Structure and function of the soil microbial community in a long-term fertilizer experiment

The effect of organic and inorganic fertiliser amendments is often studied shortly after addition of a single dose to the soil but less is known about the long-term effects of amendments. We conducted a study to determine the effects of long-term addition of organic and inorganic fertiliser amendments at low rates on soil chemical and biological properties. Surface soil samples were taken from an experimental field site near Cologne, Germany in summer 2000. At this site, five different treatments were established in 1969: mineral fertiliser (NPK), crop residues removed (mineral only); mineral fertiliser with crop residues; manure 5.2 t ha⁻¹ yr⁻¹; sewage sludge 7.6 t ha⁻¹ yr⁻¹ or straw 4.0 t ha⁻¹ yr⁻¹ with 10 kg N as CaCN₂ t straw⁻¹. The organic amendments increased the C_org content of the soil but had no significant effect on the dissolved organic C (DOC) content. The C/N ratio was highest in the straw treatment and lowest in the mineral only treatment. Of the enzymes studied, only protease activity was affected by the different amendments. It was highest after sewage amendment and lowest in the mineral only treatment. The ratios of Gram+ to Gram− bacteria and of bacteria to fungi, as determined by signature phospholipid fatty acids, were higher in the organic treatments than in the inorganic treatments. The community structure of bacteria and eukaryotic microorganisms was assessed by denaturing gradient gel electrophoresis (DGGE) and redundancy discriminate analyses of the DGGE banding patterns. While the bacterial community structure was affected by the treatments this was not the case for the eukaryotes. Bacterial and eukaryotic community structures were significantly affected by C_org content and C/N ratio.     

保护性耕作对黑土微生物群落的影响

耕作方式通过影响土壤微生物群落而影响土壤生态系统过程。本研究以传统耕作玉米连作处理为对照,通过测定土壤微生物量碳及磷脂脂肪酸含量,分析了保护性耕作(包括免耕玉米连作和免耕大豆-玉米轮作)对黑土微生物群落的影响。结果表明,保护性耕作可显著增加土壤表层(0～5cm)全碳、全氮、水溶性有机碳、碱解氮和微生物量碳(P0.05),为微生物代谢提供了丰富的资源。同时,保护性耕作显著提高了土壤表层(0～5cm)总脂肪酸量、真菌和细菌生物量(P0.05),提高了土壤的真菌/细菌值,有利于农田土壤生态系统的稳定性。研究结果对于探讨保护性耕作的内在机制具有重要意义。     

Changes in the soil microbial community structure with latitude in eastern China, based on phospholipid fatty acid analysis

Phospholipid fatty acid (PLFA) profiles were measured in soils from 14 sites in eastern China representing typical geographic zones of varying latitude from north (47.4°N) to south (21.4°N). Amounts of soil microbial biomass, measured as total amounts of PLFAs, showed no regular trend with latitude, but were positively correlated with soil organic carbon content, the concentration of humic acid and amorphous iron oxide. Soil microbial community structure showed some biogeographical distribution trends and was separated into three groups in a cluster analysis and principal coordinate analysis of log transformed PLFA concentrations (mol%). Soils in the first group came from northern China with medium mean annual temperature (1.2–15.7 °C) and rainfall (550–1021 mm). Soils in the second group originated from southern China with a relatively higher mean annual temperature (15.7–21.2 °C) and rainfall (1021–1690 mm). Soils clustered in the third group originated from the most southerly region. The northern soils contained relatively more bacteria and Gram-negative PLFAs, while the southern soils had more fungi and pressure indexed PLFAs. These differences in soil microbial community structure were largely explained by soil pH, while other site and soil characteristics were less important.     

