The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO₂. Although the stimulating effects of elevated CO₂ (eCO₂) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO₂ conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO₂. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO₂, and such significant effects of eCO₂ on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO₂. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO₂. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO₂ and environmental factors shaping the microbial community structure.     

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.     

封育年限对岩溶植被组成和土壤肥力修复的影响

岩溶植被修复是国家重大战略需求,为揭示封育年限对岩溶植被组成和土壤肥力修复的影响,该研究以空间代替时间的方法,选择不同封育年限的草丛(封育5 a)、灌丛(15 a)、灌乔林(25 a)、次顶极乔林(35 a)和顶极乔林(55 a)作为研究对象,调查分析不同封育年限岩溶植被组成和土壤肥力的特征及其修复机制。结果表明:研究样地(18 000 m ^2)共有维管植物175种,隶属74科139属,不同封育年限群落科属种组成明显不同,以封育5 a的最低(6科19属20种),封育35 a的最高(48科74属88种)。随着封育期延长,乔木生活型比例显著增加,灌木为先增后减,草本急剧减少,藤本先增后减。随着进展演替,群落不同层次的优势种替代规律不同,草本层为阳性杂草→阳性禾草→中生性或阴生性蕨类植物的有序性替代;灌木层为灌木种类被乔木幼苗幼树所替代;而乔木层却表现为常绿种类占优势到常绿与落叶树种共优势的结构性替代。封育初期群落物种组成简单,多样性较低,土壤有机质、全氮、有效氮含量较低,进入中期(25 a),多样性升高,土壤养分含量也增高,进入后期(55 a),多样性降低,土壤养分含量也相应下降,但维持在较高水平,表现出较强的协同修复效应。冗余分析(RDA)表明,群落物种组成在封育初期受土壤容重(SBD)、毛管孔隙度(CP)、全钾(TK)、速效钾(AK)、速效磷(AP)的显著影响,而在中后期则受土壤有机质(SOM)、水分含量(MC)、非毛管孔隙度(NCP)、全氮(TN)、有效氮(AN)以及碳氮磷化学计量比的显著影响。     

氮磷添加对内蒙古温带典型草原土壤微生物群落结构的影响

选取内蒙古温带典型草原,进行连续6a氮磷添加试验,采用土壤特征微生物PLFA生物标记技术,研究6个氮添加水平N0(0 kg N hm-2a-1)、N1(56 kg N hm-2a-1)、N2(112 kg N hm-2a-1)、N3(224 kg N hm-2a-1)、N4(392 kg N hm-2a-1)、N5(560 kg N hm-2a-1)和6个磷添加水平P0(0 kg P hm-2a-1)、P1(15.5 kg P hm-2a-1)、P2(31 kg P hm-2a-1)、P3(62 kg P hm-2a-1)、P4(93 kg P hm-2a-1)、P5(124 kg P hm-2a-1)对土壤特征微生物PLFA生物标记数量和土壤微生物群落结构的影响。结果表明:(1)随氮添加量增加,土壤微生物总磷脂脂肪酸(PLFA)含量和土壤细菌PLFA生物标记数量、放线菌PLFA生物标记数量呈上升趋势,土壤G+/G-呈增加趋势;各氮添加水平对土壤真菌PLFA生物标记数量无显著差异,随氮添加量增加,土壤真菌/细菌比降低。(2)随磷添加量增加,土壤总磷脂脂肪酸(PLFA)含量、土壤细菌PLFA生物标记数量、放线菌PLFA生物标记数量、真菌PLFA生物标记数量及真菌/细菌比值呈先上升后下降趋势,均以P3水平(62 kg P hm-2a-1)处理最高,说明适宜的磷添加对内蒙古温带典型草原土壤微生物繁殖和菌落结构有显著影响。     

Effects of transgenic potatoes with an altered starch composition on the diversity of soil and rhizosphere bacteria and fungi

