高寒生态系统微生物群落研究进展

高寒生态系统分布在高纬度或高海拔、气候寒冷的地区,包括北极苔原、高山苔原、青藏高原等.高寒生态系统对气候变化非常敏感,其土壤中储存大量的有机碳,对全球的碳平衡起关键作用.微生物是生物地球化学循环的主要驱动者,微生物群落对气候变化的响应和反馈影响生态系统的功能与稳定性.本文回顾了高寒生态系统微生物群落组成、多样性与空间分布,以及微生物群落对气候变化(增温、氮沉降、火干扰)的响应,为拓展我国高寒生态系统微生物研究提供基础.     

陆地和淡水生态系统新型微生物氮循环研究进展

氮生物地球化学循环是地球物质循环的重要枢纽,是决定陆地生态系统生产力水平、水资源安全、温室气体生成排放的关键过程。氮循环是由微生物介导的一系列复杂过程,不同形态、价态氮化合物的转化分别由相应的功能微生物驱动完成。随着厌氧氨氧化、完全氨氧化等新型氮转化过程的相继报道和发现更新了人们对氮循环的认识。本文综述了陆地和淡水生态系统中厌氧氨氧化(anammox)、硝酸盐异化还原为铵(DNRA)、完全氨氧化(comammox)等新型氮循环过程的发生机制、热区分布及环境效应,并总结了这三种氮循环的相互关系。     

地下水微生物功能群及生物地球化学循环

地下水系统是地球关键带的重要组成部分,为微生物提供了特殊的栖息环境和复杂的生存条件,进而演化出复杂的生物地球化学过程。随着多技术、多学科的交叉融合及发展,近几十年地下水微生物功能群及生物地球化学循环研究取得了引人瞩目的重要进展。本文从地下水中的微生物群功能分区、微生物介导的地球化学元素循环、污染与修复中的生物地球化学过程,以及生物地球化学过程数值模拟等方面对国内外相关研究进展进行了综述,并对地下水系统中微生物"暗物质、暗过程"、微生物修复、地下水医学地质学,以及地下水多学科交叉融合等研究方向和前景进行了展望。     

火腿微生物研究进展

数千年来,微生物参与的食品发酵为人类保存食物和风味多元化提供了重要的方法。这些可再生且易于操作的发酵食品为研究微生物群落提供了理想的材料。干腌火腿就是传统发酵食品之一,在微生物作用下其加工过程发生了蛋白质和脂肪的水解和氧化反应,产生的一些化合物形成了火腿的独特风味。文中描述了不同地域火腿微生物类群及其对火腿品质形成的作用,为火腿微生物今后的研究提出了参考。     

Microbial community structure and global trace gases

Global change can affect soil processes by either altering the functioning of existing organisms or by restructuring the community, modifying the fundamental physiologies that drive biogeochemical processes. Thus, not only might process rates change, but the controls over them might also change. Moreover, previously insignificant processes could become important. These possibilities raise the question ‘Will changes in climate and land use restructure microbial communities in a way that will alter trace gas fluxes from an ecosystem?’ Process studies indicate that microbial community structure can influence trace gas dynamics at a large scale. For example, soil respiration and CH₄ production both show ranges of temperature response among ecosystems, indicating differences in the microbial communities responsible. There are three patterns of NH₄⁺ inhibition of CH₄ oxidation at the ecosystem scale: no inhibition, immediate inhibition, and delayed inhibition; these are associated with different CH₄ oxidizer communities. Thus, it is possible that changes in climate, land-use, and disturbance regimes could alter microbial communities in ways that would substantially alter trace gas fluxes; we discuss the data supporting this conclusion. We also discuss approaches to developing research linking microbial community structure and activity to the structure and functioning of the whole ecosystem. Modern techniques allow us to identify active organisms even if they have not been cultivated; in combination with traditional experimental approaches we should be able to identify the linkages between these active populations and the processes they carry out at the ecosystem level. Finally, we describe scenarios of how global change could alter trace gas fluxes by altering microbial communities and how understanding the microbial community dynamics could improve our ability to predict future trace gas fluxes.     