Effects of tree identity dominate over tree diversity on the soil microbial community structure

This study investigated the possible effects of tree species diversity and identity on the soil microbial community in a species-rich temperate broad-leaved forest. For the first time, we separated the effects of tree identity and tree species diversity on the link between above and belowground communities in a near-natural forest. We established 100 tree clusters consisting of each three tree individuals represented by beech (Fagus sylvatica L.), ash (Fraxinus excelsior L.), hornbeam (Carpinus betulus L.), maple (Acer pseudoplatanus L.), or lime (Tilia spec.) at two different sites in the Hainich National Park (Thuringia, Germany). The tree clusters included one, two or three species forming a diversity gradient. We investigated the microbial community structure, using phospholipid fatty acid (PLFA) profiles, in mineral soil samples (0–10 cm) collected in the centre of each cluster.The lowest total PLFA amounts were found in the pure beech clusters (79.0 ± 23.5 nmol g⁻¹ soil dw), the highest PLFA amounts existed in the pure ash clusters (287.3 ± 211.3 nmol g⁻¹ soil dw). Using principle components analyses (PCA) and redundancy analyses (RDA), we found only for the variables ‘relative proportion of beech trees’ and ‘living lime fine root tips associated with ectomycorrhiza’ a significant effect on the PLFA composition. The microbial community structure was mainly determined by abiotic environmental parameters such as soil pH or clay content. The different species richness levels in the clusters did not significantly differ in their total PLFA amounts and their PLFA composition. We observed a tendency that the PLFA profiles of the microbial communities in more tree species-rich clusters were less influenced by individual PLFAs (more homogenous) than those from species-poor clusters.We concluded that tree species identity and site conditions were more important factors determining the soil microbial community structure than tree species diversity per se.     

Microbial community structure and functionality under peanut-based cropping systems in a sandy soil

Little information is available on soil microbial and biochemical properties, important for understanding nutrient cycling and organic matter dynamics, as affected by different peanut cropping systems and how they relate to soil functioning. Thus, we studied a Tifton loamy sand (fine-loamy, kaolinitic, thermic Plinthic Kandiudults) in Georgia, which is first in peanut production in USA, after 5 and 8 years under continuous cotton (Gossypium hirsutum, L) (CtCtCt), cotton–cotton–peanut (CtCtPt), corn (Zea mays L.)–peanut–cotton (CrPtCt), peanut–peanut–cotton (PtPtCt), and continuous peanut (PtPtPt). Soil organic carbon (OC) at 0–20 cm was already higher under PtPtPt (average, 8.7 g C kg⁻¹ soil), PtPtCt (average, 7.7 g C kg⁻¹ soil), and CrPtCt (average, 7.8 g C kg⁻¹ soil) compared with CtCtPt (average, 4.7 g C kg⁻¹ soil) and CtCtCt (average, 3.3 g C kg⁻¹ soil). Similarly, alkaline phosphatase, acid phosphatase, and phosphodiesterase as a group showed higher activities under PtPtPt, PtPtCt, and CrPtCt than under CtCtPt and CtCtCt. The activities of glycosidases (α-galactosidase, β-glucosidase, and β-glucosaminidase) as a group were more sensitive to the cropping systems than phosphastases and showed a distinctive cropping system separation as follows: PtPtPt = CrPtCt > PtPtCt > CtCtPt > CtCtCt. Similar to OC and microbial biomass C trends, distinctive differences were found in the microbial community structure of this sandy soil after 8 years between peanut-based cropping systems (CrPtCt, PtPtCt, and PtPtPt) and cotton-based cropping systems (CtCtCt and CtCtPt) as indicated by the fatty acid methyl esters profiles. Trade names and company names are included for the benefit of the reader and do not infer any endorsement or preferential treatment of the product by USDA-ARS.     

Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure

Plant-soil feedbacks are gaining attention for their ability to determine plant community development. Plant-soil feedback models and research assume that plant-soil interactions occur within days to weeks, yet, little is known about how quickly and to what extent plants change soil community composition. We grew a dominant native plant (Pseudoroegneria spicata) and a dominant non-native plant (Centaurea diffusa) separately in both native- and non-native-cultivated field soils to test if these species could overcome soil legacies and create new soil communities in the short-term. Soil community composition before and after plant growth was assessed in bulk and rhizosphere soils using phospholipid fatty acid analyses. Nematode abundance and mycorrhizal colonization were also measured following plant growth. Field-collected, native-cultivated soils showed greater bacterial, Gram (−), fungal, and arbuscular mycorrhizal PLFA abundance and greater PLFA diversity than field-collected, non-native-cultivated soils. Both plant species grew larger in native- than non-native-cultivated soils, but neither plant affected microbial composition in the bulk or rhizosphere soils after two months. Plants also failed to change nematode abundance or mycorrhizal colonization. Plants, therefore, appear able to create microbial legacies that affect subsequent plant growth, but contrary to common assumptions, the species in this study are likely to require years to create these legacies. Our results are consistent with other studies that demonstrate long-term legacies in soil microbial communities and suggest that the development of plant-soil feedbacks should be viewed in this longer-term context.     

Exotic earthworms alter soil microbial community composition and function

Exotic earthworms can profoundly alter soil carbon (C) and nitrogen (N) dynamics in northern temperate forests, but the mechanisms explaining these responses are not well understood. We compared the soil microbial community (SMC) composition (measured as PLFAs) and enzyme activity between paired earthworm-invaded and earthworm-free plots in northern hardwood forests of New York, USA. We hypothesized that differences in SMCs and enzyme activity between plots would correspond with differences in soil C content and C:N ratios. Relative abundance of several bacterial (mostly gram-positive) PLFAs was higher and that of two fungal PLFAs was lower in earthworm compared to reference plots, largely because of earthworm incorporation of the organic horizon into mineral soil. In surface mineral soil earthworms increased arbuscular mycorrhizal fungi (AMF) and gram-positive bacterial PLFAs, and decreased fungal (mostly saprotrophic) and several bacterial (gram-negative and non-specific) PLFAs. Earthworms also increased the activities of cellulolytic relative to lignolytic enzymes in surface mineral soil, and the relationships between enzyme activities and components of the SMC suggest a substrate-mediated effect on the SMC and its metabolism of C. A highly significant relationship between components of the SMC and soil C:N also suggests that earthworms reduce soil C:N through functional and compositional shifts in the SMC. Finally, changes in AMF abundances were linked to phosphatase activity, suggesting that earthworms do not necessarily inhibit P-acquisition by AMF-associated plants in our study system. We conclude that the combined influence of earthworm-related changes in physical structure, accessibility and chemistry of organic matter, and relative abundance of certain groups of fungi and bacteria promote C metabolism, in particular by increasing the activities of cellulolytic vs. lignolytic enzymes.     

土壤微生物群落结构对凋落物组成变化的响应

凋落物分解是陆地生态系统养分循环的关键过程,明确凋落物多样性如何影响土壤微生物群落构成和多度,继而潜在地改变凋落物分解的微生物学机制有助于认识生物多样性和森林生态系统功能的关系。通过小盆模拟试验,应用磷脂脂肪酸谱图的方法研究了我国南方红壤丘陵区典型物种马尾松和湿地松的凋落物分别与白栎和青冈的凋落物混合,与单一针叶凋落物分解时相比,针阔混合凋落物分解过程中土壤微生物群落结构的变化,结果显示:(1)针阔混合凋落物分解时土壤微生物群落磷脂脂肪酸(Phospholipidfatty acids,PLFA)总量低于单一针叶处理,细菌和放线菌的相对多度高于单一针叶处理,真菌则相反,群落真菌/细菌低于单一针叶处理,土壤微生物生物量的差异主要来自于真菌;(2)主成分分析表明:针阔混合凋落物分解与单一针叶凋落物分解的土壤微生物群落结构差异显著,两个时期(分解9个月和18个月)主成分一分别可以解释65.74%和89.63%的变异,第一主成分主要包括18∶2ω6,9、18∶1ω9c、17∶0和10Me18∶0等磷脂脂肪酸;(3)土壤微生物群落结构受凋落物初始C/N和木质素/N调控,土壤微生物群落细菌的相对多度与凋落物初始C/N和木质素/N显著负相关,真菌则与凋落物初始C/N和木质素/N显著正相关,群落真菌/细菌与凋落物初始C/N和木质素/N显著正相关。针阔凋落物混合分解通过改变凋落物C/N和木质素/N,提供了对分解者更为有利的微环境。     

Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil

 Particle-size fractionation of a heavy metal polluted soil was performed to study the influence of environmental pollution on microbial community structure, microbial biomass, microbial residues and enzyme activities in microhabitats of a Calcaric Phaeocem. In 1987, the soil was experimentally contaminated with four heavy metal loads: (1) uncontaminated controls; (2) light (300 ppm Zn, 100 ppm Cu, 50 ppm Ni, 50 ppm V and 3 ppm Cd); (3) medium; and (4) heavy pollution (two- and threefold the light load, respectively). After 10 years of exposure, the highest concentrations of microbial ninhydrin-reactive nitrogen were found in the clay (2–0.1 μm) and silt fractions (63–2 μm), and the lowest were found in the coarse sand fraction (2,000–250 μm). The phospholipid fatty acid analyses (PLFA) and denaturing gradient gel electrophoresis (DGGE) separation of 16S rRNA gene fragments revealed that the microbial biomass within the clay fraction was predominantly due to soil bacteria. In contrast, a high percentage of fungal-derived PLFA 18 : 2ω6 was found in the coarse sand fraction. Bacterial residues such as muramic acid accumulated in the finer fractions in relation to fungal residues. The fractions also differed with respect to substrate utilization: Urease was located mainly in the <2 μm fraction, alkaline phosphatase and arylsulfatase in the 2–63 μm fraction, and xylanase activity was equally distributed in all fractions. Heavy metal pollution significantly decreased the concentration of ninhydrin-reactive nitrogen of soil microorganisms in the silt and clay fraction and thus in the bulk soil. Soil enzyme activity was reduced significantly in all fractions subjected to heavy metal pollution in the order arylsulfatase >phosphatase >urease >xylanase. Heavy metal pollution did not markedly change the similarity pattern of the DGGE profiles and amino sugar concentrations. Therefore, microbial biomass and enzyme activities seem to be more sensitive than 16S rRNA gene fragments and microbial amino-sugar-N to heavy metal treatment. Received: 21 January 2000     

Substrate inputs and pH as factors controlling microbial biomass, activity and community structure in an arable soil

Our aim was to determine whether the smaller biomasses generally found in low pH compared to high pH arable soils under similar management are due principally to the decreased inputs of substrate or whether some factor(s) associated with pH are also important. This was tested in a soil incubation experiment using wheat straw as substrate and soils of different pHs (8.09, 6.61, 4.65 and 4.17). Microbial biomass ninhydrin-N, and microbial community structure evaluated by phospholipid fatty acids (PLFAs), were measured at 0 (control soil only), 5, 25 and 50 days and CO₂ evolution up to 100 days. Straw addition increased biomass ninhydrin-N, CO₂ evolution and total PLFA concentrations at all soil pH values. The positive effect of straw addition on biomass ninhydrin-N was less in soils of pH 4.17 and 4.65. Similarly total PLFA concentrations were smallest at the lowest pH. This indicated that there is a direct pH effect as well as effects related to different substrate availabilities on microbial biomass and community structure. In the control soils, the fatty acids 16:1ω5, 16:1ω7c, 18:1ω7c&9t and i17:0 had significant and positive linear relationships with soil pH. In contrast, the fatty acids i15:0, a15:0, i16:0 and br17:0, 16:02OH, 18:2ω6,9, 17:0, 19:0, 17:0c9,10 and 19:0c9,10 were greatest in control soils at the lowest pHs. In soils given straw, the fatty acids 16:1ω5, 16:1ω7c, 15:0 and 18:0 had significant and positive linear relationships with pH, but the concentration of the monounsaturated 18:1ω9 PLFA decreased at the highest pHs. The PLFA profiles indicative of Gram-positive bacteria were more abundant than Gram-negative ones at the lowest pH in control soils, but in soils given straw these trends were reversed. In contrast, straw addition changed the microbial community structures least at pH 6.61. The ratio: [fungal PLFA 18:2w6,9]/[total PLFAs indicative of bacteria] indicated that fungal PLFAs were more dominant in the microbial communities of the lowest pH soil. In summary, this work shows that soil pH has marked effects on microbial biomass, community structure, and response to substrate addition.     

