Minor responses of soil microbial biomass, community structure and enzyme activities to nitrogen and phosphorus addition in three grassland ecosystems

Understanding the responses, adaptations and feedback mechanisms of biological communities to climate change is critical to project future state of earth and climate systems. Although significant amount of knowledge is available on the feedback responses of aboveground communities to climate change, little is known about the responses of belowground microbial communities due to the challenges in analyzing soil microbial community structure. Thus the goal overall goal of this study is to provide system-level, predictive mechanistic understanding of the temperature sensitivity of soil carbon (C) decomposition to climate warming by using cutting-edge integrated metagenomic technologies. Towards this goal, the following four objectives will be pursued: (i) To determine phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems; (ii) To delineate the responses of microbial community structure, functions and activities to climate change in the temperate grassland and tundra ecosystems; (iii) To determine the temperature sensitivity of microbial respiration in soils with different mixtures of labile versus recalcitrant C, and the underlying microbiological basis for temperature sensitivity of these pools; and (iv) To synthesize all experimental data for revealing microbial control of ecosystem carbon processes in responses to climate change. We have achieved our goals for all four proposed objectives. First, we determined the phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems. For this objective, we have developed a novel phasing amplicon sequencing (PAS) approach for MiSeq sequencing of amplicons. This approach has been used for sequencing various phylogenetic and functional genes related to ecosystem functioning. A comprehensive functional gene array (e.g., GeoChip 5.0) has also been developed and used for soil microbial community analysis in this study. In addition, shot-gun metagenome sequencing along with the above approaches have been used to understand the phylogenetic and functional diversity, composition, and structure of soil microbial communities in both temperature grassland and tundra ecosystems. Second, we determined the response of soil microbial communities to climate warming in both temperate grassland and tundra ecosystems using various methods. Our major findings are: (i) Microorganisms are very rapid to respond to climate warming in the tundra ecosystem, AK, which is vulnerable, too. (ii) Climate warming also significantly shifted the metabolic diversity, composition and structure of microbial communities, and key metabolic pathways related to carbon turnover, such as cellulose degradation (~13%) and CO2 production (~10%), and to nitrogen cycling, including denitrification (~12%) were enriched by warming. (iii) Warming also altered the expression patterns of microbial functional genes important to ecosystem functioning and stability through GeoChip and metatranscriptomic analysis of soil microbial communities at the OK site. Third, we analyzed temperature sensitivity of C decomposition to climate warming for both AK and OK soils through laboratory incubations. Key results include: (i) Alaska tundra soils showed that after one year of incubation, CT in the top 15 cm could be as high as 25% and 15% of the initial soil C content at 25°C and 15°C incubations, respectively. (ii) analysis of 456 incubated soil samples with 16S rRNA gene, ITS and GeoChip hybridization showed that warming shifted the phylogenretic and functional diversity, composition, structure and metabolic potential of soil microbial communities, and at different stages of incubation, key populations and functional genes significantly changed along with soil substrate changes. Functional gene diversity and functional genes for degrading labile C components decrease along incubation when labile C components are exhausting, but the genes related to degrading recalcitrant C increase. These molecular data will be directly used for modeling. Fourth, we have developed novel approaches to integrate and model experimental data to understand microbial control of ecosystem C processes in response to climate change. We compared different methods to calculate Q10 for estimating temperature sensitivity, and new approaches for Q10 calculation and molecular ecological network analysis were also developed. Using those newly developed approaches, our result indicated that Q10s increased with the recalcitrance of C pools, suggesting that longer incubation studies are needed in order to assess the temperature sensitivity of slower C pools, especially at low temperature regimes. This project has been very productive, resulting in 42 papers published or in press, 4 submitted, and 13 in preparation.

Parallel shifts in plant and soil microbial communities in response to biosolids in a semi-arid grassland

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.

Summary Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations. We hypothesized that microbial biomass, activity and community structure in nutrient‐poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana. After 2 years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate‐induced respiration rate and a 5‐fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P‐fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro‐organisms at our study site. Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram‐positive : Gram‐negative ratio. The Fungi : Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities. While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure. We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.

Accounting for variability in soil microbial communities of temperate upland grassland ecosystems

Effects of tree species transition on soil microbial biomass and community structure in subtropical China

Litter quantity confers soil functional resilience through mediating soil biophysical habitat and microbial community structure on an eroded bare land restored with mono Pinus massoniana

Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates.