Changes in soil heterotrophic respiration,carbon availability,and microbial function in seven forests along a climate gradient

Soil microbial communities play an essential role in soil carbon (C) emission and C sequestration in forest ecosystems. However, little information is available regarding the relationship between soil C dynamics and microbial substrate utilization at large scales. Along the North–South Transect of Eastern China (NSTEC), seven forests representative of boreal, temperate and tropical biomes were examined. Soil heterotrophic respiration (R_h), soil dissolved organic C (DOC), microbial biomass C (MBC), and microbial community-level physiological profiles (CLPPs) were investigated using biochemical measurements, static chamber-gas chromatography analysis, and Biolog-Eco microplates, respectively. We found that soil R_h rates were significantly higher in subtropical and boreal forests than in temperate forests. Conversely, the concentrations of soil DOC and MBC, as well as microbial metabolic activity and functional diversity, were consistently higher in temperate forests than in subtropical forests. There were considerably different substrate utilization profiles among the boreal, temperate, and subtropical forests. Soil microorganisms from the temperate and boreal forests mainly metabolized high-energy substrates, while those from the subtropical forests used all substrates equally. In addition, soil R_h rates were significantly and negatively related to soil labile C concentrations, total metabolic activity, and the intensity of individual substrate utilization, indicating that soil microbes assimilated more soil substrates, thereby reducing CO₂ emissions. Overall, our study suggests that climate factors, as well as substrate availability, dominate the activities and functions of soil microbes at large scales.     

Impact of elevated atmospheric CO2 concentration on soil microbial biomass and activity in a complex, weedy field model ecosystem

Although soil organisms play an essential role in the cycling of elements in terrestrial ecosystems, little is known of the impact of increasing atmospheric CO₂ concentrations on soil microbial processes. We determined microbial biomass and activity in the soil of multitrophic model ecosystems housed in the Ecotron (NERC Centre for Population Biology, Ascot, UK) under two atmospheric CO₂ concentrations (ambient vs. ambient + 200 ppm). The model communities consist of four annual plant species which naturally co-occur in weedy fields and disturbed ground throughout southern England, together with their herbivores, parasitoids and soil biota. At the end of two experimental runs lasting 9 and 4.5 months, respectively, root dry weight and quality showed contradictory responses to elevated CO₂ concentrations, probably as a consequence of the different time-periods (and hence number of plant generations) in the two experiments. Despite significant root responses no differences in microbial biomass could be detected. Effects of CO₂ concentration on microbial activity were also negligible. Specific enzymes (protease and xylanase) showed a significant decrease in activity in one of the experimental runs. This could be related to the higher C:N ratio of root tissue. We compare the results with data from the literature and conclude that the response of complex communities cannot be predicted on the basis of oversimplified experimental set-ups.     

The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche-driven microbial community assembly processes

Shallow thermokarst ponds are a conspicuous landscape element of the Arctic Siberian tundra with high biogeochemical variability. Little is known about how microbes from the regional species pool assemble into local pond communities and how the resulting patterns affect functional properties such as dissolved organic carbon (DOC) remineralization and greenhouse gas (GHG) turnover. We analysed the pelagic microbiomes of 20 ponds in north-eastern Siberia in the context of their physico-chemical properties. Ponds were categorized as polygonal or trough according to their geomorphological origin. The diversity of bacteria and eukaryotic microbes was assessed by ribosomal gene tag sequencing. Null model analysis revealed an important role of stochastic assembly processes within ponds of identical origin, in particular for genotypes only occurring in few systems. Nevertheless, the two pond types clearly represented distinct niches for both the bacterial and eukaryotic microbial communities. Carbon dioxide concentration, indicative of heterotrophic microbial processes, varied greatly, especially in the trough ponds. Methane concentrations were lower in polygonal ponds and were correlated with the estimated abundance of methanotrophs. Thus, the overall functional variability of Arctic ponds reflects the stochastic assembly of their microbial communities. Distinct functional subcommunities can, nevertheless, be related to GHG concentrations.     