The aim of this study was to investigate potential effects on the composition of the bacterial and fungal diversity in rhizosphere and soil of a transgenic potato line (SIBU S1) which was modified in its starch composition by RNA anisensing, compared to the non-transgenic parental cultivar (SIBU) at the flowering stage in 2000. Furthermore a second non-transgenic cultivar (SOLANA) was included in the study. To avoid artefacts derived from cultivation depending approaches, molecular techniques based on 16S-(bacteria) and 18S-(fungi) rDNA respectively were used to describe the microbial community structure. Comparing 16S- and 18S-rDNA DGGE fingerprints from the different bulk soil samples, it could be shown that no significant differences between the two cultivars and the transgenic line were found. Similar results were obtained for the rhizosphere samples using the eubacterial, α-and β-proteobacterial and fungal specific primers with the exception of, the eubacterial DGGE patterns obtained for the rhizosphere of SOLANA. These patterns revealed that the relative abundance of one band was enhanced compared with the patterns of SIBU and SIBU S1 and the sequence of the differentiating band showed the highest similarity with Enterobacter amnigenus. When Pseudomonas specific primers were used, relevant differences were found between the rhizosphere patterns of the transgenic potato line (SIBU S1) and the parental cultivar (SIBU). However, clear effects of the cultivar SOLANA on the structure of the Pseudomonas community compared to SIBU were also detected.     

西藏色季拉山垂直植被带土壤细菌群落组成及功能潜势

研究青藏高原土壤微生物群落组成和功能的空间分布特征有助于深入理解典型高寒生态系统中土壤微生物的重要生态功能.本研究采用16S rDNA高通量测序方法,分析了西藏色季拉山4个不同海拔土壤细菌群落物种组成和功能潜势的变化特征及其驱动因子.结果 表明:随着海拔的升高,土壤细菌的丰富度和Shannon多样性指数显著降低;酸杆菌...     

轮作与休闲对日光温室黄瓜连作土壤微生物和酶活性的影响

采用盆栽试验,研究了不同作物轮作和休闲方式对日光温室黄瓜连作土壤微生物数量、酶活性及后茬黄瓜生长和产量的影响.结果表明： 与连作相比,轮作有利于改善土壤微生物结构,增加细菌和放线菌数量,减少真菌数量;轮作与休闲有利于提高土壤转化酶、脲酶、过氧化氢酶和多酚氧化酶活性.在不同作物轮作和休闲方式下,后茬黄瓜结果期的细菌、放线菌数量和土壤转化酶活性均呈先升后降趋势,在盛瓜期达到最大值;真菌数量随生育期延长而增加;脲酶、过氧化氢酶和多酚氧化酶活性则随生育期延长而降低,在初瓜期最高.不同栽培模式下,以大葱-黄瓜轮作和糯玉米-黄瓜轮作的效果更佳,明显改善了后茬黄瓜的生长,提高了产量.     

五大连池新期火山熔岩台地不同植被类型土壤微生物群落的功能多样性

土壤微生物群落是陆地生态系统的重要生物活性成分,其结构和功能多样性直接影响到系统的碳、氮等生态过程,微生物群落功能多样性与地上植被类型变化密切相关,开展植被类型对土壤微生物群落功能多样性的影响研究具有重要意义。以五大连池新期火山熔岩台地苔藓、草本、灌丛、矮曲林、针阔混交林5种典型植被类型为对象,利用BIOLOG微孔板法研究不同演替阶段植被类型土壤微生物群落功能多样性特征。结果表明：不同植被类型土壤微生物群落功能多样性存在显著差异。平均颜色变化率（AWCD）随培养时间延长而逐渐增加,大小顺序为：苔藓 > 针阔混交林 > 矮曲林 > 草本 > 灌丛。灌丛土壤微生物多样性指数与其他植被类型间差异显著。主成分分析结果表明,主成分1和主成分2分别能解释变量方差的56.24%和29.59%,不同植被类型下土壤微生物的碳源利用格局差异主要是由氨基酸类和带磷基糖类引起,二者合计解释总变异量的47.51%。冗余分析表明,速效磷、铵态氮、C：N和pH对微生物功能多样性具有显著的影响,羧酸类、氨基酸类、酯类和胺类的降解更易受到环境因素的影响。研究结果为进一步探讨植被类型与土壤微生物之间在植被演替过程中的关系提供参考。     