A meta-analysis on the responses of soil microbial biomass and community structure to antibiotics

Soil microbial community structure is determined by environmental conditions and influenced by other factors, such as the intensity of the land use management. Studies addressing the effect of environmental factors and management on grassland soil microbial communities at the continental scale are missing, and the wide range of ecosystem services provided by these ecosystems are thus also wanting. To address this knowledge gap, this study presents data on grassland soil microbial communities along a pan-European agro-ecological gradient. The transect included five geographical locations (Sweden, Germany, Switzerland, Portugal mainland, Portugal Azores). At each location, soils were collected in two regions characterized by favourable and less favourable conditions for plant growth. In each of these ten regions, grasslands along a gradient of management intensity were selected, i.e. grassland under intensive, less intensive and extensive management. Phospholipid fatty acid analysis (PLFA) was used to characterize the microbial community structure (PLFA pattern) in relation to climatic and soil properties. Over the whole geographical range, the environmental properties determined the soil microbial community structure. In Sweden and Switzerland, the regional growth conditions had the strongest influence on the soil microbial communities, while in Germany, Portugal mainland and Azores the management intensity was more important. Splitting up this whole community response into individual groups reveals that, in general, saprotrophic fungal biomarkers were highest in extensively managed grasslands while bacterial biomarkers differed mainly between the regions. We conclude that at the transect level, climate and soil properties were the most important factors influencing soil bacterial community structure, while soil fungal groups were more responsive to grassland management intensity. Overall agricultural sustainability could benefit from informed soil health promoting management practices, and this study contributes to such knowledge, showing the importance of management for the soil microbial biomass and community structure.

Soil microbial stoichiometry reflects carbon (C) and nutrient (e.g., nitrogen (N) and phosphorus (P)) elemental balances under land-use change (LUC). However, how soil microbial community (SMC) structure and stoichiometry respond to long-term LUC in forests is still unclear. Here, we investigated three 36-year-old typical plantations, Cryptomeria fortunei, Metasequoia glyptostroboides, and Cunninghamia lanceolata, and the natural forest to assess their soil microbial stoichiometry and SMC structure. Three plots (30×30 m2) were randomly set in each forest site. In each plot of every forest site, soil samples of three depths (0-10, 10-30, and 30-60 cm) were collected. Dissolved organic C, N, and P (abbreviated as DOC, DON, and DOP, respectively) and environmental factors were measured. We also detected microbial biomass C, N, and P as well as SMC structure. The results showed that the soil microbial C:N:P stoichiometry had a strong or strict homeostasis regardless of soil depth and exhibited decoupling from the SMC structure at each depth. The SMC structure across forest types was mainly driven by mean annual soil temperature (MAST) and DOC at 0-10 cm depth, by soil water content and MAST at 10-30 cm depth, and by DOC to DOP ratio at 30-60 cm depth. Thus, SMC structure could be jointly regulated by available resources and environment. These results suggest that the C dynamics in forests tend to gain resilience or re-equilibrium over more than three decades after forest conversion. These findings highlight the importance of reforested plantations forest management for sustaining soil C over a long term.

Consistent effects of nitrogen addition on soil microbial communities across three successional stages in tropical forest ecosystems

Soil microbial communities and enzyme activities play key roles in soil ecosystems. Both are sensitive to changes in environmental factors, including seasonal temperature, precipitation variations and soil properties. To understand the interactive mechanisms of seasonal changes that affect soil microbial communities and enzyme activities in a subtropical masson pine (Pinus massoniana) forest, we investigated the soil microbial community structure and enzyme activities to identify the effect of seasonal changes on the soil microbial community for two years in Jinyun Mountain National Nature Reserve, Chongqing, China. The soil microbial community structure was investigated using phospholipid fatty acids (PLFAs). The results indicated that a total of 36 different PLFAs were identified, and 16:0 was found in the highest proportions in the four seasons, moreover, the total PLFAs abundance were highest in spring and lowest in winter. Bacteria and actinomycetes were the dominant types in the study area. Seasonal changes also had a significant (P < 0.05) influence on the soil enzyme activity. The maximum and minimum values of the invertase and catalase activities were observed in autumn and winter, respectively. However, the maximum and minimum values of the urease and phosphatase acid enzymatic activities were found in spring and winter, respectively. Canonical correspondence analysis (CCA) analysis revealed that the seasonal shifts in soil community composition and enzyme activities were relatively more sensitive to soil moisture and temperature, but the microbial community structure and enzyme activity were not correlated with soil pH in the study region. This study highlights how the seasonal variations affect the microbial community and function (enzyme activity) to better understand and predict microbial responses to future climate regimes in subtropical area.

PDF HTML阅读 XML下载 导出引用 引用提醒 南亚热带红椎和格木人工幼龄林土壤微生物群落结构特征 DOI: 10.5846/stxb201411242328 作者: 作者单位: 中国林科院森环森保所,中国林科院森环森保所,中国林科院森环森保所,四川省林业科学研究院 作者简介: 通讯作者: 中图分类号: 基金项目: 国家科技支撑计划项目（2012BAD22B01） Characteristics of soil microbial community structure in two young plantations of Castanopsis hystrix and Erythrophleum fordii in subtropical China Author: Affiliation: Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry,Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry,, Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:采用氯仿熏蒸浸提法和磷脂脂肪酸法（Phospholipids fatty acid，PLFA）研究了我国南亚热带地区非固氮树种红椎（Castanopsis hystrix）和固氮树种格木（Erythrophleum fordii）人工幼龄林土壤微生物生物量与微生物群落结构特征。结果表明，在旱季和雨季，红椎幼龄林土壤微生物总PLFAs量，细菌PLFAs量、放线菌PLFAs量及丛枝菌根真菌PLFAs量均大于格木幼龄林。红椎幼龄林土壤PLFA Shannon多样性指数（HPLFA）在旱季和雨季均大于格木幼龄林。主成分分析表明，土壤微生物群落结构组成受到林分类型和季节的双重影响。冗余分析表明，土壤硝态氮（NO3--N）含量、土壤含水量、pH及土壤微生物生物量氮（MBN）与特征磷脂脂肪酸之间呈显著相关关系。以上结果表明固氮树种格木与非固氮树种红椎人工幼龄林对土壤微生物生物量和群落结构的影响存在显著差异。 Abstract:The effects of two plantation stands of non-N-fixing Castanopsis hystrix and N-fixing Erythrophleum fordii on soil microbial biomass and microbial community structure in south subtropical China were studied by fumigation-extraction and phospholipid fatty acid (PLFA) analyses. The results showed that soil pH, soil N status (total N, NH4+-N and NO3--N), soil microbial total PLFAs, bacterial PLFAs, actinomycetes PLFAs and arbuscular mycorrhizal fungi PFLAs were significantly influenced by plantation type and season, while only season significantly influenced soil microbial biomass carbon and fungal PLFAs, but soil microbial biomass nitrogen(MBN) was not significantly affected by plantation type and season. The content of soil NH4+-N and NO3--N in C. hystrix plantation were significantly higher than those in E. fordii plantation during both the dry and rainy seasons. In addition, the amounts of soil microbial total PLFAs and bacterial, actinomycete, and arbuscular mycorrhizal fungi PFLAs in C. hystrix plantation were significantly higher than those in E. fordii plantation during both the seasons as well. Furthermore, the richness and Shannon diversity index of soil microbial PLFAs were significantly altered by plantation type, Shannon diversity index of soil microbial PLFAs in C. hystrix plantation was significantly higher than that in E. fordii plantation during both the seasons. Principal component analysis indicated that variations in the soil microbial community structure were affected by both the plantation types and seasons. Redundancy analysis of soil microbial community structure and environmental factors showed that NO3-, soil water content, soil pH, and microbial biomass nitrogen had significant correlations with PLFA signatures. Thus, our study results showed significantly different effects of non-N-fixing C. hystrix and N-fixing E. fordii plantation stands on the soil microbial biomass and community structure. Overall, soil pH and N status may be the main factors that could regulate soil microbial biomass and community structure in the studied plantations. 参考文献 相似文献 引证文献

The application of organic mulches as a soil cover is effective in improving the quality of soil. However, very little information is available on the effect of mulches on the soil microbial community. In this study, we investigated the effect of various organic mulches on soil dehydrogenase activity (DHA) and microbial community structures in the top 1 cm and 5 cm below the soil surface 1 year after application of the mulches. DHA was stimulated at both depths in plots mulched with grass clippings (GC), but was not significantly different from the control for the other mulch treatments. Fatty acid methyl ester (FAME) analysis and denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction-amplified 16S rDNA fragments were used to assess changes in the soil microbial community structure. Cluster analysis and principle component analysis of FAME profiles showed that only soil mulched with pine chips distinctively clustered from the other treatments. At the soil surface, bacterial DGGE profiles revealed that distinct shifts in several bacterial populations occurred in soils mulched with GC and eucalyptus yardwaste (EY), while DGGE profiles from soil at the 5 cm depth revealed no distinct changes. Changes in bacterial diversity at the soil surface under different mulches were calculated based on the number of bands in the DGGE profile using the Shannon-Weaver index of diversity ( H). Compared to the control ( H =0.9), the GC- and EY-treated soils showed slightly increased bacterial diversity, with an H of 1.1 and 1.0, respectively. These results indicate that the long-term effect of organic mulches on the soil microbial activity and community structure is highly dependent upon the type of mulch and is mostly exerted in the top few centimeters of the soil profile.