Above‐ and belowground linkages in Sphagnum peatland: climate warming affects plant‐microbial interactions

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above‐ and belowground linkages that regulate soil organic carbon dynamics and C‐balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top‐predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum‐polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above‐ and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands     

The trade-off between growth rate and yield in microbial communities and the consequences for under-snow soil respiration in a high elevation coniferous forest

Soil microbial respiration is a critical component of the global carbon cycle, but it is uncertain how properties of microbes affect this process. Previous studies have noted a thermodynamic trade-off between the rate and efficiency of growth in heterotrophic organisms. Growth rate and yield determine the biomass-specific respiration rate of growing microbial populations, but these traits have not previously been used to scale from microbial communities to ecosystems. Here we report seasonal variation in microbial growth kinetics and temperature responses (Q₁₀) in a coniferous forest soil, relate these properties to cultured and uncultured soil microbes, and model the effects of shifting growth kinetics on soil heterotrophic respiration (R_h). Soil microbial communities from under-snow had higher growth rates and lower growth yields than the summer and fall communities from exposed soils, causing higher biomass-specific respiration rates. Growth rate and yield were strongly negatively correlated. Based on experiments using specific growth inhibitors, bacteria had higher growth rates and lower yields than fungi, overall, suggesting a more important role for bacteria in determining R_h. The dominant bacteria from laboratory-incubated soil differed seasonally: faster-growing, cold-adapted Janthinobacterium species dominated in winter and slower-growing, mesophilic Burkholderia and Variovorax species dominated in summer. Modeled R_h was sensitive to microbial kinetics and Q₁₀: a sixfold lower annual R_h resulted from using kinetic parameters from summer versus winter communities. Under the most realistic scenario using seasonally changing communities, the model estimated R_h at 22.67 mol m⁻² year⁻¹, or 47.0% of annual total ecosystem respiration (R_e) for this forest.     

Applying population and community ecology theory to advance understanding of belowground biogeochemistry

Approaches to quantifying and predicting soil biogeochemical cycles mostly consider microbial biomass and community composition as products of the abiotic environment. Current numerical approaches then primarily emphasise the importance of microbe–environment interactions and physiology as controls on biogeochemical cycles. Decidedly less attention has been paid to understanding control exerted by community dynamics and biotic interactions. Yet a rich literature of theoretical and empirical contributions highlights the importance of considering how variation in microbial population ecology, especially biotic interactions, is related to variation in key biogeochemical processes like soil carbon formation. We demonstrate how a population and community ecology perspective can be used to (1) understand the impact of microbial communities on biogeochemical cycles and (2) reframe current theory and models to include more detailed microbial ecology. Through a series of simulations we illustrate how density dependence and key biotic interactions, such as competition and predation, can determine the degree to which microbes regulate soil biogeochemical cycles. The ecological perspective and model simulations we present lay the foundation for developing empirical research and complementary models that explore the diversity of ecological mechanisms that operate in microbial communities to regulate biogeochemical processes.     

土壤微生物生物量碳氮磷与土壤酶化学计量对气候变化的响应机制

微生物和土壤酶是陆地生态系统中生物地球化学循环的重要驱动力,深入理解微生物在生态系统中的调节作用以及气候变化过程中微生物量和土壤酶的响应机制是生态学领域关注的重要科学问题.本研究从气候因素角度出发,基于生态化学计量学理论,综述了微生物和土壤酶在陆地生态系统碳氮磷循环中的作用,以及土壤微生物生物量碳氮磷和土壤酶化学计量对气候变化的响应机制,即: 改变微生物代谢速率和酶活性;调整微生物群落结构;调整微生物生物量碳氮磷与土壤酶化学计量特征;改变碳氮磷养分元素利用效率.最后分析当前研究的不足,并提出了该领域亟待解决的科学问题: 综合阐明土壤微生物和土壤酶对气候变化的响应机制;探究土壤微生物和胞外酶养分耦合机理;深入探究土壤微生物量和土壤酶化学计量特征对气候变化的适应对策.     