Decoupling plant-growth from land-use legacies in soil microbial communities

Differences in soil microbial communities between ex-arable and undisturbed soils are often assumed to reflect long-term legacies of agricultural practices. Ex-arable soils, however, are commonly dominated by different plant species than undisturbed soils making it difficult to separate the importance of land-use and plant-growth legacies. In a system where non-native plants dominate ex-arable soils, we decoupled land-use (ex-arable, undisturbed) and plant-growth (native, non-native) effects on soil microbial communities using a factorial sampling design. Soils were removed from 14 sites that formed a 52-year chronosequence of agricultural abandonment. Microbial abundance and composition were measured using whole-soil phospholipid fatty acid analyses and microbial activity was measured in a subset of samples using sole-carbon-source utilization analyses. We found that both non-native-cultivated and ex-arable soils were independently associated with lower microbial abundance and diversity than native and undisturbed soils. We also found a correlation between microbial abundance and age-since-agricultural abandonment in ex-arable/non-native-cultivated soils suggesting that non-native plant effects accumulate over time. Microbial activity was consistent with microbial abundance; microbial communities in non-native-cultivated, ex-arable soils were slow to respire most carbon sources. Our data suggests that agricultural practices create soil conditions that favor non-native plant growth and non-native plants maintain these conditions. Potential mechanisms explaining how non-natives create soils with small microbial communities and how small microbial communities may benefit non-natives are discussed.     

PLFA方法研究连作对加工番茄根际土壤微生物群落结构的影响

通过在石河子大学农学院试验站开展加工番茄连作定点微区试验,采用氯仿熏蒸和磷脂脂肪酸(PLFA)法相结合,研究了不同连作处理(种植1 a、连作3 a、5 a和7 a)对新疆加工番茄花果期和成熟期根际土壤微生物群落结构及土壤微生物量的影响。结果表明,连作导致土壤微生物量碳(SMBC)、微生物量氮(SMBN)和微生物熵(q MB)下降,SMBC/SMBN升高,而微生物量磷(SMBP)随连作年限和生育期的变化而不同。连作显著增加了真菌PLFAs含量,降低了细菌PLFAs含量、土壤PLFAs总量及细菌/真菌PLFAs的比值,而放线菌PLFAs含量变化无规律。连作7 a时,成熟期的细菌PLFAs含量、土壤PLFAs总量较对照分别减少62.9%、50.3%(P0.05),而真菌PLFAs含量较对照升高60.2%(P0.05)。从多样性指数分析看,Shannon-Wiener指数、Simpson指数、Brillouin指数和Pielou指数均随连作年限的延长呈先升后降的变化,其中连作3 a时各项指数最大,连作7 a时最小,表明在本试验年限范围内,连作使得微生物群落多样性与均匀程度皆出现了一定程度的降低。相关性分析表明,土壤微生物各类群PLFAs量、微生物量及土壤肥力之间存在相关性,说明土壤微生物量与土壤肥沃程度相关,可作为评价土壤肥力的生物学指标。可见,加工番茄连作改变了土壤微生物群落结构,降低了土壤微生物量,最终在根际土壤微生态系统和环境因子等因素的综合作用下产生连作障碍。     

Defoliation and fertiliser influences on the soil microbial community associated with two contrasting Lolium perenne cultivars