祁连山北坡退化林地植被群落的自然恢复过程及土壤特征变化

采用长期定位观测的方法,研究了祁连山北坡退化林地人工抚育下2001-2008年间植被群落的自然恢复过程和土壤特征变化。结果表明:人为干扰消除后,退化林地群落环境逐渐优化,群落的科、属、种均明显增加,物种成员更替频繁;灌木和乔木物种出现后,群落垂直高度增大,群落结构出现成层现象;群落总体多样性指数呈不断增大的趋势,在空间结构上,Patrick丰富度指数、Shannon-Wiener多样性指数和Simpson优势度指数表现出:草本层>灌木层>乔木层的规律,而Pielou均匀度指数变化相反;土壤含水量、土壤有机碳和全氮含量随植被恢复均不断增加。在实施封育禁牧措施后,退化林地实现了由草本群落-灌木群落-乔木群落方向的快速演替,当恢复到早期的先锋乔灌混交阶段时,群落的物种组成、结构和多样性趋于复杂化,土壤性状也得到一定改善,显示出相对较好的适应性和恢复效果。     

树种多样性对土壤微生物群落结构和元素生物地球化学循环的影响研究进展

森林是陆地生态系统的重要组成部分,其巨大的生产力和生态服务功能对人类的生存和发展至关重要。森林树种多样性增加能够显著提高森林生产力,关于树种多样性如何影响地下生物多样性及生态功能逐渐受到国内外学者的广泛关注。从土壤微生物及其介导的元素生物地球化学循环这一视角出发,综述了树种多样性对土壤细菌和真菌多样性、群落结构及功能的影响,提出需要进一步深入研究的方向。总体来说,树种多样性有利于增加土壤细菌生物量和多样性,是预测病原性真菌和菌根真菌多样性及群落结构的重要生物因子。树种多样性能增加土壤有机碳储量,增强森林土壤的甲烷氧化能力,并提高土壤磷周转速率及有效磷含量。关于树种多样性对森林土壤氮循环的影响需考虑多样性假说和质量比假说的相对贡献。今后应加强树种多样性对多个营养级之间相互作用的研究;关注树种多样性对生态系统多功能的影响;加强学科交叉,引入微生物种群动态模型和气候模型等模型预测方法,研究树种多样性对全球气候变化的应对机制,以期促进地上植物多样性与地下生态系统功能关系的研究,增强森林生态系统应对未来全球环境变化的能力。     

内生真菌感染对禾草宿主生境土壤特性和微生物群落的影响

以羊草(Leymus chinensis)-内生真菌共生体为研究对象, 分别在野外样地和室内盆栽两种实验条件下研究了内生真菌感染对土壤特性和微生物群落结构的影响。结果显示：在处理时间较长并伴随有枯落物分解的羊草样地中, 内生真菌感染促进了土壤氮(N)的积累, 提高了30天培养时间内土壤初始碳(C)矿化速率和前3天土壤矿化量和土壤矿化总量; 而在处理时间较短且没有地上枯落物分解的盆栽羊草中, 内生真菌感染对土壤的C、N含量及C矿化均无显著影响。无论是野外样地还是室内盆栽实验, 内生真菌感染均未引起土壤微生物磷脂脂肪酸种类的变化, 但内生真菌感染均有提高土壤微生物生物量的趋势, 内生真菌显著增加了盆栽羊草土壤中细菌、革兰氏阴性细菌、真菌磷脂脂肪酸含量和磷脂脂肪酸总量, 增加了羊草样地土壤中革兰氏阳性细菌和放线菌的磷脂脂肪酸含量。总体看来, 内生真菌感染能够改变土壤N积累和C矿化率, 并且改变土壤中微生物群落的结构, 这有助于进一步认识内生真菌与羊草之间的共生关系及其在生态系统C、N循环中所起的作用。     

The effects of insect pathogenic soil fungi and ectomycorrhizal inoculation of birch seedlings on the survival of Otiorhynchus larvae

