Experimental warming effects on the microbial community of a temperate mountain forest soil

Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO₂ (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.     

Comparison of chloroform fumigation-extraction, phospholipid fatty acid, and DNA methods to determine microbial biomass in forest humus

Techniques developed to measure microbial biomass in mineral soils may not give reliable results in humus. We evaluated the relationships between three techniques to estimate microbial biomass in forest humus: chloroform fumigation-extraction (CFE), total extractable phospholipid fatty acids (PLFA), and extractable DNA. There was a good relationship between PLFA and CFE (R²=0.96), with a slope slightly different from that previously reported for mineral soils (1 nmol PLFA corresponded to a flush of 3.2 μg C released by fumigation in humus cf. 2.4 μg C in mineral soil). There was no relationship between DNA concentration and the other two measurements of microbial biomass. This may be due, in part, to the high fungal biomass in forest humus, as DNA concentration per unit biomass is much more variable for fungi than bacteria.     

The microbial PLFA composition as affected by pH in an arable soil

The influence of soil pH on the phospholipid fatty acid (PLFA) composition of the microbial community was investigated along the Hoosfield acid strip, Rothamsted Research, UK - a uniform pH gradient between pH 8.3 and 4.5. The influence of soil pH on the total concentration of PLFAs was not significant, while biomass estimated using substrate induced respiration decreased by about 25%. However, the PLFA composition clearly changed along the soil pH gradient. About 40% of the variation in PLFA composition along the gradient was explained by a first principal component, and the sample scores were highly correlated to pH (R² = 0.97). Many PLFAs responded to pH similarly in the Hoosfield arable soil compared with previous assessments in forest soils, including, e.g. monounsaturated PLFAs 16:1ω5, 16:1ω7c and 18:1ω7, which increased in relative concentrations with pH, and i16:0 and cy19:0, both of which decreased with pH. Some PLFAs responded differently to pH between the soil types, e.g. br18:0. We conclude that soil pH has a profound influence on the microbial PLFA composition, which must be considered in all applications of this method to detect changes in the microbial community.     

Soil microbial dynamics in maize-growing soil under different tillage and residue management systems

The long-term impact of tillage and residue management on soil microorganisms was studied over the growing season in a sandy loam to loamy sand soil of southwestern Quebec, growing maize (Zea mays L.) monoculture. Tillage and residue treatments were first imposed on plots in fall 1991. Treatments consisted of no till, reduced tillage, and conventional tillage with crop residues either removed from (−R) or retained on (+R) experimental plots, laid out in a randomized complete block design. Soil microbial biomass carbon (SMB-C), soil microbial biomass nitrogen (SMB-N) and phospholipid fatty acid (PLFA) contents were measured four times, at two depths (0-10 and 10-20 cm), over the 2001 growing season. Sample times were: May 7 (preplanting), June 25, July 16, and September 29 (prior to corn harvest). The effect of time was of a greater magnitude than those attributed to tillage or residue treatments. While SMB-C showed little seasonal change (160 μg C g⁻¹ soil), SMB-N was responsive to post-emergence mineral nitrogen fertilization, and PLFA analysis showed an increase in fungi and total PLFA throughout the season. PLFA profiles showed better distinction between sampling time and depth, than between treatments. The effect of residue was more pronounced than that of tillage, with increased SMB-C and SMB-N (61 and 96%) in +R plots compared to −R plots. This study illustrated that measuring soil quality based on soil microbial components must take into account seasonal changes in soil physical and chemical conditions.     

不同利用方式下红壤微生物生物量及代谢功能多样性的变化

研究了不同农林利用方式下红壤微生物生物量和代谢功能多样性等土壤质量指标的变化.结果表明:不同利用方式对土壤质量各指标造成了显著的影响;稻田的微生物生物量碳、氮最高,林地和草地微生物生物量次之,旱地的微生物生物量碳、氮最低(分别是稻田利用方式的4.3% 和 13.7%);稻田的微生物代谢功能多样性最高,旱地、林地和草地的细菌代谢功能多样性较低,旱地的真菌代谢功能多样性最低;微生物生物量和代谢功能多样性可以作为反映土壤质量变化的早期敏感的指标,用来衡量管理措施的改变对土壤质量造成的影响.     

