Microbial diversity and soil functions

Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high‐resolution techniques with which to detect inactive and active microbial cells in the soil matrix. Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function. The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated ¹³C‐ and ¹²C‐DNA, both extracted from soil treated with a ¹³C source, by density‐gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of ¹³C‐DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C‐substrate added to soil.     

苯醚甲环唑胁迫下农田土壤微生物群落和多样性分析

为研究三唑类杀菌剂苯醚甲环唑(dif)施用后土壤中微生物群落结构的响应变化,通过模拟生产中的施用剂量,监测35 d后土壤的理化性质并利用高通量测序技术分析土壤中细菌和真菌的群落组成变化,通过db-RDA分析建立环境因子与微生物群落响应关系。研究结果显示,随着dif施用浓度的增加,土壤中有机质(SOM)、总氮(TN)、碱解氮(AN)均有所提高,有效磷(AP)呈下降趋势,Alpha多样性指数中细菌Chao1、ACE和Shannon指数均低于未处理土壤,真菌Shannon指数高于未处理土壤;所有样本中细菌共检出31门、91纲、206目、315科、553属,真菌共检测出11门、34纲、79目、174科、370属;苯醚甲环唑施用浓度为50 mg/kg时,土壤细菌中变形菌门和拟杆菌门的相对丰度分别提高了14.2%和1.81%,酸杆菌门和绿弯菌门相对丰度分别降低了8.28%和3.44%,绝对优势菌属节杆菌属相对丰度下降7.85%,真菌中赤霉属和被孢霉属逐渐成为优势菌群;细菌的优势菌群中变形菌门与TN呈显著正相关,真菌优势菌门中子囊菌门与AN、TN和dif呈显著正相关,被孢霉门与SOM呈显著负相关;TN和AN对细菌的Shannon指数影响较大。以上说明,高浓度苯醚甲环唑的施用对土壤的理化性质以及微生物的丰富度和群落结构均产生了影响。     

Microbial community development and unseen diversity recovery in inoculated sterile soil

Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurrence, and role of its different microbial populations are largely unknown. Here, two sterilized soils (from England and Italy) were inoculated with a subsample of their initial microbial communities and/or those from the other soil to study their microbial community evolution. This approach compared two driving factors (original community and soil physico-chemical characteristics) for microbial community definition. After 2 months of incubation and based on metagenomic datasets, the two inoculated communities (from an English grassland and an Italian forest) possessed similar functional and taxonomical structures when inoculated in the same sterile soil. For example, the newly colonized Italian soil was dominated by Actinobacteria related organisms (>66 % of the detected community) with a functional distribution independent of the inoculated soil origin. In addition, some of the organisms that dominated the different inoculated communities after 2 months were similar for a given sterile soil whether they came from the English grassland or the Italian forest, and they had not been detected in the original microbial community from either soil. Thus, similar microorganisms with low representation from the two distinct communities emerged in each sterilized soil, thus increasing the microbial diversity recovered from the microbial community of the donor soil. So far, these observations support the idea that different temperate soil microbial communities have different evenness due to environmental physico-chemical variations, yet have similar community composition (richness), and thus develop similarly when colonizing the same habitat.     

Microbial diversity and activity of disturbed soil in the northern Chihuahuan Desert

 The effects of intense grazing, seasonal drought, and fire on soil microbial diversity (substrate utilization) and activity in a northern Chihuahuan Desert grassland were measured in summer 1997, winter 1998, and spring 1998. Intense livestock grazing was initiated in winter 1995, burning occurred in August 1994, and drought stresses were imposed from October 1994 to June 1997. Microbial diversity was inferred from the carbon substrate utilization patterns in both gram (+) and gram (–) Biolog plates. Microbial activity was estimated by the activity of selected enzymes. Neither microbial diversity nor activity was affected by grazing. The interaction of intense grazing and stress sub-treatments only occurred in spring for one set of diversity measurements. The maximum microbial diversity and activity occurred in the winter-drought-stress sub-plots in summer and spring. Burning reduced microbial diversity and most enzyme activities as compared to the control in summer and spring. Microbial diversity was also lower in summer-drought-stress sub-plots than in the control in summer and spring. Microbial diversity was highest in summer, intermediate in winter, and lowest in spring. Microbial activity was generally higher in summer and lower in winter. It was concluded that substrate availability was the most important factor affecting the diversity and activity of soil microorganisms within a season. Soil moisture was not the factor causing differences in microbial diversity and activity among the stress treatments, but it was a predictor for some microbial responses under a particular stress. Received: 12 August 1999     

长期无机有机肥配施对红壤性水稻土微生物群落多样性及酶活性的影响

【目的】长期有机与无机肥配合施用是促进农田生产力和土壤有机碳固定的重要技术途径。本文以江西省红壤研究所长期不同施肥试验田的表土(0—15 cm)为对象,探讨不同施肥措施对土壤微生物群落多样性和酶活性的影响。【方法】在水稻收获后,采集表土壤样品,提取土壤总DNA。采用聚合酶链反应结合变性梯度凝胶电泳(PCR-DGGE)的方法研究土壤微生物的群落结构多样性,并结合克隆测序研究土壤微生物的群落组成;用实时荧光定量PCR(q PCR)的方法研究土壤微生物的丰度。土壤细菌定量和群落结构分析的分子标靶基因分别为16S rRNA基因V3区和V6区片段,土壤真菌定量和群落结构分析的标靶基因均为18S rRNA基因。DGGE分析采用8%的聚丙烯酰胺凝胶分离细菌和真菌,所用变性梯度分别为35%65%和20%40%。同时采用荧光微孔板检测技术测定土壤几丁质酶、α-葡萄糖苷酶、β-葡萄糖苷酶、纤维素酶、酸性磷酸单脂酶和木聚糖酶活性;用紫外分光光度计法测定土壤过氧化物酶活性。【结果】PCR-DGGE分析表明,与不施肥对照(CK)相比,有机无机肥配施(NPKM),土壤细菌的香农指数和丰富度指数显著增大,而土壤真菌的香农指数和丰富度指数在不同施肥处理间无显著差异。DGGE图谱聚类分析显示,NPKM处理的土壤细菌和真菌的群落结构显著区别于其他3个处理。后续的切胶测序得出,土壤细菌分属于Chloroflexi(绿弯菌门),Proteobacteria(变形菌门)和Firmicutes(厚壁菌门);NPKM处理下隶属于Clostridum(梭菌属)和Anaerolineaceae(厌氧绳菌科)的两类细菌显著增加。土壤真菌主要分属于Basidiomycota(担子菌门)和Ascomycota(子囊菌门),这些真菌条带在DGGE图谱上的分布不同处理间均无明显的规律性,因而不同处理间真菌的群落分布未出现较清晰的变化。q PCR的结果显示,土壤细菌和真菌拷贝数在不同处理间无显著差异。土壤酶的检测结果表明,与CK相比,单施氮肥(N)处理的土壤几丁质酶活性显著提高,常规氮磷钾处理(NPK)处理的几丁质酶和α-葡萄糖苷酶活性显著增强,NPKM处理提高了土壤几丁质酶、纤维素酶和过氧化物酶活性;酸性磷酸单酯酶和木聚糖酶活性在各处理间无显著差异。归一化酶活性值,NPKM处理显著高于CK和其他施肥处理。【结论】长期有机无机肥配施可显著提高土壤细菌多样性,并改变土壤细菌和真菌的群落结构,提高土壤酶活性,因而提高了农田生态系统的生产力并对生态系统健康有改善作用。     

Nitrous oxide and methane emissions from different soil suspensions: effect of soil redox status

Four soil samples from fields of different land use [US (paddy field), China (paddy field) and Belgium (maize and wheat fields)] were incubated as soil suspension (soil:water ratio 1:4) to study the N₂O and CH₄ emission under different soil redox potential conditions. The results show that the N₂O emission was regulated within a narrow redox potential range of +120 to +250 mV, due to the balance of N₂O production and its further reduction to N₂. Methane emission occurred below a soil specific redox potential point, and the emission rates were inversely related to soil redox potentials. Both linear and exponential relationships between CH₄ emission and the soil redox potential were significant. By extrapolating the linear relationship of CH₄ emission against soil redox potential, the critical redox potentials for CH₄ production were estimated at about -170 (US paddy soil), -150 (Chinese paddy soil), -215 (Belgian maize soil), and -195 mV (Belgian wheat soil), respectively. In addition, the results indicate that a soil with a lower critical redox potential for CH₄ production had a higher CH₄ production potential. In this study, N₂O and CH₄ emissions were found to occur at a distinctly different soil redox potential condition. The range of soil redox potential values where both N₂O and CH₄ emissions were low was different for different soils, but it was situated between +120 and -170 mV. This is a wide redox potential range enabling field management practices to minimize both N₂O and CH₄ emissions from wetland ecosystems.     

Microbial removal of lead from solid media and soil

We have isolated a Pseudomonas aeruginosa strain designated CHL004 which is able to remove lead from solidified media and soil. The process for testing removal was generally the same for all experiments. A piece of sterile filter paper was placed on the surface of a plate containing solidified media and lead carbonate or lead contaminated soil and incubated at 29 °C for 30 days. Lead was removed from yeast malt plates but generally not from R2A plates. Dextrose was shown to be a critical component in the YM; without it almost no lead was removed. Sucrose, maltose and lactose could not be substituted for the dextrose although these carbon sources allowed for survival and growth of the isolate. In order to study the initial kinetics of lead uptake, lead nitrate was used in an aqueous environment. The rate of uptake of lead nitrate by CHL004 was very rapid initially then decreased greatly. Sodium azide treated cells did not remove lead. The removal of lead from an urban soil was affected by the pH of the soil. The pH of the soil in YM was 6.9 and 3.3% of the total lead in the soil was removed. When the pH was adjusted to a pH of 5, 8% of the total lead was removed but at a pH of 6, 6.4% was removed.     

可装配式土壤温度传感器设计与试验

土壤温度是土壤墒情监测的重要参数之一,它影响着土壤中一系列的物理、化学和生物化学过程,并与作物生长、发育及生理过程关系密切。目前土壤温度测量技术与设备主要源于工业领域,应用比较成熟,但在农田土壤墒情、气象环境、水文、地理等领域具体应用过程中,存在结构针对性不足、敏感元件及探头选择盲目、测量方式不科学等问题。该文针对以上问题,在分析农田土壤温度测量特殊需求、常用传感器结构与特征、敏感元件选型的基础上,对土壤温度传感器进行优化设计,将感知区域缩短为2cm,提出探头导管分离可装配式结构,采用不同长度玻璃钢塑料管组合装配方式,能够灵活满足地温单点、多点、多层测量,并通过试验分析比较了该传感器与传统传感器在结构、封装材料、测量精度、测量插入方式的差异。结果表明,该传感器精度不超过±0.2℃,20℃跨度响应时间小于100s,水平、垂直测量差异稳定缩小到±0.2℃以下。该传感器减少了结构、封装、测量方式等因素的影响,提高了土壤温度测量科学性、准确性。     

Microbial functional diversity can be influenced by the addition of simple organic substrates to soil

The influence of the composition of added organic C on microbial functional diversity was investigated in an arable soil. Soil was treated with single large additions of organic C compounds (asparagine, gluconic acid, glutamic acid, mannose, methyl–glucamine and urocanic acid) or repeated additions of compounds (asparagine, glucosamine, -ketovaleric acid or urocanic acid) over 4 d. The effects on microbial functional diversity were assessed by measurement of patterns of in situ catabolic potential (ISCP) in each experiment at 1, 7 and 20 weeks, and 1, 4 and 7 d, respectively. Microbial biomass C was generally increased by the substrate additions in both experiments and remained greater than the control over 7 d in the repeated-addition experiment. After 20 weeks, however, only the microbial biomass C in the asparagine and mannose treatments remained increased in the single-addition experiment. The direction of changes in the patterns of ISCP were distinctly different between most treatments in both the single- and repeated-substrate addition experiments. Over 20 weeks, factor analysis showed that the patterns of ISCP in the glutamic acid, mannose, methyl–glucamine and urocanic acid treatments tended to converge with that in the non-amended treatment. The changes in patterns of ISCP were also different after repeated additions of different substrates. However, respiration responses to the added substrate in each of the treatments were not specifically increased relative to the respiration responses to other organic C compounds. These results support the hypothesis that addition of different types of organic C can influence patterns of ISCP. However, it is difficult to distinguish the direct effects of the added compounds on the respiration response to individual substrates.     