• 1 Weevil larvae of the genus Otiorhynchus are a serious problem in agriculture and forestry, causing damage to a wide range of plant species, primarily by larval feeding on roots. Otiorhynchus larvae are a serious pest in forest plantations in Iceland, causing 10–20% mortality of newly‐planted seedlings.
• 2 We studied the effects of soil fungi on the survival of Otiorhynchus sulcatus larvae. The larvae were introduced into pots with birch seedlings grown in: (i) nursery peat; (ii) nursery peat inoculated with three different species of ectomycorrhizal fungi; (iii) nursery peat inoculated with insect pathogenic fungi; (iv) nursery peat inoculated with ectomycorrhizal fungi and insect pathogenic fungi; and (v) nursery peat inoculated with natural forest soil from Icelandic birch woodland.
• 3 Larval survival was negatively affected by inoculation of: (i) the ectomycorrhizal fungus Laccaria laccata; (ii) the ectomycorrhizal fungus Cenococcum geophylum; (iii) the insect pathogenic fungus Metarhizium anisopliae; and (iv) forest soil. Inoculation with the ectomycorrhizal fungus Phialophora finlandia did not have any significant effect on larval survival. No significant synergistic effect was found between insect pathogenic and ectomycorrhizal fungi.
• 4 It is concluded that ectomycorrhizal and insect pathogenic fungi have a significant potential in biological control of Otiorhynchus larvae in afforestation areas in Iceland. Further studies are needed to establish the effect of these fungi in the field and to analyse how mycorrhizal fungi affect root‐feeding larvae.

     

The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis (‘everything is everywhere, but, the environment selects'') was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.     

The effect of long-term nitrate treatment on SRB activity,corrosion rate and bacterial community composition in offshore water injection systems

Biogenic production of hydrogen sulphide (H₂S) is a problem for the oil industry as it leads to corrosion and reservoir souring. Continuous injection of a low nitrate concentration (0.25–0.33 mM) replaced glutaraldehyde as corrosion and souring control at the Veslefrikk and Gullfaks oil field (North Sea) in 1999. The response to nitrate treatment was a rapid reduction in number and activity of sulphate-reducing bacteria (SRB) in the water injection system biofilm at both fields. The present long-term study shows that SRB activity has remained low at ≤0.3 and ≤0.9 μg H₂S/cm²/day at Veslefrikk and Gullfaks respectively, during the 7–8 years with continuous nitrate injection. At Veslefrikk, 16S rRNA gene based community analysis by PCR–DGGE showed that bacteria affiliated to nitrate-reducing sulphide-oxidizing Sulfurimonas (NR–SOB) formed major populations at the injection well head throughout the treatment period. Downstream of deaerator the presence of Sulfurimonas like bacteria was less pronounced, and were no longer observed 40 months into the treatment period. The biofilm community during nitrate treatment was highly diverse and relative stable for long periods of time. At the Gullfaks field, a reduction in corrosion of up to 40% was observed after switch to nitrate treatment. The present study show that nitrate injection may provide a stable long-term inhibition of SRB in sea water injection systems, and that corrosion may be significantly reduced when compared to traditional biocide treatment.     

Plant presence and species combination, but not diversity, influence denitrifier activity and the composition of nirK-type denitrifier communities in grassland soil

To explore potential links between plant communities, soil denitrifiers and denitrifier function, the impact of presence, diversity (i.e. species richness) and plant combination on nirK -type denitrifier community composition and on denitrifier activity was studied in artificial grassland plant assemblages over two consecutive years. Mesocosms containing zero, four and eight species and different combinations of two species were set up. Differences in denitrifier community composition were analysed by canonical correspondence analyses following terminal restriction fragment length polymorphism analysis of PCR-amplified nirK gene fragments coding for the copper-containing nitrite reductase. As a measure of denitrifier function, denitrifier enzyme activity (DEA) was determined in the soil samples. The presence as well as the combination of plants and sampling time, but not plant diversity, affected the composition of the nirK -type denitrifier community and DEA. Denitrifier activity significantly increased in the presence of plants, especially when they were growing during summer and autumn. Overall, we found a strong and direct linkage of denitrifier community composition and functioning, but also that plants had additional effects on denitrifier function that could not be solely explained by their effects on nirK -type denitrifier community composition.     

