Microbial community responses reduce soil carbon loss in Tibetan alpine grasslands under short-term warming

Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems

Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.

Quantifying thermal adaptation of soil microbial respiration

Quantifying the rate of thermal adaptation of soil microbial respiration is essential in determining potential for carbon cycle feedbacks under a warming climate. Uncertainty surrounding this topic stems in part from persistent methodological issues and difficulties isolating the interacting effects of changes in microbial community responses from changes in soil carbon availability. Here, we constructed a series of temperature response curves of microbial respiration (given unlimited substrate) using soils sampled from around New Zealand, including from a natural geothermal gradient, as a proxy for global warming. We estimated the temperature optima ([Formula: see text]) and inflection point ([Formula: see text]) of each curve and found that adaptation of microbial respiration occurred at a rate of 0.29 °C ± 0.04 1SE for [Formula: see text] and 0.27 °C ± 0.05 1SE for [Formula: see text] per degree of warming. Our results bolster previous findings indicating thermal adaptation is demonstrably offset from warming, and may help quantifying the potential for both limitation and acceleration of soil C losses depending on specific soil temperatures.

A functional metagenomics study of soil carbon and nitrogen degradation networks and limiting factors on the Tibetan plateau

Introduction

The Three-River Source Nature Reserve is located in the core area of the Qinghai-Tibetan Plateau, with the alpine swamp, meadow and steppe as the main ecosystem types. However, the microbial communities in these alpine ecosystems, and their carbon and nitrogen degrading metabolic networks and limiting factors remain unclear.

Methods

We sequenced the diversity of bacteria and fungi in alpine swamps, meadows, steppes, and their degraded and artificially restored ecosystems and analyzed soil environmental conditions.

Results

The results indicated that moisture content had a greater influence on soil microbial community structure compared to degradation and restoration. Proteobacteria dominated in high moisture alpine swamps and alpine meadows, while Actinobacteria dominated in low moisture alpine steppes and artificial grasslands. A metabolic network analysis of carbon and nitrogen degradation and transformation using metagenomic sequencing revealed that plateau microorganisms lacked comprehensive and efficient enzyme systems to degrade organic carbon, nitrogen, and other biological macromolecules, so that the short-term degradation of alpine vegetation had no effect on the basic composition of soil microbial community. Correlation analysis found that nitrogen fixation was strong in meadows with high moisture content, and their key nitrogen-fixing enzymes were significantly related to Sphingomonas. Denitrification metabolism was enhanced in water-deficient habitats, and the key enzyme, nitrous oxide reductase, was significantly related to Phycicoccus and accelerated the loss of nitrogen. Furthermore, Bacillus contained a large number of amylases (GH13 and GH15) and proteases (S8, S11, S26, and M24) which may promote the efficient degradation of organic carbon and nitrogen in artificially restored grasslands.

Discussion

This study illustrated the irrecoverability of meadow degradation and offered fundamental information for altering microbial communities to restore alpine ecosystems.

Elevational changes in the bacterial community composition and potential functions in a Tibetan grassland

In the Tibetan grasslands, the distribution patterns of the microbial community structure and function along elevation gradients have attracted considerable attention due to the wide distribution of mountain slopes, but the controlling factors of these patterns are still unclear. Here we investigated the taxonomy and potential functions of soil bacteria along an elevation gradient in a Tibetan mountainous grassland in 2 years, aiming to explore the elevation patterns of the bacterial structure and function and the underlying drivers. High-throughput sequencing and environment attribute measurements were conducted to survey the bacterial and environment characters. Furthermore, PICRUSt2 for prediction of bacterial functions, iCAMP for unraveling the drivers controlling community assembly, and HMSC for variance partitioning of bacterial community composition were used. Elevation did not significantly affect the bacterial diversity but changed their composition, driven by both deterministic and stochastic processes. In addition, elevation did not significantly affect the relative importance of deterministic and stochastic processes. Soil carbon, nitrogen, and temperature were important deterministic factors in driving bacterial community structure. The genus Solirubrobacter in Actinobacteriota was identified as most elevation discriminatory. Based on these observations, the bacterial community in the Tibetan mountainous grasslands was more controlled by edaphic factors than temperature, indicating their relative stability under climate change scenarios.

Distinct Elevational Patterns and Their Linkages of Soil Bacteria and Plant Community in An Alpine Meadow of the Qinghai-Tibetan Plateau

Soil microbes play important roles in determining plant community composition and terrestrial ecosystem functions, as well as the direction and extent of terrestrial ecosystem feedback to environmental changes. Understanding the distribution patterns of plant and soil microbiota along elevation gradients is necessary to shed light on important ecosystem functions. In this study, soil bacteria along an elevation gradient in an alpine meadow ecosystem of the Qinghai−Tibetan Plateau were investigated using Illumina sequencing and GeoChip technologies. The community structure of the soil bacteria and plants presented a continuous trend along the elevation gradient, and their alpha diversity displayed different distribution patterns; however, there were no linkages between them. Beta diversity of the soil bacteria and plants was significantly influenced by elevational distance changes (p < 0.05). Functional gene categories involved in nitrogen and phosphorus cycling had faster changes than those involved in carbon degradation, and functional genes involved in labile carbon degradation also had faster variations than those involved in recalcitrant carbon degradation with elevational changes. According to Pearson’s correlation, partial Mantel test analysis, and canonical correspondence analysis, soil pH and mean annual precipitation were important environmental variables in influencing soil bacterial diversity. Soil bacterial diversity and plant diversity had different distribution patterns along the elevation gradient.