Effects of tetracycline on the soil microflora: function,diversity, resistance

Background  Tetracycline is a widely used antibiotic in animal production. Significant amounts of the substance reach the soil via feces, urine and manure application. As tetracycline is a persistent compound with antibacterial activity, its presence in soil may have undesired direct and indirect effects. These have been investigated so far focusing on effects on selected microbial functions. Objectives  The aim of the present study was to obtain comprehensive information on potential effects of tetracycline on the soil microflora under environmentally relevant conditions. The investigations included function and structure of the microbial biocoenosis and the distribution of resistance genes. Methods  Pig manure rich in tetracycline resistance genes was applied to a sandy soil. This soil as well as an unamended soil were additionally treated with several concentrations of tetracycline. The spiked soils were incubated in outdoor lysimeters for several months. Substrate induced respiration, PLFAs, ten selected resistance genes, and the concentrations of tetracycline were determined. Results  The test concentrations, though far exceeding environmental relevance, caused only small effects. An establishment of resistance could not be detected. Applied resistance genes were not detectable at the end of the study even in the presence of added tetracycline. Conclusion  Due to the high sorption capacity of the antibiotic, environmentally relevant concentrations of tetracycline do not seem to cause undesired effects on the soil microflora.     

Sampling soil microfloras: Optimization of density gradient centrifugation in percoll to separate microorganisms from soil suspensions

Suspensions of non-filamentous microorganisms and clay were prepared by dispersing soil with an ion-exchange resin, sieving, elutriation and ultrafiltration. Cells were separated from clay by density gradient centrifugation in linear gradients of Percoll (limiting densities 1.101 and l.139 gcm⁻³). By fractionating the density gradient, the mixed population could be separated into components of differing density. Percoll could be separated from microorganisms by gel chromatography on columns of Sephacryl S-1000 or centrifugation after dilution.     

Determination of exchangeable potassium in soil using ion-selective electrodes in soil suspensions

Summary Methods of determining exchangeable K⁺ of soil by mixing extracting solutions and analysing the soil suspension with ion‐selective electrodes were developed and evaluated on 30 samples of soils. From preliminary comparisons of the K⁺ extracted by BaCl₂ and NH₄OAc solutions and by batch and leaching treatments of soils, we established that suspensions of 5 g soil in 100 ml 0.5 m BaCl₂ and single batch treatments of 1 h should be used. The exchangeable K⁺ was determined with a K‐selective, valinomycin‐based PVC membrane electrode and electrochemical cells that did or did not include a liquid junction (the reference electrode being a double‐junction reference electrode assembly with a 10 m LiOAc salt bridge solution or a Cl‐selective electrode, respectively). The Ba‐exchangeable K⁺ values were sensibly the same whether a liquid junction was involved or not, a result that can be attributed to the beneficial effects of the salt bridge and the ionic strength of the extractant. Comparisons of these Ba‐exchangeable results with those obtained by various combinations of batch or leaching treatments, BaCl₂ or NH₄OAc extractants and filtrate analysis by the ion‐selective electrode method or atomic absorption spectrometry showed they were all highly correlated (r≥ 0.996). The selectivity of the K⁺‐selective electrode (k^pot_KNH4 = 0.004) significantly reduced the interference from indigenous soil NH₄⁺ in the BaCl₂ suspensions. Overall, the results show potentiometric measurements of K⁺ in soil suspensions can provide a simple, rapid, and reliable means of determining exchangeable K⁺ in soils.     

淋洗过程预分离细颗粒悬液重金属去除的研究

研究了4种絮凝剂对在土壤淋洗过程中预分离出来的细颗粒悬液中的Cd、Pb、Zn的去除效果以筛选最佳絮凝剂及其用量。结果表明,随着硫酸铝添加量的增加,悬液中Cd、Pb、Zn浓度呈先逐渐降低后上升的趋势;3种元素浓度均随着聚合氯化铝(PAC)和CaO添加量的增加而迅速降低;随着硫酸亚铁添加量的增加,悬液中Pb、Zn浓度逐渐降低,而Cd浓度先迅速降低后逐渐回升。综合悬液中Cd、Pb、Zn的去除效果,选择硫酸铝、PAC、硫酸亚铁和CaO的最佳添加量分别为:0.25、0.04、1.0、0.3 g/L,此时3种元素浓度均达到农田灌溉水质标准。在最佳添加量下按每万吨悬液处理量换算,4种絮凝剂絮凝成本依次为:硫酸亚铁(4500元)>硫酸铝(1900元)>PAC(1000元)>CaO(900元)。因此,选择CaO作为最佳絮凝剂,相应最佳絮凝pH范围为10～11。     

Genetic and phenotypic diversity and random association of DNA markers of isolates of the fungal plant pathogen Sclerotinia sclerotiorum from soil on a fine geographic scale