Comparison of phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME) for characterizing soil microbial communities

Phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME), both lipid-based approaches used to characterize microbial communities, were compared with respect to their reliable detection limits, extraction precision, and ability to differentiate agricultural soils. Two sets of soil samples, representing seven crop types from California's Central Valley, were extracted using PLFA and TSFAME procedures. PLFA analysis required 10 times more soil than TSFAME analysis to obtain a reliable microbial community fingerprint and total fatty acid content measurement. Although less soil initially was extracted with TSFAME, total fatty acid (FA) content g⁻¹ soil (DW) was more than 7-fold higher in TSFAME- versus PLFA-extracted samples. Sample extraction precision was much lower with TSFAME analysis than PLFA analysis, with the coefficient of variation between replicates being as much as 4-fold higher with TSFAME extraction. There were significant differences between PLFA- and TSFAME-extracted samples when biomarker pool sizes (mol% values) for bacteria, actinomycetes, and fungi were compared. Correspondence analysis (CA) of PLFA and TSFAME samples indicated that extraction method had the greatest influence on sample FA composition. Soil type also influenced FA composition, with samples grouping by soil type with both extraction methods. However, separate CAs of PLFA- and TSFAME extracted samples depicted strong differences in underlying sample groupings. Recommendations for the selection of extraction method are presented and discussed.     

长期不同施肥条件下红壤性水稻土微生物群落结构的变化

以位于江西省红壤研究所内长期定位试验的水稻土(始于1981年)为研究对象,运用磷脂脂肪酸(phospholipid fatty acid,PLFA)和BIOLOG分析技术研究了不施肥(CK)、单施化肥(NPK)及有机肥与化肥混施(NPKM)三种施肥方式对土壤微生物群落结构的影响。结果表明:长期施化肥和有机肥与化肥混施处理的PLFA总量均高于未施肥处理,两者分别较未施肥处理高91%和309%;PLFA主成分分析(PCA)显示施肥促进了土壤微生物群落结构的变化,其中NPKM处理增加了革兰氏阴性细菌(G-细菌)、真菌、放线菌和原生动物的数量,NPK处理增加了革兰氏阳性细菌(G+细菌)的数量,不施肥处理较施肥处理提高了真菌/细菌比例,CK和NPK处理的微生物群落结构更为相似;各施肥处理间土壤的AWCD值(平均每孔颜色变化率,average well color development,AWCD)表明,NPKM处理能够促进土壤微生物群落对碳源的利用能力,进而增加土壤中微生物的整体活性,而NPK处理减弱了土壤微生物的活性。代谢功能多样性分析同时表明,NPKM处理增加了微生物群落的多样性,而NPK处理使土壤微生物的多样性降低;土壤PLFA与土壤养分的相关性分析显示,土壤总PLFA量与土壤有机质和全氮呈极显著相关(p0.01),与速效养分相关性不大。     

Functional resilience of soil microbial communities depends on both soil structure and microbial community composition

The effects of soil structure and microbial community composition on microbial resistance and resilience to stress were found to be interrelated in a series of experiments. The initial ability of Pseudomonas fluorescens to decompose added plant residues immediately after a copper or heat stress (resistance) depended significantly on which of 26 sterile soils it was inoculated into. Subsequent studies showed that both the resistance and subsequent recovery in the ability of P. fluorescens to decompose added plant residues over 28 days after stress (resilience) varied significantly between a sandy and a clay-loam soil. Sterile, sandy and clay-loam soil was then inoculated with a complex microbial community extracted from either of the soils. The resulting microbial community structure depended on soil type rather than the source of inoculum, whilst the resistance and resilience of decomposition was similarly governed by the soil and not the inoculum source. Resilience of the clay-loam soil to heat stress did not depend on the water content of the soil at the time of stress, although the physical condition of the soil when decomposition was measured did affect the outcome. We propose that soil functional resilience is governed by the physico-chemical structure of the soil through its effect on microbial community composition and microbial physiology.     

