森林母土异地迁播后的土壤真菌和细菌变化

【背景】森林土壤中携带了大量种子和微生物,已经被广泛用于各种退化生态系统的植被恢复。但是,关于土壤迁播到退化生态系统后的真菌和细菌群落变化研究较少。【目的】研究土壤迁播后真菌和细菌的组成和多样性,比对其与森林母土和受体土壤之间的物种组成与群落差异。【方法】通过Illumina HiSeq高通量测序,获取迁播15个月的土壤、森林母土及受体土壤中真菌和细菌特征值,比对其多样性和丰富度。【结果】3类样地真菌优势菌门为担子菌门和子囊菌门,细菌优势菌门为酸杆菌门、变形菌门、放线菌门和绿弯菌门,土壤迁播后显著改变了真菌和细菌优势菌门的相对丰度。主成分分析表明3类样地真菌和细菌群落组成存在显著差异。聚类分析表明迁播土壤与受体土壤聚类距离更近,物种组成更相似,真菌和细菌优势属与受体土壤无显著差异。迁播土壤的真菌和细菌丰富度和多样性与森林母土差异显著(P0.05)。【结论】森林土壤迁播15月后,其细菌和真菌物种组成逐步趋同于受体土壤。该结果为进一步研究石漠化微生物生态系统、改善和提升土壤迁播技术提供支撑。     

Soil drying as a model for the action of stress factors on the natural bacterial population

The drying of soil samples reduced the abundance (especially of predominant species) and the diversity of bacteria isolated from these samples, making easier the isolation of rare bacterial species. Some bacterial species that were minor before soil drying became dominant in dried soil samples. In general, soil drying allowed the diversity of soil bacteria to be determined more adequately. The bacteria that were isolated from dried soil samples turned out to be resistant to gamma radiation (with LD90 = 2.8-4.6 kGy) and desiccation. It is concluded that soil drying may serve as a model for the action of stress factors on natural bacterial populations. The hypothesis that periodic desiccation was the primary cause of formation of bacterial radioresistance in nature is discussed.     

Soil Drying As a Model for the Action of Stress Factors on Natural Bacterial Populations

The drying of soil samples reduced the abundance (especially of predominant species) and the diversity of bacteria isolated from these samples, making easier the isolation of rare bacterial species. Some bacterial species that were minor before soil drying became dominant in dried soil samples. In general, soil drying allowed the diversity of soil bacteria to be determined more adequately. The bacteria that were isolated from dried soil samples turned out to be resistant to gamma radiation (with LD₉₀ = 2.8–4.6 kGy) and desiccation. It is concluded that soil drying may serve as a model for the action of stress factors on natural bacterial populations. The hypothesis that periodic desiccation was the primary cause of formation of bacterial radioresistance in nature is discussed.     

Sensitivity of soil bacteria isolated from the alienated zone around the Chernobyl Nuclear Power Plant to various stress factors

Seventy strains of chemoorganotrophic bacteria isolated by our group in 1993-1994 from soil sampled in the zone around the Chernobyl Nuclear Power Plant (ChNPP) were studied with respect to their sensitivity to various stress factors damaging DNA. Bacillus subtilis, B. cereus (both spores and vegetative cells), Methylobacterium extorquens, M. mesophilicum, and unidentified pigmented bacteria were found to be the most resistant to ultraviolet (UV) radiation, exhibiting LD90 values of 40 to more than 211 J/m2. The same bacteria, as well as Bacillus polymyxa, were tolerant to hydrogen peroxide (lethal concentrations of H2O2 ranged from 0.3 to 1.0 M); i.e., UV-resistant strains were also tolerant to hydrogen peroxide and vice versa. Fluorescent pseudomonads were the most sensitive to both UV radiation and H2O2, showing LD90 from 6 to 18 J/m2 and a lethal concentration of H2O2 lower than 0.1 M. All of the soil samples collected in the alienated zone around the ChNPP, where the radioactivity of the soil had decreased from 1000 to 2 microCi/kg soil over the period from 1987 to 1995, contained not only resistant bacteria but also a small number of bacteria sensitive to UV radiation and H2O2.     