Sclerotia of the soil-borne plant pathogen Sclerotinia sclerotiorum were collected from 1 m² area of the top 1.27 cm layer of soil in an alfalfa field in southeastern Washington state of the US. Out of 272 sclerotia collected, 40 were randomly selected and analyzed for genetic diversity in terms of microsatellite loci, mycelial compatibility groups (MCGs) and phenotypic diversity using five phenotypic traits (fungicide sensitivity, oxalic acid production, growth rate, colony color and virulence). Sixteen microsatellite haplotypes and 15 MCGs were found among the 40 isolates. The isolates showed three colony colors (beige, dark and white) on Difco PDA and exhibited significant differences in growth rate, oxalic acid production, and sensitivity to three fungicides, benomyl, fluazinam and iprodione. However, these isolates did not show differences in their ability to colonize detached pea leaves. No apparent relationship among the neutral genetic markers and the phenotypic traits was detected. Two of the haplotypes accounted 40% of the isolates, suggesting isolates of these haplotypes might be better adapted to the environmental conditions in this alfalfa field. Several lines of evidence indicated high levels of genetic diversity and potential outcrossing within the population of S. sclerotiorum: 1) high likelihood of five genetic populations based on Bayesian probability and the presence of admixed isolates; 2) random association of alleles in every pair-wise linkage disequilibrium test among eight independent microsatellite loci; 3) discordances between microsatellite haplotypes and MCGs and 4) lack of correspondence among the genetic markers and phenotypic traits. Multilocus Index of Association test suggested that outcrossing occurs only within interbreeding subpopulations of S. sclerotiorum.     

Microbial induced nitrous oxide emissions from an arable soil during winter

Nitrous oxide (N₂O) release rates were measured from an fertilized and unfertilized plot on silty loam (Gleyic Luvisol) cropped with winter wheat. Rates were estimated using a closed soil cover box technique throughout a continuous investigation period of 12 months. The 12 months of investigation were separated into the cropping period (March to November) and the winter period (December to February). Soil management and all N-applications were made during the cropping period. The application of 220 kg N to the soil induced significantly higher N₂O losses throughout the cropping season compared to the unfertilized soil. No significant differences were found during winter, where 70% of the annual N₂O emissions were found. The temporal changes of the N₂O emission rates on both soils were highly correlated (r=0.96; P≤0.001), and could be attributed to temporal changes in soil temperature (r=0.65; P≤0.01) resulting from freezing and thawing cycles. In order to decide whether the N₂O production can be attributed to microbial or non-microbial processes in soil, the time courses of the N₂O emissions from a γ-ray sterilized and a non-sterilized soil were compared in a laboratory experiment, where the freezing and thawing cycles were simulated according to field conditions. The results indicated, that microbial processes were responsible for N₂O production in thawing and even frozen soils.     

Seasonal variation rather than stand age determines bacterial diversity in the rhizosphere of wolfberry (Lycium barbarum L.) associated with soil degradation

Journal of Soils and Sediments - Soil degradation occurs in wolfberry (Lycium barbarum L.) fields with increasing stand age, but the effect of stand age on rhizosphere microbial communities is...     

Microbial response of an acid forest soil to experimental soil warming

 Effects of increased soil temperature on soil microbial biomass and dehydrogenase activity were examined on organic (O) horizon material in a low-elevation spruce-fir ecosystem. Soil temperature was maintained at 5  °C above ambient during the growing season in the experimental plots, and soil temperature, moisture, microbial biomass, and dehydrogenase activity were measured during the experiment. An incubation study was also conducted under three temperature regimes, 5, 15, and 25  °C, and under four moisture regimes of 20, 120, 220, and 320% to further evaluate these environmental factors on dehydrogenase activity and microbial biomass. Soil moisture content and microbial biomass controls were significantly lower (30% and 2 μg g^–1 soil, respectively) in the heated plots during the treatment period, suggesting that moisture content was important in controlling microbial biomass. In the incubation study, temperature appeared more important than moisture in controlling microbial biomass and dehydrogenase activity. Increasing temperature between 5  °C and 25  °C resulted in significant decreases in microbial biomass and dehydrogenase activity. Received: 7 August 1998     