土壤微生物群落抵抗力和恢复力研究进展

人类活动的不断加剧使得土壤生态系统承受着环境干扰压力。土壤微生物受到环境干扰的响应程度（抵抗力）及恢复至原来状态的能力（恢复力）决定着土壤生态系统的可持续性。梳理和总结了土壤微生物群落对环境干扰的抵抗力和恢复力方面的研究进展。首先,在介绍土壤微生物群落抵抗力和恢复力概念的基础上,阐述了通过评估微生物群落的结构和功能的变化来系统表征抵抗力和恢复力;随后,分析了最近十年（2012-2021年）有关文献,发现土壤微生物群落的结构和（或）功能在环境干扰后的恢复力总体较弱,但耕作、有机物料添加和轮作等农田管理措施下的响应趋势表现出一定的规律性;继而,从个体水平的休眠和胁迫忍耐、种群水平的生存策略、群落水平的多样性和相互作用以及生态系统水平的历史遗留效应等方面分析了土壤微生物群落抵抗力和恢复力的维持机制;最后,从功能性状、多功能性和植物-土壤微生物整体性对未来研究做出了展望,以期为构建土壤健康评价体系及预测环境干扰对土壤功能的影响提供科学依据。     

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

Changes in labile carbon (LC) pools and microbial communities are the primary factors controlling soil heterotrophic respiration (R_h) in warming experiments. Warming is expected to initially increase R_h but studies show this increase may not be continuous or sustained. Specifically, LC and soil microbiome have been shown to contribute to the effect of extended warming on R_h. However, their relative contribution is unclear and this gap in knowledge causes considerable uncertainty in the prediction of carbon cycle feedbacks to climate change. In this study, we used a two‐step incubation approach to reveal the relative contribution of LC limitation and soil microbial community responses in attenuating the effect that extended warming has on R_h. Soil samples from three Tibetan ecosystems—an alpine meadow (AM), alpine steppe (AS), and desert steppe (DS)—were exposed to a temperature gradient of 5–25°C. After an initial incubation period, soils were processed in one of two methods: (a) soils were sterilized then inoculated with parent soil microbes to assess the LC limitation effects, while controlling for microbial community responses; or (b) soil microbes from the incubations were used to inoculate sterilized parent soils to assess the microbial community effects, while controlling for LC limitation. We found both LC limitation and microbial community responses led to significant declines in R_h by 37% and 30%, respectively, but their relative contributions were ecosystem specific. LC limitation alone caused a greater R_h decrease for DS soils than AMs or ASs. Our study demonstrates that soil carbon loss due to R_h in Tibetan alpine soils—especially in copiotrophic soils—will be weakened by microbial community responses under short‐term warming.     

The role of amoeboid protists and the microbial community in moss-rich terrestrial ecosystems: biogeochemical implications for the carbon budget and carbon cycle, especially at higher latitudes

Moss-rich terrestrial communities are widely distributed in low- and high-latitude environments, covering vast surface areas in the boreal forests and tundra. The microbial biota in these organic-rich communities may contribute substantially to the carbon budget of terrestrial communities and the carbon cycle on a global scale. Recent research is reported on the carbon content of microbial communities in some temperate and high-latitude moss communities. The total carbon content and potential respiratory carbon dioxide (CO(2)) efflux is reported for bacteria, microflagellates, naked amoebae, and testate amoebae within sampling sites at a northeastern forest and the tundra at Toolik, Alaska. Quantitative models of the predicted total CO(2) efflux from the microbes, based on microscopic observations and enumeration of the microbiota in samples from the research sites, are described and predictions are compared with published field-based data of CO(2) efflux. The significance of the predictions for climate change and global warming are discussed.     