Changes in microbial community structure in soil as a result of different amounts of nitrogen fertilization

The changes in size, activity and structure of soil microbial community caused by N fertilization were studied in a laboratory incubation experiment. The rates of N fertiliser applied (KNO₃) were 0 (control), 100 and 2,000 μg N g⁻¹ soil. Despite no extra C sources added, a high percentage of N was immobilized. Whereas no significant increase of microbial C was revealed during incubation period, microbial growth kinetics as determined by the substrate-induced growth-response method demonstrated a significant decrease in the specific growth rate of microbial community in soil treated with 2,000 μg N g⁻¹ soil. Additionally, a shift in microbial community structure resulting in an increase in fungal biomarkers, mainly in the treatment with 2,000 μg N g⁻¹ soil was visible.     

The effect of tropical forest conversion on soil microbial biomass

We investigated the effects of converting forest to savanna and plough land on the microbial biomass in tropical soils of India. Conversion of the forest led to a significant reduction in soil organic C (40–46%), total N (47–53%), and microbial biomass C (52–58%) in the savanna and the plough land. Among forest, savanna, and plough land, basal soil respiration was maximum in the forest, but the microbial metabolic quotient (qCO₂ was estimated to be at a minimum in the forest and at a maximum in the plough land.     

喀斯特生态系统中乔木和灌木林根际土壤微生物生物量及其多样性的比较

我国喀斯特区域面积分布较广,而喀斯特生态系统的退化已成为当前西南地区面临的严重的生态问题。本研究选取贵州中部两种不同植被类型的生态系统—乔木林和灌木林,以乔木林中的白栎、园果化香和灌木林中的火棘、竹叶椒等主要优势树种为对象,研究不同的植物树种对根际土壤微生物生物量及其细菌群落结构的影响。结果显示:乔木林系统中根际土壤微生物生物量碳、氮显著性高于灌木林,植物的根际效应在乔木林中表现更为显著;同时乔木林中的优势树种通过根系分泌物的作用显著提高根际土壤细菌多样性指数,而灌木林中优势树种的根际土壤微生物量及多样性均未表现出明显的根际效应。因此,植被的演替通过改变土壤微生物的特性影响植物-微生物-土壤之间的物质和能量循环,进一步影响喀斯特生态系统的稳定和健康功能。     

Long-term exclusion of plant-inputs to soil reduces the functional capacity of microbial communities to mineralise recalcitrant root-derived carbon sources

Microbial communities in soil are highly species-rich, recognition of which has led to the view that functional redundancy within communities may buffer many impacts of altered community structure on soil functions. In this study we investigated the impact of long-term (>50 years) exclusion of plant-inputs (bare-fallow treatment) on soil microbial community structure and on the ability of the microbial biomass to mineralise tracer additions of ¹³C-labelled plant-derived C-substrates. Exclusion of plant-inputs resulted in depletion of soil organic matter (SOM) and a reduction in microbial biomass size. The microbial community structure was also strongly affected, as indicated by the distinct phospholipid fatty acid (PLFA) profiles in bare-fallow and grassland soils. Mineralisation of labile plant-derived substrates was not perturbed by the bare-fallow treatment. The incorporation of labile plant-derived C into PLFA biomarkers was found to differ between soils, reflecting the distinct community structures of the soils and indicating that these substrates were utilised by a broad range of microbial groups. In contrast, the mineralisation of recalcitrant plant-derived substrates was reduced in bare-fallow soil and the fate of substrate-derived C within PLFA biomarkers was, initially, similar between the soils. These results indicate that utilisation of these recalcitrant substrates was a function restricted to specific groups, and that exclusion of plant-derived inputs to soil had reduced the capacity of bare-fallow microbial communities to utilise this substrate type. Therefore, the study suggests that long-term selective pressure on microbial communities, resulting in altered community structure, may also result in altered functional attributes. This structure-function relationship was apparent for utilisation of recalcitrant plant-derived substrates, but not for the more widely distributed attribute of labile C-substrate utilisation.     