The influence of repeated defoliation on soil microbial community (SMC) structure and root turnover was assessed in two contrasting Lolium perenne cultivars (AberDove and S23) grown in fertilised (+F) and non-fertilised (NF) soil. BiOLOG sole carbon source utilisation profiles (SCSUPs) indicated consistently greater potential carbon utilisation in defoliated (+D) compared to non-defoliated (ND) soils regardless of cultivar and fertiliser, and was accounted for in a variety of substrate groups (sugars, carboxylic, amino and phenolic acids). Potential carbon utilisation was also stimulated in +F compared to NF soils, primarily through increased potential utilisation of carboxylic acids. PLFA indicators for the bacterial biomass did not significantly differ between cultivar, soil fertilisation, or defoliation. Defoliated swards grown in fertilised soil (+F+D) had a higher fungal:bacterial ratio and a greater bacterial stress index (cy19:0/18:1w7c), compared to that of +F ND, NF ND and NF+D, and regardless of cultivar. Overall SMC structure (canonical variate (CV) analysis of PLFAs) discriminated based on cultivar, defoliation and soil fertilisation. Primary discrimination of the SMCs could be related to differences in root density and total plant biomass, and in the case of NF soils, secondary community shifts, evident with defoliation, related to root disappearance over the growing season. Despite the strong common effects of defoliation, and to a lesser extent soil fertilisation, cultivar specific drivers of the soil microbial community were maintained, resulting in consistent, but subtle, discrimination of the SMC associated with the contrasting L. perenne cultivars.     

不同培肥方式对土壤有机碳与微生物群落结构的影响

为揭示旱作区耕地土壤有机碳累积规律及其与土壤微生物群落间的相互作用机制,试验采用磷脂脂肪酸(PLFA)指纹图谱及土壤腐殖质形态分组的方法,通过田间定位试验,研究了马铃薯-马铃薯-油用向日葵-马铃薯-油用向日葵轮作模式下,有机、无机肥配施(不施肥、单施化肥、化肥配施牛粪、化肥配施羊粪、化肥配施生物有机肥、化肥配施黄腐酸钾)对土壤有机碳累积、土壤腐殖质形态的影响及其与土壤微生物群落结构间的相互关系。结果表明:在连续培肥5年间,随培肥时间延长,土壤有机碳呈波动性上升趋势。与对照相比,化肥配施牛粪、化肥配施羊粪处理土壤有机碳以年6.61%和8.97%的增长率累积增加,不同处理外源有机碳含量及有机肥种类的差异影响了土壤有机碳的累积速率。化肥配施高量有机肥(化肥+羊粪、化肥+牛粪)处理显著提高了土壤稳结态、松结态腐殖质含量及松结态/紧结态腐殖质的比例,且以PLFA表征的土壤细菌、真菌、放线菌、原生动物、土壤微生物群落总生物量与对照处理间均有显著性差异(P0.05)。与对照相比,各施肥处理的革兰氏阳性菌/革兰氏阴性菌(G+/G-)值均呈降低趋势;但不同有机无机相结合的土壤培肥方式对土壤G+/G-的比例没有显著差异。多元分析表明,基于土壤微生物主要类群磷脂脂肪酸含量的排序轴与基于土壤有机碳、腐殖质形态的排序轴之间相关性(P1=0.568,P2=0.611)较好,累积变量在98.69%上揭示不同有机无机培肥措施影响下的土壤微生物群落生物量与环境因子间的相互关系。土壤松结态腐殖质含量与土壤G+/G-比值正相关。外源有机碳的施入促进了土壤紧结态腐殖碳向稳结态、松结态腐殖质转化;较高量外源有机碳施入有助于提升土壤细菌、真菌的生物量。总体而言,土壤微生物群落结构的变化是受有机无机培肥措施所引起的土壤有机碳含量、腐殖质形态变化驱动;化肥配施牛粪和化肥配施羊粪有利于土壤有机碳积累和松结态腐殖质的形成,促进土壤中微生物生物量提高。研究结果可为宁夏中部干旱区土壤合理培肥提供科学依据。     