Microbial assemblies associated with temperature sensitivity of soil respiration along an altitudinal gradient

Identifying the drivers of the response of soil microbial respiration to warming is integral to accurately forecasting the carbon-climate feedbacks in terrestrial ecosystems. Microorganisms are the fundamental drivers of soil microbial respiration and its response to warming; however, the specific microbial communities and properties involved in the process remain largely undetermined. Here, we identified the associations between microbial community and temperature sensitivity (Q₁₀) of soil microbial respiration in alpine forests along an altitudinal gradient (from 2974 to 3558 m) from the climate-sensitive Tibetan Plateau. Our results showed that changes in microbial community composition accounted for more variations of Q₁₀ values than a wide range of other factors, including soil pH, moisture, substrate quantity and quality, microbial biomass, diversity and enzyme activities. Specifically, co-occurring microbial assemblies (i.e., ecological clusters or modules) targeting labile carbon consumption were negatively correlated with Q₁₀ of soil microbial respiration, whereas microbial assemblies associated with recalcitrant carbon decomposition were positively correlated with Q₁₀ of soil microbial respiration. Furthermore, there were progressive shifts of microbial assemblies from labile to recalcitrant carbon consumption along the altitudinal gradient, supporting relatively high Q₁₀ values in high-altitude regions. Our results provide new insights into the link between changes in major microbial assemblies with different trophic strategies and Q₁₀ of soil microbial respiration along an altitudinal gradient, highlighting that warming could have stronger effects on microbially-mediated soil organic matter decomposition in high-altitude regions than previously thought.

Soil microbial trait-based strategies drive metabolic efficiency along an altitude gradient

Trait-based approaches provide a candidate framework for linking soil microbial community to ecosystem processes, yet how the trade-offs in different microbial traits regulate the community-level metabolic efficiency remains unknown. Herein we assessed the roles of the microbial taxa with particular trait strategies in mediating soil microbial metabolic efficiency along an altitude gradient on the Tibetan Plateau. Results showed that soil microbial metabolic efficiency declined with increasing altitude, as indicated by the increasing metabolic quotient (microbial respiration per unit biomass, qCO2) and decreasing carbon use efficiency (CUE). Both qCO2 and CUE were predominantly predicted by microbial physiological and taxonomic attributes after considering key environmental factors including soil pH, substrate quantity and quality. Specifically, the reduced metabolic efficiency was associated with higher investment into nutrient (particularly for phosphorus) acquisitions via enzymes. Furthermore, we identified key microbial assemblies selected by harsh environments (low substrate quality and temperature) as important predictors of metabolic efficiency. These results suggest that particular microbial assemblies adapted to nutrient limited and cold habitats, but at the expense of lower metabolic efficient at higher altitude. Our findings provide a candidate mechanism underlying community-level metabolic efficiency, which has important implications for microbial-mediated processes such as carbon dynamics under global climate changes.

High microbial diversity stabilizes the responses of soil organic carbon decomposition to warming in the subsoil on the Tibetan Plateau

Soil microbes are directly involved in soil organic carbon (SOC) decomposition, yet the importance of microbial biodiversity in regulating the temperature sensitivity of SOC decomposition remains elusive, particularly in alpine regions where climate change is predicted to strongly affect SOC dynamics and ecosystem stability. Here we collected topsoil and subsoil samples along an elevational gradient on the southeastern Tibetan Plateau to explore the temperature sensitivity (Q₁₀ ) of SOC decomposition in relation to changes in microbial communities. Specifically, we tested whether the decomposition of SOC would be more sensitive to warming when microbial diversity is low. The estimated Q₁₀ value ranged from 1.28 to 1.68, and 1.80 to 2.10 in the topsoil and subsoil, respectively. The highest Q₁₀ value was observed at the lowest altitude of forests in the topsoil, and at the highest altitude of alpine meadow in the subsoil. Variations in Q₁₀ were closely related to changes in microbial properties. In the topsoil the ratio of gram-positive to gram-negative bacteria (G+:G-) was the predominant factor associated with the altitudinal variations in Q₁₀ . In the subsoil, SOC decomposition showed more resilience to warming when the diversity of soil bacteria (both whole community and major groups) and fungi was higher. Our results partly support the positive biodiversity-ecosystem stability hypothesis. Structural equation modeling further indicates that variations in Q₁₀ in the subsoil were directly related to changes in microbial diversity and community composition, which were affected by soil pH. Collectively our results provide compelling evidence that microbial biodiversity plays an important role in stabilizing SOC decomposition in the subsoil of alpine montane ecosystems. Conservation of belowground biodiversity is therefore of great importance in maintaining the stability of ecosystem processes under climate change in high-elevation regions of the Tibetan Plateau.

Unaltered soil microbial community composition, but decreased metabolic activity in a semiarid grassland after two years of passive experimental warming

Soil microbial communities regulate soil carbon feedbacks to climate warming through microbial respiration (i.e., metabolic rate). A thorough understanding of the responses of composition, biomass, and metabolic rate of soil microbial community to warming is crucial to predict soil carbon stocks in a future warmer climate. Therefore, we conducted a field manipulative experiment in a semiarid grassland on the Loess Plateau of China to evaluate the responses of the soil microbial community to increased temperature from April 2015 to December 2017. Soil temperature was 2.0°C higher relative to the ambient when open-top chambers (OTCs) were used. Warming did not affect microbial biomass or the composition of microbial functional groups. However, warming significantly decreased microbial respiration, directly resulting from soil pH decrease driven by the comediation of aboveground biomass increase, inorganic nitrogen increase, and moisture decrease. These findings highlight that the soil microbial community structure of semiarid grasslands resisted the short-term warming by 2°C, although its metabolic rate declined.