Diverse UV-B Resistance of Culturable Bacterial Community from High-Altitude Wetland Water

Isolation of most ultraviolet B (UV-B)-resistant culturable bacteria that occur in the habitat of Laguna Azul, a high-altitude wetland [4554 m above sea level (asl)] from the Northwestern Argentinean Andes, was carried out by culture-based methods. Water from this environment was exposed to UV-B radiation under laboratory conditions during 36 h, at an irradiance of 4.94 W/m². It was found that the total number of bacteria in water samples decreased; however, most of the community survived long-term irradiation (312 nm) (53.3 kJ/m²). The percentage of bacteria belonging to dominant species did not vary significantly, depending on the number of UV irradiation doses. The most resistant microbes in the culturable community were Gram-positive pigmented species (Bacillus megaterium [endospores and/or vegetative cells], Staphylococcus saprophyticus, and Nocardia sp.). Only one Gram-negative bacterium could be cultivated (Acinetobacter johnsonii). Nocardia sp. that survived doses of 3201 kJ/m² were the most resistant bacteria to UV-B treatment. This study is the first report on UV-B resistance of a microbial community isolated from high-altitude extreme environments, and proposes a method for direct isolation of UV-B-resistant bacteria from extreme irradiated environments. This article is dedicated to the memory of Carolina Colin.     

Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking

Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.     

Microwave irradiation is a useful tool for improving isolation of actinomycetes from soil

Actinomycetes are an important source of novel, biologically active compounds. New methods need to be developed for isolating previously unknown actinomycetes from soil. The objective of this experiment was to study microwave irradiation of soil as a means for isolating previously unknown actinomycetes. Soil samples were collected at ten elevations between 800 m and 3670 m on Taibai Mountain, Shaanxi Province, China. Moistened soil samples were irradiated at 120 W heating power (2450 MHz) for 3 min using a household microwave oven. Irradiation increased total actinomycete, streptomycete, and antagonistic actinomycete counts on three types of culture media. Irradiation also increased the number of culturable actinomycete isolates. Some actinomycete isolates were culturable only after the soil was irradiated, whereas other isolates could not be cultured after irradiation. Irradiation of soil from elevations >3000 m increased actinomycete counts significantly but had little effect on the number of culturable actinomycete isolates. In contrast, irradiation of samples from elevations <3000 m had relatively little effect on actinomycete counts, but significantly increased the number of culturable actinomycete isolates. We used 16S rDNA sequence analysis to identity 14 actinomycete isolates that were only culturable after irradiation. Microwave irradiation of soil was helpful for isolating Streptomyces spp., Nocardia spp., Streptosporangium spp., and Lentzea spp. Slightly more than 90% of the identified actinomycete species were biologically active. In conclusion, microwave irradiation is a useful tool for isolating biologically active actinomycetes from soil.     

The metagenomics of soil

Phylogenetic surveys of soil ecosystems have shown that the number of prokaryotic species found in a single sample exceeds that of known cultured prokaryotes. Soil metagenomics, which comprises isolation of soil DNA and the production and screening of clone libraries, can provide a cultivation-independent assessment of the largely untapped genetic reservoir of soil microbial communities. This approach has already led to the identification of novel biomolecules. However, owing to the complexity and heterogeneity of the biotic and abiotic components of soil ecosystems, the construction and screening of soil-based libraries is difficult and challenging. This review describes how to construct complex libraries from soil samples, and how to use these libraries to unravel functions of soil microbial communities.     

Respiration and metabolic processes of bacteria in autoclaved and gamma-irradiated soil

Samples of chernozem and brown soils were irradiated with gamma rays using doses of 1.5 to 4.5 Mrad, or fractionally autoclaved at 1 and 2 kp/cm². Consumption of oxygen by cellular suspensions of bacteria added to suspensions of sterilized soils was higher than in untreated samples. The increased oxygen consumption indicated an increase in the quantity of a biologically oxidizable substrate which could be released during the irradiation or autoclaving of soils. The amount of oxygen consumed was proportional to the radiation dose or autoclaving time and the pressure used, and was dependent also on the type of soil. The accessible substrate could be immediately, without a lag phase, oxidized by the added microorganism. The extent and rate of oxygen consumption in the sterilized soil samples varied in different microorganisms. It was observed that decomposition of vanillie acid by a cell suspension ofCellulomonas sp. was stimulated in the soil sterilized by radiation. The significance of these findings for the soil metabolic studies is discussed.     

土壤细菌类克隆群落及其结构的生态学特征

以16SrDNA分析方法为基础,获得来自不同土壤环境的细菌克隆群落（Cloning community),并分析了这些土壤细菌群落结构特征,在不同土壤环境中,细菌种类非常丰富,但其多样性将受到植被,土壤水分或土壤层次等因子的影响,表层土壤环境中细菌种类最丰富,多样性最高,且基因型中无明显的优势类群,不同土壤环境间细菌群落的相似性好低,表明群落结构以及空间隔离的复杂性。     

土壤纤毛虫群落对退耕还林生态恢复的响应——以侧柏林为例

为了了解土壤纤毛虫群落对退耕还林区生态恢复下土壤环境变化的响应及尝试利用土壤纤毛虫群落特征评价退耕还林生态恢复的效果,于2010年3月至9月采用"非淹没培养皿法"、活体观察法、蛋白银染色法和Foissner计数法对甘肃陇南武都退耕还林区5个不同恢复阶段的样点和1个荒草坡对照样点的土壤纤毛虫群落特征进行了研究,同时测定了p H值、温度、含水量及速效磷、有效钾、铵态氮、有机质和有机碳含量等土壤环境因子并分析了生态恢复条件下土壤纤毛虫群落特征与土壤环境因子的相关性。研究中共鉴定到71种纤毛虫,隶属于3纲、10目、22科、29属。研究发现,不同恢复年限的土样中土壤纤毛虫的物种分布存在明显差异,并随恢复时间的延长,样点间物种相似性减小,群落组成复杂化,物种数、种群密度和物种多样性指数总体均呈增长趋势。优势类群也发生了演替,由恢复初期的肾形目演替到后期的下毛目。相关性分析结果表明,在生态恢复条件下,土壤有机质和铵态氮含量是影响土壤纤毛虫群落结构稳定性的主要因素,不同纤毛虫类群对生态恢复的响应存在差异。冗余分析显示,土壤纤毛虫群落很好地响应了生态恢复过程中土壤环境条件的变化。     

桂北喀斯特峰丛洼地植物群落特征及其与土壤的耦合关系

基于喀斯特峰丛洼地草丛、灌丛、次生林、原生林4个生态系统24个样地(20 m × 20 m)的系统取样调查, 研究了喀斯特峰丛洼地不同生态系统群落的结构组成与生物多样性特征, 选取代表植物群落和土壤性质的35个指标, 对不同生态系统及整个喀斯特脆弱生态系统植物群落与土壤主要养分、土壤矿质养分和土壤微生物间的相互关系进行了主成分分析与典范相关分析。结果表明: 沿草丛、灌丛、次生林、原生林的顺向演替发展, 重要值(importance value, IV)>10.00的科、属、种及物种多样性最大值出现在次生林, 群落结构最佳值出现在顶级群落原生林; 喀斯特峰丛洼地景观异质性高, 各生态系统影响因子不同, 土壤微生物在喀斯特脆弱生态系统处于主导地位, 其次为灌丛; 不同集团因子的典范相关分析表明, 植物多样性指标与土壤氮素、Al₂O₃、Fe₂O₃、土壤微生物生物量碳(C_mic)、真菌和细菌关系密切。因此, 在喀斯特脆弱生态系统恢复与重建过程中, 应针对不同生态系统制定相应的培育管理措施。     

Nitrification and occurrence of salt-tolerant nitrifying bacteria in the Negev desert soils

Ammonia oxidation potential, major ammonia oxidizers and occurrence of salt-tolerant nitrifying bacteria were studied in soil samples collected from diverse ecosystems along the northern Negev desert. Great diversity in ammonia oxidation potential was observed among the soil samples, and ammonia oxidizers were the rate-limiting step of nitrification. Denaturing gradient gel electrophoresis and partial 16S rRNA gene sequences indicate that members of the genus Nitrosospira are the major ammonia oxidizers in the natural desert soil samples. Upon enrichment with different salt concentrations, salt-tolerant nitrifying enrichments were established from several soil samples. In two enrichments, nitrification was not inhibited by 400 mM NaCl. Electrophoretic analysis and partial 16S rRNA gene sequences indicate that Nitrosomonas species were dominant in the 400 mM salt enrichment. The results point towards the potential of the desert ecosystem as a source of stress-tolerant nitrifying bacteria or other microorganisms with important properties.     

Diversity and distribution of soil fungal communities in a semiarid grassland

The fungal loop model of semiarid ecosystems integrates microtopographic structures and pulse dynamics with key microbial processes. However limited data exist about the composition and structure of fungal communities in these ecosystems. The goal of this study was to characterize diversity and structure of soil fungal communities in a semiarid grassland. The effect of long-term nitrogen fertilization on fungi also was evaluated. Samples of rhizosphere (soil surrounding plant roots) and biological soil crust (BSC) were collected in central New Mexico, USA. DNA was amplified from the samples with fungal specific primers. Twelve clone libraries were generated with a total of 307 (78 operational taxonomic units, OTUs) and 324 sequences (67 OTUs) for BSC and rhizosphere respectively. Approximately 40% of soil OTUs were considered novel (less than 97% identity when compared to other sequences in NCBI using BLAST). The dominant organisms were dark-septate (melanized fungi) ascomycetes belonging to Pleosporales. Effects of N enrichment on fungi were not evident at the community level; however the abundance of unique sequences, sampling intensity and temporal variations may be uncovering the effect of N in composition and diversity of fungal communities. The fungal communities of rhizosphere soil and BSC overlapped substantially in composition, with a Jaccard abundance similarity index of 0.75. Further analyses are required to explore possible functions of the dominant species colonizing zones of semiarid grassland soils.     

Biodegradation of decabromodiphenyl ether (BDE-209) by bacterial mixed cultures in a soil/water system

Decabromodiphenyl ether (DBDE) is a brominated flame retardant that is commonly used in many commercial products. Sorption of DBDE within a soil/water system can result in serious bioaccumulation within the ecological system and be a threat to human health. Little is known about aerobic DBDE biodegradation, and the influence of the UV light radiation on DBDE biodegradation has not been considered. This study, for the first time, isolates DBDE biodegrading aerobic mixed bacterial cultures from DBDE-contaminated soil/water systems in Taiwan. The aerobic biodegradation of DBDE as a sole carbon source in the presence of 365 nm UVA irradiation over 10 months was investigated using a clay/water system. The rate constants for DBDE degradation gave values ranging from 0.0121 to 0.0134 day⁻¹ in the presence of UV irradiation, which were significantly higher than the 0.0092–0.0102 day⁻¹ values obtained in complete darkness. The aerobic metabolites: 2′,3′-dihydroxy-4-bromodiphenyl ether and 2′,3′-dihydroxy-diphenyl ether were identified by GC–MS. Debromination was ascribed to UV irradiation and biodegradation by facultative aerobic bacteria in the micro-anaerobic environment of the clay/water system. The products of debromination included 12 PBDE congeners (tri- to hexa-BDEs) and their concentrations ranged from 34.28 to 83.80 mg l⁻¹. Specific bacteria capable of degrading PBDEs and carrying out nitrification/denitrification were identified. The present findings suggest that systems using a novel combination of photolysis and biodegradation could be developed to carry out DBDE remediation in the future.     

西南岩溶生态系统土壤微生物的初步研究

探讨微生物在岩溶作用中的作用 ,需要考察土壤微生物在岩溶地区的生态分布和特性。本文对采自中国西南 4个不同岩溶地区 (重庆金佛山、六盘水米苏嘎、广西弄拉和桂林丫吉村岩溶试验场 )生态系统土壤样品中的细菌、放线菌和真菌进行了数量测定 ,结果表明 ,微生物的数量和组成与赋予不同地形和植被特征的岩溶生态系统的特性高度相关。本文还分析了马山弄拉和岩溶试验场的优势细菌 ,并且进行了初步鉴定 ,结果显示 ,固氮菌科细菌在两个岩溶生态系统土壤中都占优势 ,表明其土壤肥力都在改善。     

Global change and biological soil crusts: effects of ultraviolet augmentation under altered precipitation regimes and nitrogen additions

Biological soil crusts (BSCs), a consortium of cyanobacteria, lichens, and mosses, are essential in most dryland ecosystems. As these organisms are relatively immobile and occur on the soil surface, they are exposed to high levels of ultraviolet (UV) radiation and atmospheric nitrogen (N) deposition, rising temperatures, and alterations in precipitation patterns. In this study, we applied treatments to three types of BSCs (early, medium, and late successional) over three time periods (spring, summer, and spring–fall). In the first year, we augmented UV and altered precipitation patterns, and in the second year, we augmented UV and N. In the first year, with average air temperatures, we saw little response to our treatments except quantum yield, which was reduced in dark BSCs during one of three sample times and in Collema BSCs two of three sample times. There was more response to UV augmentation the second year when air temperatures were above average. Declines were seen in 21% of the measured variables, including quantum yield, chlorophyll a, UV‐protective pigments, nitrogenase activity, and extracellular polysaccharides. N additions had some negative effects on light and dark BSCs, including the reduction of quantum yield, β‐carotene, nitrogenase activity, scytonemin, and xanthophylls. N addition had no effects on the Collema BSCs. When N was added to samples that had received augmented UV, there were only limited effects relative to samples that received UV without N. These results indicate that the negative effect of UV and altered precipitation on BSCs will be heightened as global temperatures increase, and that as their ability to produce UV‐protective pigments is compromised, physiological functioning will be impaired. N deposition will only ameliorate UV impacts in a limited number of cases. Overall, increases in UV will likely lead to lowered productivity and increased mortality in BSCs through time, which, in turn, will reduce their ability to contribute to the stability and fertility of soils in dryland regions.     

呼和浩特市大青山白桦根际土壤细菌群落结构研究

采用高通量测序技术对天然次生林生态系统演替过程中先锋树种白桦的根际土壤细菌多样性及群落结构进行了分析。研究结果表明:白桦根际土壤细菌隶属于28门、90纲、126目、213科、286属,在3个采样地中排名前8的优势细菌门的相对丰度均大于1%,分别为变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、芽单胞菌门(Gemmatimonadetes)、绿弯菌门(Chloroflexi)、硝化螺旋菌门(Nitrospirae)、疣微菌门(Verrucomicrobia)和拟杆菌门(Bacteroidetes)。各样地中前3个门的相对丰度之和均在60%以上。对白桦根际土壤细菌的α多样性指数、门水平的聚类热图以及PCoA聚类结果的分析表明,3个采样地中,小井沟(B2)和哈达门森林公园(C2)白桦根际土壤细菌的物种组成更为接近,与井儿梁(A2)的物种组成有一定差异;且小井沟和哈达门森林公园的物种多样性及丰度(ACE指数)显著高于井儿梁,表明细菌对不同环境的适应能力有明显差异。对细菌群落结构与土壤理化性质的RDA分析及相关性分析表明,环境因子对白桦根际土壤细菌的影响顺序为:全氮TN酸碱度pH含水量WC速效钾AK硝态氮NN铵态氮AN有机质OM有效磷EP,其中,TN、pH和WC是白桦根际土壤优势细菌的主要影响因子。研究结果为深入认识森林生态系统中根际土壤细菌的群落结构和影响因子提供了理论依据。     

Tolerance of soil bacterial complexes to salt shock

Investigations showed that bacteria present in soil are resistant to one-day exposure to a saturated solution of ammonium nitrate and can well develop when transferred to laboratory nutrient media. The evaluated number of bacteria in NH4NO3-treated soil samples was nearly the same as in native soil samples, while was 1.5-2.5 times smaller in the former than in the latter case when microbial succession in the soil samples was initiated by wetting them. Bacteria (particularly gram-negative ones) occurring at the early stages of succession were the most sensitive to salt stress. Bacteria in soil were found to be much more resistant to salt stress than the same bacteria isolated in pure cultures.     

冰川棘豆(Oxytropis glacialis)根系土壤细菌多样性特征

冰川棘豆是青藏高原高寒草原和荒漠草原主要伴生毒草之一,对青藏高原草地退化及畜牧业的发展产生严重影响。对4种不同生态环境中冰川棘豆根系土壤细菌的16S rRNA进行高通量测序及生物信息学分析,结合土壤的理化性质,分析了不同生态环境下冰川棘豆根系土壤细菌群落多样性及其与土壤理化因子的关系,探讨了根系土壤细菌对冰川棘豆在高寒生态系统中形成优势种可能的影响。结果表明,在不同生态环境下冰川棘豆根系土壤细菌多样性丰富,且受土壤pH和有机物影响最大,同时,能够保持稳定的核心菌群网络,对冰川棘豆在高寒生态系统中形成优势种具有促进作用。