棉花连作对北疆土壤酶活性、致病菌及拮抗菌多样性的影响

本文通过测定土壤酶活性与微生物PCR-DGGE指纹图谱研究了北疆棉区5年棉花连作(CtN5)、10年棉花连作(CtN10)及15年棉花连作(CtN15)对土壤过氧化氢酶、蔗糖酶、芳基硫酸酯酶、脱氢酶和蛋白酶酶活性的影响,分析了土壤细菌、真菌、镰刀菌和枯草芽孢杆菌群落结构多样性对北疆棉田长期连作的响应。结果表明:过氧化氢酶、蔗糖酶、脱氢酶活性随棉花连作年限延长而下降。CtN15处理的过氧化氢酶、蔗糖酶和脱氢酶活性分别比CtN10处理下降15.0%、6.4%和12.0%,比CtN5处理下降16.8%、58.6%和49.5%(P0.05);芳基硫酸酯酶与蛋白酶活性随连作年限的增加呈先下降后升高的特点。土壤细菌、真菌多样性指数随连作年限的增加明显下降。CtN15的细菌条带数比CtN10下降7.41%,Ct N10比CtN5降低1.72%。CtN15真菌条带数和Shannon-Wiener多样性指数分别为78和3.22,比CtN5处理低17.02%和5.29%。土壤镰刀菌和枯草芽孢杆菌的条带数、多样性指数均表现为先下降后升高。CtN15枯草芽孢杆菌Shannon-Wiener和Simpson指数分别比CtN10处理高54.8%和14.5%。北疆长期连作棉田的土壤酶活性和土壤微生物群落多样性总体呈下降趋势,长期连作对棉田土壤生物性状有明显负面影响。     

Plant species richness does not attenuate responses of soil microbial and nematode communities to a flood event

Human activities are causing climatic changes and alter the composition and biodiversity of ecosystems. Climate change has been and will be increasing the frequency and severity of extreme climate events and natural disasters like floods in many ecosystems. Therefore, it is important to investigate the effects of disturbances on ecosystems and identify potential stabilizing features of ecological communities. In this study, soil microbial and nematode communities were investigated in a grassland biodiversity experiment after a natural flood to investigate if plant diversity is able to attenuate or reinforce the magnitude of effects of the disturbance on soil food webs. In addition to community analyses of soil microorganisms and nematodes, the stability indices proportional resilience, proportional recovery, and proportional resistance were calculated. Generally, soil microbial biomass decreased significantly due to the flood with the strongest reduction in gram-negative bacteria, while gram-positive bacteria were less affected by flooding. Fungal biomass increased significantly three months after the flood compared to few days before the flood, reflecting elevated availability of dead plant biomass in response to the flood. Similar to the soil microbial community, nematode community structure changed considerably due to the flood by favoring colonizers (in the broadest sense r-strategists; c–p 1, 2 nematodes), particularly so at high plant diversity. None of the soil microbial community stability indices and few of the nematode stability indices were significantly affected by plant diversity, indicating limited potential of plant diversity to buffer soil food webs against flooding disturbance. However, plant diversity destabilized colonizer populations, while persister populations (in the broadest sense K-strategists; c–p 4 nematodes) were stabilized, suggesting that plant diversity can stabilize and destabilize populations depending on the ecology of the focal taxa. The present study shows that changes in plant diversity and subsequent alterations in resource availability may significantly modify the compositional shifts of soil food webs in response to disturbances.     