不同树叶凋落物对人参土壤理化性质及微生物群落结构的影响

树种选择是林下山参护育成败的关键,研究树叶凋落物对人参土壤养分、微生物群落结构组成的影响,旨在为林下山参护育选择适宜林地及农田栽参土壤改良提供科学依据和理论指导。通过盆栽试验,研究添加5.0 g色木槭Acer mono.Maxim.var.mono(A)、赤松Pinus densiflora Sieb.et Zucc.(B)、胡桃楸Juglans mandshurica Maxim.(C)、紫椴Tilia amurensis Rupr.(D)、蒙古栎Quercus mongolica Fisch.ex Ledeb.(E)树叶凋落物到土壤中,种植人参(Panax ginseng C.A.meyer)后研究土壤理化性质以及微生物群落结构的变化。结果表明:添加不同树叶处理后人参土壤性质发生改变,土壤p H值显著高于对照土壤5.91(P0.05),土壤全氮、速效氮磷、微生物碳氮在所有树叶处理中显著增加(P0.05),而土壤容重、速效钾和C/N在添加树叶处理中降低。18个土壤样品基因组,经16S和ITS1测序分别得到6064和1900个OUTs。其中细菌涵盖了42门、117纲、170目、213科、225属,真菌涵盖了24门、98纲、196目、330科、435属。不同树叶处理人参土壤细菌和真菌地位发生改变,细菌Proteobacteria是树叶分解的关键微生物,添加树叶后其多样性显著高于对照(P0.05)。而细菌Bacteroidetes和真菌Basidiomycota可能是区别阔叶林和针叶林树种的关键微生物,针叶林中含量显著低于阔叶林(P0.05),而真菌Ascomycota是针叶林分解的关键微生物。进一步从不同分类水平上得到特定树叶凋落物的特异细菌和真菌。典型相关分析(CDA)表明细菌Bacteroidetes、Chloroflexi、Actinobacteria及真菌Basidiomycota、Zygomycota、Chytridiomycota及Ascomycota的位置及多样性的改变均与土壤因子SMBN、TN、AP、SOC、AK、C/N、p H有关。综上所述,添加不同树叶后不仅提高土壤微生物量碳氮、改善土壤理化性质,同时改变微生物群落结构组成,不同树叶处理土壤理化性质不同导致人参土壤微生物组成的差异,本结果对于林下参选地和农田栽参土壤微生物改良具有理论指导作用。     

The influence of moisture regimes on the population and activity of soil microorganisms

This paper deals with the influence of soil moisture on the fungal population, bacterial population, CO₂-evolution and dehydrogenase activity. Correlation coefficients of various parameters of the soil with different moisture regimes are given. It is demonstrated that soil moisture significantly alters the microbial population, its activity and the relationships between various parameters.     

克隆整合对遮荫白夹竹分株根际土壤细菌生物特征的影响

克隆整合被认为是克隆植物维持生态优势的重要手段,其通过分株间生理整合缓解资源异质性带来的压力。文章以根状茎克隆植物白夹竹(Phyllostachys bissetii)为研究对象,探讨异质性光照下克隆整合对白夹竹分株根际土壤细菌生物特征的影响。白夹竹克隆片段包含一个近端分株(proximal ramet)和一个远端分株(distal ramet),近端分株或远端分株分别置于80%遮荫环境,另一分株置于全光照环境;同时,分株间根状茎保持连接或割断处理。研究结果表明,不论白夹竹克隆片段近端分株遮荫还是远端分株遮荫,克隆整合均显著促进了遮荫分株根际土壤溶解性有机碳(DOC)含量和微生物生物量碳、氮含量(MBC,MBN);根状茎连接条件下遮荫分株根际土壤胞外N-乙酰基-β-氨基葡萄糖苷酶(NAGase)、脲酶(Urease)活性显著高于根状茎割断处理的遮荫分株;对遮荫分株根际土壤基因组DNA的16S rDNA V3、V4可变区的测序结果表明,可操作分类单元(OTUs)归于13个门,415个属。与根际土壤氮素转化相关的菌群Nitrosomonadaceae(uncultured),Nitrospira,Nitrospinaceae(uncultured),Xanthobacteraceae(uncultured),Bradyrhizobium相对丰度较小(最高值为11.8%)。基于OTUs的主成分分析(PCA)表明,根状茎割断处理并没有对遮荫分株根际土壤细菌生物群落结构产生显著性影响。克隆整合显著促进了遮荫分株根际土壤C有效性,进而刺激了微生物调控的土壤有机质(SOM)周转过程。克隆整合对异质生境下克隆植物土壤细菌生物特征的影响可能部分解释了克隆植物的生态优势。