Microbial Communities Associated with Tree Bark Foliose Lichens: A Perspective on their Microecology

Tree‐bark, foliose lichens occur widely on a global scale. In some locales, such as forests, they contribute a substantial amount of biomass. However, there are few research reports on microbial communities including eukaryotic microbes associated with foliose lichens. Lichens collected from tree bark at 11 locations (Florida, New York State, Germany, Australia, and the Arctic) were examined to determine the density and C‐biomass of bacteria and some eukaryotic microbes, i.e. heterotrophic nanoflagellates (HNF) and amoeboid protists. A rich microbial diversity was found, including large plasmodial slime molds, in some cases exceeding 100 μm in size. The densities of HNF and amoeboid protists were each positively correlated with densities of bacteria, r = 0.84 and 0.80, respectively (p < 0.01, N = 11 for each analysis) indicating a likely bacterial‐based food web. Microbial densities (number/g lichen dry weight) varied markedly across the geographic sampling sites: bacteria (0.7–13.1 × 10⁸), HNF (0.2–6.8 × 10⁶) and amoeboid protists (0.4–4.6 × 10³). The ranges in C‐biomass (μg/g lichen dry weight) across the 11 sites were: bacteria (8.8–158.5), HNF (0.03–0.85), and amoeboid protists (0.08–540), the latter broad range was due particularly to absence or presence of large slime mold plasmodia.     

The effect of fire on microbial biomass: a meta-analysis of field studies

Soil microbes regulate the transfer of carbon (C) from ecosystems to the atmosphere and in doing so influence feedbacks between terrestrial ecosystems and global climate change. Fire is one element of global change that may influence soil microbial communities and, in turn, their contribution to the C dynamics of ecosystems. In order to improve our understanding of how fire influences belowground communities, we conducted a meta-analysis of 42 published microbial responses to fire. We hypothesized that microbial biomass as a whole, and fungal biomass specifically, would be altered following fires. Across all studies, fire reduced microbial abundance by an average of 33.2% and fungal abundance by an average of 47.6%. However, microbial responses to fire differed significantly among biomes and fire types. For example, microbial biomass declined following fires in boreal and temperate forests but not following grasslands fires. In addition, wildfires lead to a greater reduction in microbial biomass than prescribed burns. These differences are likely attributable to differences in fire severity among biomes and fire types. Changes in microbial abundance were significantly correlated with changes in soil CO₂ emissions. Altogether, these results suggest that fires may significantly decrease microbial abundance, with corresponding consequences for soil CO₂ emissions.     

A Synthesis of Climate and Vegetation Cover Effects on Biogeochemical Cycling in Shrub-Dominated Drylands

Semi-arid and arid ecosystems dominated by shrubs (“dry shrublands”) are an important component of the global C cycle, but impacts of climate change and elevated atmospheric CO₂ on biogeochemical cycling in these ecosystems have not been synthetically assessed. This study synthesizes data from manipulative studies and from studies contrasting ecosystem processes in different vegetation microsites (that is, shrub or herbaceous canopy versus intercanopy microsites), to assess how changes in climate and atmospheric CO₂ affect biogeochemical cycles by altering plant and microbial physiology and ecosystem structure. Further, we explore how ecosystem structure impacts on biogeochemical cycles differ across a climate gradient. We found that: (1) our ability to project ecological responses to changes in climate and atmospheric CO₂ is limited by a dearth of manipulative studies, and by a lack of measurements in those studies that can explain biogeochemical changes, (2) changes in ecosystem structure will impact biogeochemical cycling, with decreasing pools and fluxes of C and N if vegetation canopy microsites were to decline, and (3) differences in biogeochemical cycling between microsites are predictable with a simple aridity index (MAP/MAT), where the relative difference in pools and fluxes of C and N between vegetation canopy and intercanopy microsites is positively correlated with aridity. We conclude that if climate change alters ecosystem structure, it will strongly impact biogeochemical cycles, with increasing aridity leading to greater heterogeneity in biogeochemical cycling among microsites. Additional long-term manipulative experiments situated across dry shrublands are required to better predict climate change impacts on biogeochemical cycling in deserts.     

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

Despite microbes'' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO₂) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO₂ efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling.