克拉玛依石油污染土壤微生物群落结构及其代谢特征

为了分析克拉玛依油区内土壤中正构烷烃含量间的差异,微生物群落生理多样性、微生物代谢活性在不同石油污染梯度土壤中的变化规律。本研究采用GC、平板稀释法、Biolog微平板技术探讨了土壤微生物群落特征在3种不同污染程度下的变化情况。研究表明,石油污染土壤烷烃含量与微生物代谢活性呈显著负相关(r=-0.783, p<0.05)。随着石油污染程度增加微生物数量呈下降趋势,不同石油污染土壤中细菌数量占决定优势,细菌>真菌>放线菌。不同石油污染土壤微生物群落对6大碳源的利用体现出差异。主成分分析(PCA)表明,清洁土壤与石油污染土壤对底物利用有明显差异。石油污染严重土样碳源利用率为"酯类>酸类>胺类>氨基酸类>单糖/糖苷/聚合糖类>醇类"。本研究成果为后期修复污染土壤时调整投入的碳源底物等提供科学帮助。     

Effect of Metal Oxide Nanoparticles on Microbial Community Structure and Function in Two Different Soil Types

Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe₃O₄) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe₃O₄ changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity.     

Microbial Diversity and Community Structure in Two Different Agricultural Soil Communities

Abstract In this study, two different agricultural soils were investigated: one organic soil and one sandy soil, from Stend (south of Bergen), Norway. The sandy soil was a field frequently tilled and subjected to crop rotations. The organic soil was permanent grazing land, infrequently tilled. Our objective was to compare the diversity of the cultivable bacteria with the diversity of the total bacterial population in soil. About 200 bacteria, randomly isolated by standard procedures, were investigated. The diversity of the cultivable bacteria was described at phenotypic, phylogenetic, and genetic levels by applying phenotypical testing (Biolog) and molecular methods, such as amplified rDNA restriction analysis (ARDRA); hybridization to oligonucleotide probes; and REP-PCR. The total bacterial diversity was determined by reassociation analysis of DNA isolated from the bacterial fraction of environmental samples, combined with ARDRA and DGGE analysis. The relationship between the diversity of cultivated bacteria and the total bacteria was elucidated. Organic soil exhibited a higher diversity for all analyses performed than the sandy soil. Analysis of cultivable bacteria resulted in different resolution levels and revealed a high biodiversity within the population of cultured isolates. The difference between the two agricultural soils was significantly higher when the total bacterial population was analyzed than when the cultivable population was. Thus, analysis of microbial diversity must ultimately embrace the entire microbial community DNA, rather than DNA from cultivable bacteria.     

Differences of Soil Microbial Biomass and Nitrogen Transformation under Two Forest Types in Central Germany

In order to observe the tree species effect on soil N status, soil microbial biomass C and N (C_mic, N_mic), potential N mineralization and potential nitrification (under laboratory incubation conditions, 22 °C) in different subhorizons (LOf₁, Of₂, Oh and mineral soil at 0–10 cm depth) were determined at three forest sites in central Germany. At each site, two contrasting stands (Beech, Norway spruce or Scots pine) were selected, where the initial soil conditions were similar. Three sampling dates that represented different stages of tree growth were selected: growing season - August, dormant season - November, after budbreak – April. In organic layers, C_mic-to-total C (C_t) ratios under beech and under conifer were 0.72–4.74% and 0.34–2.11%, respectively. N_mic-to-total N (N_t) ratios were 2.47–11.61% and 0.71–5.77%, respectively. Both concentrations of C_mic and N_mic were significantly affected by the stand type and sampling time. Potential N mineralization rates, ranging from 3.7 to 19.7 mg N kg⁻¹ d⁻¹, showed no clear pattern in relation to stand type. However, potential nitrification rates were mostly significantly higher under beech than under contrasting conifer. In mineral soils, concentrations of C_mic and N_mic showed a clear temporal pattern in the order: August>November>April. The average N_mic and N_mic-to-N_t were higher in soils from beech than conifer, while C_mic and C_mic-to-C_t ratios were similar between the two forest types. In organic layers, the highest values of C_mic-to-N_mic ratio and C_mic were found in November samples, especially under beech. By contrast, in mineral soils the highest value of C_mic-to-N_mic ratios were found in April samples, and at that time the C_mic concentrations were the lowest, especially under conifer. These results revealed the differences in microbial growth form and survival strategy associated with different tree species and soil layers.     

Relationships between Soil Organic Status and Microbial Community Density and Genetic Structure in Two Agricultural Soils Submitted to Various Types of Organic Management

The effects of soil organic management on indigenous microorganisms were studied by comparing mulching straw (S), conifer compost (CC), and conifer bark (CB) as well as grass landing with grass (G), clover (Cl), and fescue (F) in a silty–clay soil (Macon), and by incorporating vine shoot (VS) and single and double doses of farmyard manure (FM) and mushroom manure (MM) in a calcareous sandy soil (Chinon). Soil physicochemical and microbial characteristics were assessed at each site at two depths by sampling at 0–5 and 5–20 cm for the Macon site and 0–10 and 10–20 cm for the Chinon site. Changes in the quantity of soil organic matter (SOM), through an increase in C_org and N_org contents, and in its quality, through modifications in the C/N and humic acid/fulvic acid ratios, were essentially recorded at the surface layer of treated plots with differential magnitudes according to the inputs and soil type. Quantitative modifications in microbial communities were assessed by means of C-biomass measurements and resulted in an increase in microbial densities fitted with the increase of C_org and N_org contents. However, the deduced C incorporation in microbial biomass was negatively correlated with the C/N ratio, demonstrating a strong influence of the type of organic management on the rate of microbial processes. Qualitative modifications in microbial communities were evaluated by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using bacterial and fungal automated ribosomal intergenic spacer analysis. Organic amendments led to changes in the bacterial and fungal communities of both sites. However, the magnitude and the specificity of these changes were different between sites, organic amendments, and microorganisms targeted, revealing that the impact of organic management is dependent on the soil and organic input types as well as on the particular ecology of microorganisms. A co-inertia analysis was performed to specify the role of the quantity and quality of SOM on the modifications of the genetic structure. A significant costructure was only observed for Macon plots at 0–5 cm between the bacterial genetic structure and the SOM characteristics, demonstrating the influence of the relative amount of the different humic substances (humic and fulvic acids) on microbial composition.     

Microbial Biomass, Community Structure and Metal Tolerance of a Naturally Pb-Enriched Forest Soil

The effect of long-term elevated soil Pb levels on soil microbiota was studied at a forest site in Norway, where the soil has been severely contaminated with Pb since the last period of glaciation (several thousand years). Up to 10% Pb (total amount, w/w) has been found in the top layer. The microbial community was drastically affected, as judged from changes in the phospholipid fatty acid (PLFA) pattern. Specific PLFAs that were high in Pb-enriched soil were branched (especially br17:0 and br18:0), whereas PLFAs common in eukaryotic organisms such as fungi (18:2ω6,9 and 20:4) were low compared with levels at adjacent, uncontaminated sites. Congruent changes in the PLFA pattern were found upon analyzing the culturable part of the bacterial community. The high Pb concentrations in the soil resulted in increased tolerance to Pb of the bacterial community, measured using both thymidine incorporation and plate counts. Furthermore, changes in tolerance were correlated to changes in the community structure. The bacterial community of the most contaminated soils showed higher specific activity (thymidine and leucine incorporation rates) and higher culturability than that of control soils. Fungal colony forming units (CFUs) were 10 times lower in the most Pb-enriched soils, the species composition was widely different from that in control soils, and the isolated fungi had high Pb tolerance. The most commonly isolated fungus in Pb-enriched soils was Tolypocladium inflatum. Comparison of isolates from Pb-enriched soil and isolates from unpolluted soils showed that T. inflatum was intrinsically Pb-tolerant, and that the prolonged conditions with high Pb had not selected for any increased tolerance.     

北亚热带两种森林类型的土壤呼吸研究

对皖西大别山区2种森林植被类型土壤呼吸速率进行统计分析,结果表明,不同季节2种植被类型土壤呼吸速率随时间呈先升后降的变化趋势;土壤呼吸速率与地下5 cm、10 cm的土壤温度有较好的相关性;杉木林土壤呼吸速率与5~10 cm土层有机质含量呈极显著相关,相关系数为0.978(p<0.01);麻栎林土壤呼吸速率与0~5 cm土层有机质含量呈显著相关,相关系数为0.928(p<0.05)。     

Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar

Abstract

To develop a greater understanding of hyporheic zone microbial biogeochemistry, we sampled pore fluids from a piezometer array associated with the McCarran Ranch channel bar (MRCB); a partially submerged cobble island in the Truckee River, NV, USA. Flowing surface water and pumped pore fluids were characterized by prokaryotic community structure, metabolic potential, and aqueous physicochemistry. Concentrations of potential respiratory electron acceptors were highest in surface water and riverbed porewater and sequentially depleted in porewaters along the inferred flowpath (O₂, then NO₃^?, then SO₄^2?). Correspondingly, cultivable nitrate reducers/denitrifiers were most abundant in surface water and riverbed porewater, despite oxic conditions. Cultivable sulfate reducers were overall most abundant in surface water. Prokaryotic community reconstruction from 16S rRNA gene sequences indicates that the surface water community was less diverse than that of porewater and supports a shift in metabolic strategy, from aerobic heterotrophy in surface water (e.g., Comamonadaceae and Sporichthyaceae) to chemolithotrophy and anaerobic metabolisms (e.g., Hydrogenophaga spp., Ferribacterium spp., Methanobacterium spp.) along the hyporheic flow path. These data indicate that prokaryotic communities within the MRCB are phylogenetically and metabolically diverse and contribute to biogeochemical cycling in this common yet relatively understudied habitat.     

两种湿地松群落的小气候特点及其与林分结构的关系

由生物学和生态学特性相互适应的树种组成的混交林,是一个较为稳定的森林生态系统。我国混交林营造、研究的历史不长,大量的工作仅在生长效果等表征调查研究居多,对其内在规律的研究尚处于萌芽阶段。混交林的生态效应是这种变化规律的重要内容,国内学者也曾做了一些工作。本文研究的目的在于:了解湿地松(Pinus elliottii)与大叶相     

Insights into the Phylogeny and Metabolic Potential of a Primary Tropical Peat Swamp Forest Microbial Community by Metagenomic Analysis

A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem.     

Potential Changes in Tree Species Richness and Forest Community Types following Climate Change

Potential changes in tree species richness and forest community types were evaluated for the eastern United States according to five scenarios of future climate change resulting from a doubling of atmospheric carbon dioxide (CO₂). DISTRIB, an empirical model that uses a regression tree analysis approach, was used to generate suitable habitat, or potential future distributions, of 80 common tree species for each scenario. The model assumes that the vegetation and climate are in equilibrium with no barriers to species migration. Combinations of the individual species model outcomes allowed estimates of species richness (from among the 80 species) and forest type (from simple rules) for each of 2100 counties in the eastern United States. Average species richness across all counties may increase slightly with climatic change. This increase tends to be larger as the average temperature of the climate change scenario increases. Dramatic changes in the distribution of potential forest types were modeled. All five scenarios project the extirpation of the spruce–fir forest types from New England. Outputs from only the two least severe scenarios retain aspen–birch, and they are largely reduced. Maple–beech–birch also shows a large reduction in area under all scenarios. By contrast, oak–hickory and oak–pine types were modeled to increase by 34% and 290%, respectively, averaged over the five scenarios. Although many assumptions are made, these modeled outcomes substantially agree with a limited number of predictions from researchers using paleoecological data or other models. Received 12 May 2000; accepted 20 October 2000.     

Soil Bacterial Community Structure Responses to Precipitation Reduction and Forest Management in Forest Ecosystems across Germany

Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season.     

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area

Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P. elliottii plantations.     

Two Invasive Plants Alter Soil Microbial Community Composition in Serpentine Grasslands

Plant invasions pose a serious threat to native ecosystem structure and function. However, little is known about the potential role that rhizosphere soil microbial communities play in facilitating or resisting the spread of invasive species into native plant communities. The objective of this study was to compare the microbial communities of invasive and native plant rhizospheres in serpentine soils. We compared rhizosphere microbial communities, of two invasive species, Centaurea solstitialis (yellow starthistle) and Aegilops triuncialis (barb goatgrass), with those of five native species that may be competitively affected by these invasive species in the field (Lotus wrangelianus, Hemizonia congesta, Holocarpha virgata, Plantago erecta, and Lasthenia californica). Phospholipid fatty acid analysis (PLFA) was used to compare the rhizosphere microbial communities of invasive and native plants. Correspondence analyses (CA) of PLFA data indicated that despite yearly variation, both starthistle and goatgrass appear to change microbial communities in areas they invade, and that invaded and native microbial communities significantly differ. Additionally, rhizosphere microbial communities in newly invaded areas are more similar to the original native soil communities than are microbial communities in areas that have been invaded for several years. Compared to native plant rhizospheres, starthistle and goatgrass rhizospheres have higher levels of PLFA biomarkers for sulfate reducing bacteria, and goatgrass rhizospheres have higher fatty acid diversity and higher levels of biomarkers for sulfur-oxidizing bacteria, and arbuscular mycorrhizal fungi. Changes in soil microbial community composition induced by plant invasion may affect native plant fitness and/or ecosystem function.     

Microbial Community Structure and Density Under Different Tree Species in an Acid Forest Soil (Morvan, France)

Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of “Breuil-Chenue” in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0–5, 5–10, and 10–15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation–extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.     

Microbial Community Structure and Oxidative Enzyme Activity in Nitrogen-amended North Temperate Forest Soils

Large regions of temperate forest are subject to elevated atmospheric nitrogen (N) deposition which can affect soil organic matter dynamics by altering mass loss rates, soil respiration, and dissolved organic matter production. At present there is no general model that links these responses to changes in the organization and operation of microbial decomposer communities. Toward that end, we studied the response of litter and soil microbial communities to high levels of N amendment (30 and 80 kg ha^–1 yr^–1) in three types of northern temperate forest: sugar maple/basswood (SMBW), sugar maple/red oak (SMRO), and white oak/black oak (WOBO). We measured the activity of extracellular enzymes (EEA) involved directly in the oxidation of lignin and humus (phenol oxidase, peroxidase), and indirectly, through the production of hydrogen peroxide (glucose oxidase, glyoxal oxidase). Community composition was analyzed by extracting and quantifying phospholipid fatty acids (PLFA) from soils. Litter EEA responses at SMBW sites diverged from those at oak-bearing sites (SMRO, BOWO), but the changes were not statistically significant. For soil, EEA responses were consistent across forests types: phenol oxidase and peroxidase activities declined as a function of N dose (33–73% and 5–41%, respectively, depending on forest type); glucose oxidase and glyoxal oxidase activities increased (200–400% and 150–300%, respectively, depending on forest type). Principal component analysis (PCA) ordinated forest types and treatment responses along two axes; factor 1 (44% of variance) was associated with phenol oxidase and peroxidase activities, factor 2 (31%) with glucose oxidase. Microbial biomass did not respond to N treatment, but nine of the 23 PLFA that formed >1 mol% of total biomass showed statistically significant treatment responses. PCA ordinated forest types and treatment responses along three axes (36%, 26%, 12% of variance). EEA factors 1 and 2 correlated negatively with PLFA factor 1 (r = –0.20 and –0.35, respectively, n = 108) and positively with PLFA factor 3 (r = +0.36 and +0.20, respectively, n = 108). In general, EEA responses were more strongly tied to changes in bacterial PLFA than to changes in fungal PLFA. Collectively, our data suggests that N inhibition of oxidative activity involves more than the repression of ligninase expression by white-rot basidiomycetes.This revised version was published online in November 2004 with corrections to Volume 48.