沂蒙山林区不同森林群落土壤水分贮存与入渗特征

为给沂蒙山区森林植被建设中合理群落类型的选择与配置提供参考,采用森林水文学方法,对淮河流域沂蒙山林区典型森林群落的土壤水分贮存与人渗特征进行研究。结果表明：1）森林群落具有显著提高林地土壤孔隙度、土壤贮水量和土壤入渗速率的作用,其作用程度混交林大于纯林,阔叶林大于针叶林;2）森林群落对土壤（非毛管）滞留贮水量的提高程度明显大于土壤毛管吸持贮水量,因而具有明显的涵养水源作用;3）Horton模型和Kostiakov模型能较好模拟研究区森林群落的土壤人渗过程,但通用经验模型和Philip模型的适用性较差;土壤入渗速率与孔隙度之间具有明显的线性正相关关系。     

Soil microbial communities in (sub)alpine grasslands indicate a moderate shift towards new environmental conditions 11 years after soil translocation

A change in environmental conditions may result in altered soil microbial communities in alpine grasslands but the extent and direction of the change is largely unknown. The aim of our study was to investigate (i) differences in soil microbial communities across an elevation gradient of (sub)alpine grassland soils in the Swiss Alps, and (ii) the long-term effect of translocation of soil cores from a higher to a lower elevation site. The translocation of undisturbed soil cores from a high alpine site (2525 m asl) to a subalpine site near the timberline (1895 m asl) induced an effective artificial warming of 3.3 °C. We hypothesized that after longer than a decade, soil microbial community in translocated cores would differ from that at the original site but resemble the community at the new site. Results from soil phospholipid fatty acid (PLFA) analysis confirm significant differences in microbial communities between sites and a shift in total microbial biomass (TMB) and proportional distribution of structural groups in the translocated cores towards the lower elevation community. Patterns related to translocation were also observed as shifts in the fractional biomass of ectomycorrhizal and arbuscular fungi, and in relative contents of several structural groups. Hence, soil microbial community activity and diversity indicate a moderate shift towards new site conditions after 11 years and therefore, our data suggest slow responses of microbial communities to environmental changes in alpine soils.     

Tree influence on soil microbial community structure

Biological communities differ over time and in space, and in the forest these communities often vary according to trees and tree gaps, mediated by mechanisms that are likely to change over time and as a tree are removed. In this paper we ask the questions: What is the influence of individual trees on soil microbial community structure? Does the soil microbial community change in the short-term when a tree is removed, and does this change depend on the initial influence of the tree? We use phospholipid fatty acid (PLFA) analysis and a geostatistical approach to study effects of trees and tree removal (thinning) on soil microbial community structure in a young boreal Norway spruce (Picea abies) forest. An experiment was setup where half (four) of the included trees were cut and soil was collected prior to (t0) and one month after (t1) tree felling. The samples were collected along two perpendicular transects originating from each of the eight study trees. A tree influence index was calculated for each sample point from the distances to neighbouring trees, weighted by tree diameter. We found that individual trees are important in structuring the soil microbial community as microbial community structure responded to the gradient in tree influence. Also strong spatial structure was found corresponding to the patch structure induced by trees. Changes in microbial community structure before and after tree felling (t0 and t1) was found to differ significantly between felled and non-felled trees: samples from felled trees came to resemble samples with a low value of tree influence and samples from below non-felled trees came to resemble samples with a high value for tree influence. We thus found that soil microbial community structure in a boreal forest is spatially structured by the distribution of single trees, and that soil microbial community structure varies seasonally and is affected by tree removal, in an intricate manner that reflects the initial influence of trees.     

Seasonal and long-term resource-related variations in soil microbial communities in wheat-based rotations of the Canadian prairie

Like all other living organisms, microorganisms depend on nutrients, carbon and energy. Since microorganisms are central to most soil processes, the sustainable management of agricultural soils may need to consider the impact of soil fertility management on the soil microbial community. We tested the hypothesis that different rates of N and P fertilizers, and cropping frequency (modifying C input to soil) influence the size, structure and physiological condition of soil microbial populations residing in the plough layer (top 7.5 cm). For this study, we used a 37-yr old long-term wheat-based rotation experiment located in the semiarid Brown soil zone of Saskatchewan. The experiment included (1) four input treatments: (i) no N or (ii) no P fertilizer application to wheat (Triticum aestivum L.) grown in fallow-wheat-wheat (F-W-W) rotations, and (iii) recommended rates of both N and P fertilizer applied to fallow-wheat (F-W) and (iv) to F-W-W; (2) two rotation phases: fallow and wheat-after-fallow; and (3) four sampling times: 8 June, 4 July, 5 August and 16 September 2003. Increased partitioning into storage lipids of the arbuscular mycorrhizal fungi (AMF) fatty acid methyl ester (FAME) biomarker 16:1ω5 (P=0.04), suggested the accumulation of storage material under low soil N availability. Discriminant analysis detected modifications in soil microbial community structure due to cropping frequency (P=0.001) and sampling time, the effect of which was different in the fallow (P<0.0001) and wheat-after-fallow (P<0.0001) phases of the rotations. Correlation analysis of soil variables conducted in plots growing wheat revealed a dual effect of plants, which stimulated active soil microbial biomass (SMB), possibly through the release of soluble extractable C (C_sol−ext) in soil and, at the same time, SMB competed with wheat for soil water and N. The 37 y of different nutrient input treatments had no effect upon the active soil microbial biomass according to PLFA measurements, despite changes in soil resource-related variables (soil water potential, soil PO₄-P and NO₃-N fluxes, and C_sol−ext concentrations) (P?0.003). The biomass of each of three microbial populations monitored was lowest on 4 July, when the amounts of the soil resources monitored were average, and greatest on 5 August, when N, P and soil moisture availability was lowest. The temporal effect on the biomass of microbial populations seemed unrelated to variation in nutrient or water availability. We conclude that the soil microbial community is adaptable to a wide range of soil conditions. We propose therefore that the occurrence of sudden and dramatic events, such as a heavy rainfall on a dry soil, is the most important determinant of seasonal variation in active soil microbial biomass.     

氮素浓度和水分对水稻土硝化作用和微生物特性的影响

为了明确不同氮素浓度和水分对土壤硝化作用和微生物特性的影响,特别是高氮素浓度下的响应特异性,以红壤水稻土为供试土壤,设置4个硫铵用量水平[0(CK)、120 mg(N).kg-1(A1)、600 mg(N).kg-1(A2)、1 200 mg(N).kg-1(A3)],调节土壤水分为饱和持水量(WHC)的40%、60%和80%,研究了短期内不同氮素浓度和不同水分条件下土壤硝化作用、微生物生物量碳和微生物功能多样性的变化。结果表明:在40%、60%和80%WHC水分条件时,硫铵A2、A3浓度处理土壤硝化率和硝化速率普遍较低,硫铵A1浓度处理硝化率和硝化速率随土壤含水量的升高而升高;同含水量时随硫铵用量的升高而显著降低。在40%、60%和80%WHC水分条件时,微生物生物量碳随硫铵浓度的升高而降低;同浓度硫铵用量水平时,微生物生物量碳的变化基本表现为:60%WHC80%WHC40%WHC。分析发现不同水分和硫铵处理之间存在交互作用。BIOLOG分析显示:不同氮素浓度和不同水分处理,60%WHC下A1处理的平均吸光值(AWCD)和Shannon、Simpson、McIntosh指数最大,其次为60%WHC的硫铵CK处理,而不同水分下硫铵A2、A3处理,其AWCD值和Shannon、Simpson、McIntosh多样性指数都较低,进一步说明过量施肥导致微生物活性降低。不同氮素浓度和水分条件下土壤微生物和生化性状不同,过量施用化肥后将有可能造成土壤微生物性状和生化功能衰减。     