Phospholipid fatty acid profiles as indicators for the microbial community structure in soils along a climatic transect in the Judean Desert

 Analyses of phospholipid fatty acids (PLFAs) were used to assess variations in soil microbial biodiversity, community structure and biomass, and consequently, the soil microbial successions in time along the climate gradient of the Judean Desert. Principal component analysis of the PLFA data revealed that the degree of time- and space-related variations in PLFA composition and microbial community structure was high among the desert habitats. Significant shifts of specific groups of fatty acids caused by climatic variations were observed. The biomass represented by the total amounts of PLFAs indicated that the greater the average amount of precipitation, the higher the biomass. The results indicate that at least three different microorganism strategies were probably followed: (1) in soils with a high biomass during the rainy period, a significant biomass decrease occurred during the dry period, mainly due to an extraordinary decrease of Gram-negative bacteria as indicated by the decrease of typical monounsaturated fatty acids and hydroxy-substituted phospholipid fatty acids in semi-arid climates; (2) in soils with low biomass content during the rainy period, a significant increase of biomass during the dry period occurred, due mainly to the increase of eukaryotes, Gram-positive, and Gram-negative bacteria characterized by polyunsaturated, branched chain and some of the monounsaturated fatty acids, respectively; and (3) relatively low and constant biomass during the entire observation period in the more arid zones of the Judean Desert. Received: 12 January 1998     

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.     

Rock fragments in soil support a different microbial community from the fine earth

Two sandstone-derived soils under pure stands of silver fir (Abies alba Mill.) and European beech (Fagus sylvatica L.) were studied to determine if the fine earth (<2 mm material) and two size-classes of porous rock fragments (>2 mm material) supported different microbial communities. Samples from three soil horizons (A, Bw, and BC) were analysed under both optical and scanning electron microscopes. Small stones (2-10 mm in average diameter) appeared more altered than larger ones (40-60 mm) and the effects of weathering became more obvious with shallower depth. In both soils, numerous hyphae and other living forms were observed on the surface of the stones from the A and Bw horizons; this contrasted with the stones from the BC horizon, which showed little or no colonisation. The microbial community of each fraction was characterised using Biolog-Community Level Physiological Profiles (CLPP) and phospholipid fatty acid analyses (PLFA) for samples in the A and B horizons. Significant potential microbial activity (C source utilisation) was associated with rock fragments, from the A horizon and, to a lesser extent, the B, although this was lower than for the equivalent fine earth fraction. The microbial colonisation of the stones appeared inversely related with their size and sampling depth. The PLFA analysis showed not only quantitative differences in the microbial biomass between horizons and size-fractions but also highlighted that the communities differed between soils, horizons (for the sole beech soil) and fractions. These findings demonstrate that by considering rock fragments as a microbiologically inert fraction and discarding them before analysis, as usually is done, can lead to an incomplete picture of both the total amount and, perhaps more importantly, the structure of soil microbial community.     

Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities

Understanding the influence of long-term crop management practices on the soil microbial community is critical for linking soil microbial flora with ecosystem processes such as those involved in soil carbon cycling. In this study, pyrosequencing and a functional gene array (GeoChip 4.0) were used to investigate the shifts in microbial composition and functional gene structure in a medium clay soil subjected to various cropping regimes. Pyrosequencing analysis showed that the community structure (β-diversity) for bacteria and fungi was significantly impacted among different cropping treatments. Functional gene array-based analysis revealed that crop rotation practices changed the structure and abundance of genes involved in C degradation. Significant correlations were observed between the activities of four enzymes involved in soil C degradation and the abundance of genes responsible for the production of respective enzymes, suggesting that a shift in the microbial community may influence soil C dynamics. We further integrated physical, chemical, and molecular techniques (qPCR) to assess relationships between soil C, microbial derived enzymes and soil bacterial community structure at the soil micro-environmental scale (e.g. within different aggregate-size fractions). We observed a dominance of different bacterial phyla within soil microenvironments which was correlated with the amount of C in the soil aggregates suggesting that each aggregate represents a different ecological niche for microbial colonization. Significant effects of aggregate size were found for the activity of enzymes involved in C degradation suggesting that aggregate size distribution influenced C availability. The influence of cropping regimes on microbial and soil C responses declined with decreasing size of soil aggregates and especially with silt and clay micro-aggregates. Our results suggest that long term crop management practices influence the structural and functional potential of soil microbial communities and the impact of crop rotations on soil C turnover varies between different sized soil aggregates. These findings provide a strong framework to determine the impact of management practices on soil C and soil health.