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

Background, aim, and scope  Fertilization is an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shifts of soil microorganisms, which control the cycling of many nutrients in the soil. Here, culture-dependent and culture-independent approaches were used to analyze the soil bacterial and fungal quantities and community structure under seven fertilization treatments, including Control, Manure, Return (harvested peanut straw was returned to the plot), and chemical fertilizers of NPK, NP, NK, and PK. The objective of this study was to examine the effects on soil microbial composition and diversity of long-term organic and chemical fertilizer regimes in a Chinese upland red soil. Materials and methods  Soil samples were collected from a long-term experiment station at Yingtan (28°15′N, 116°55′E), Jiangxi Province of China. The soil samples (0–20 cm) from four individual plots per treatment were collected. The total numbers of culturable bacteria and fungi were determined as colony forming units (CFUs) and selected colonies were identified on agar plates by dilution plate methods. Moreover, soil DNAs were extracted and bacterial 16S rRNA genes and fungal 18S rRNA genes were polymerase chain reaction amplified, and then analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Results  The organic fertilizers, especially manure, induced the least culturable bacterial CFUs, but the highest bacterial diversity ascertained by DGGE banding patterns. Chemical fertilizers, on the other hand, had less effect on the bacterial composition and diversity, with the NK treatment having the lowest CFUs. For the fungal community, the manure treatment had the largest CFUs but much fewer DGGE bands, also with the NK treatment having the lowest CFUs. The conventional identification of representative bacterial and fungal genera showed that long-term fertilization treatments resulted in differences in soil microbial composition and diversity. In particular, 42.4% of the identified bacterial isolates were classified into members of Arthrobacter. For fungi, Aspergillus, Penicillium, and Mucor were the most prevalent three genera, which accounted for 46.6% of the total identified fungi. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Discussion  It was evident that more representative fungal genera appeared in organic treatments than other treatments, indicating that culturable fungi were more sensitive to organic than to chemical fertilizers. A very notable finding was that fungal CFUs appeared maximal in organic manure treatments. This was quite different from the bacterial CFUs in the manure, indicating that bacteria and fungi responded differently to the fertilization. Similar to bacteria, the minimum fungal CFUs were also observed in the NK treatment. This result provided evidence that phosphorus could be a key factor for microorganisms in the soil. Thus, despite the fact that culture-dependent techniques are not ideal for studies of the composition of natural microbial communities when used alone, they provide one of the more useful means of understanding the growth habit, development, and potential function of microorganisms from soil habitats. A combination of culture-dependent and culture-independent approaches is likely to reveal more complete information regarding the composition of soil microbial communities. Conclusions  Long-term fertilization had great effects on the soil bacterial and fungal communities. Organic fertilizer applications induced the least culturable bacterial CFUs but the highest bacterial diversity, while chemical fertilizer applications had less impact on soil bacterial community. The largest fungal CFUs were obtained, but much lower diversity was detected in the manure treatment. The lowest bacterial and also fungal CFUs were observed in the NK treatment. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Phosphorus fertilizer could be considered as a key factor to control the microbial CFUs and diversity in this Chinese upland red soil. Recommendations and perspectives  Soil fungi seem to be a more sensitive indicator of soil fertility than soil bacteria. Since the major limitation of molecular methods in soil microbial studies is the lack of discrimination between the living and dead, or active and dormant microorganisms, both culture-dependent and culture-independent methods should be used to appropriately characterize soil microbial diversity.     

Effects of oxygen tension on growth,respiration, and types of bacteria isolated from soil suspensions

Fifty-seven bacteria were isolated from soil suspensions incubated under pO₂ of 1.5 or 159 mm Hg and their growth and generic characteristics were elucidated.The isolates were cultured under both high (159 mm Hg) and low (3 mm Hg) pO₂. On the basis of their growth responses to the different pO₂, the isolates were classified into two types; (A-type) the lag time, specific growth rate, and/or maximum growth depended on pO₂, and (B-type) these three growth characteristics did not depend on pO₂. B-types were found only among isolates from soil suspensions incubated under the low pO₂. The respiration of some B-type isolates was inhibited by higher pO₂. No A-type isolates were inhibited by high pO₂.The isolates were classified into eight generic groups: Under 159 mm Hg O₂, Groups I(Bacillus spp) and IV(Pseudomonas spp etc.) dominated the others; under 1.5 mm Hg O₂, Group I, III(coryneform bacteria) and V(Alcaligenes spp etc.) dominated. Microaerophilic isolates (isolated only from the soil suspension incubated under 1.5 mm Hg O₂) were classified into Group V. Isolates belonging to the B-type were classified into the coryneform and Group V bacteria.