Response of soil respiration to nitrogen addition in two subtropical forest types

Anthropogenic activities have increased nitrogen (N) deposition in terrestrial ecosystems, which directly and indirectly affects soil biogeochemical processes, including soil respiration. However, the effects of the increases in N availability on soil respiration are not fully understood. In this study, soil respiration was measured using an infrared gas analyzer system with soil chambers under four N treatments (0, 5, 15, and 30 g N m^-2 year^-1 as control, low N (LN), moderate N (MN), and high N (HN), respectively) in camphor tree and slash pine forests in subtropical China. Results showed that soil respiration rates decreased by 37% in the camphor tree forest and 27% in the slash pine forest on average on an annual base, respectively, in the N-fertilized treatments when compared with the control. No significant differences were found in the soil respiration rate among the LN, MN, and HN treatments in both forest types as these fertilized plots reached an adequate N content zone. In addition, soil microbial biomass carbon (C) content and fine root biomass declined in N-treated plots compared to the control. Our results indicated that elevated N deposition might alter the tree growth pattern, C partitioning, and microbial activity, which further affect soil C sequestration by reducing soil respiration in subtropical forests of China.     

基于BIOLOG指纹解析三种不同森林类型土壤细菌群落功能差异

土壤微生物是生态系统的重要组成部分,直接参与土壤碳氮循环及土壤有机质矿化过程,在生态系统中具有不可替代的作用[1].土壤微生物群落多样性反映了群落总体的动态变化,而微生物对不同碳源的利用能力很大程度上取决于微生物的种类和固有性质,因此分析土壤微生物对不同碳源利用能力能够在一定程度上反映土壤碳源转化和土壤微生物多样性情况.     

Environmental conditions rather than microbial inoculum composition determine the bacterial composition,microbial biomass and enzymatic activity of reconstructed soil microbial communities

The composition of microbial communities and the level of enzymatic activity in the soil are both important indicators of soil quality, but the mechanisms by which a soil bacterial community is generated and maintained are not yet fully understood. Two soil samples were collected from the same location, but each had been subjected to a different long-term fertilization treatment and was characterized by different microbial diversity, biomass and physicochemical properties. These samples were γ-sterilized and swap inoculated. Non-sterilized soil samples along with sterilized and inoculated soil samples were incubated for eight months before their nutrient content, microbial biomass, enzymatic activity and bacterial composition were analyzed. Total phosphorus, and potassium concentrations along with the overall organic matter content of the non-sterilized soil were all equal to those of the same soil that had been sterilized and self/swap inoculated. Additionally, the microbial biomass carbon concentration was not affected by the specific inoculum and varied only by soil type. The activities of catalase, invertase, urease, protease, acid phosphatase and phytase were smaller in the sterilized soils that had been inoculated with organisms from chemical fertilizer amended soil (NPK) when compared to sterilized soil inoculated with organisms from manure and chemical fertilizer amended soil (NPKM) and non-sterilized soil samples. Bacterial 16S rRNA examined by 454-pyrosequencing revealed that the composition of bacterial community reconstructed by immigrant microbial inoculum in the soil was mainly influenced by its physicochemical properties, although the microbial inoculum contained different abundances of bacterial taxa. For example, the pH of the soil was the dominant factor in reconstructing a new bacterial community. Taken together, these results demonstrated that both soil microbial composition and functionality were primarily determined by soil properties rather than the microbial inoculum, which contributed to our understanding of how soil microbial communities are generated and maintained.