Analysis of bacterial populations in a grassland soil according to rates of development on solid media

Abstract The process of colony formation by bacteria from grassland soil sampled in April, July and September was simulated by a colony-forming curve (CFC). The CFC was a super-imposition of several component curves (cCFC) given theoretically by the first order reaction (FOR) model [3,6]. The pattern of FOR model curves was not influenced by the time of sampling and four cCFCs were always recognized during an incubation period of 160 h. It was considered that the CFC describes an inherent property of the bacterial population of the field. Bacterial isolates were obtained from colonies produced in each of four cCFCs on agar plates. Isolates corresponding to one cCFC were classified as one group. The bacterial isolates were characterized by morphological and physiological tests and subsequently clustered. Few oligotrophic bacteria were obtained among bacteria which produced visible colonies within 63 h of incubation time. On the other hand, approx. 50% of bacteria which produced v colonies after 63 h were oligotrophic bacteria. The time required for the appearance of the first colony, t _r of the FOR model, was very similar in the isolates belonging to one group. A close linear relationship was observed between t _r value and doubling time of isolates.     

Indigenous microflora responses to introduction of cyanogenic strains of Pseudomonas fluorescens into soil.

The effects of cyanogenic Pseudomonas fluorescens strains introduced into soil on the kinetic of colony formation and bacterial community structure were investigated. About 7.8 x 10(8) and 1.2 x 10(9) cfu per g dry soil of TA1 and B2 were added to the soil portions, respectively. The parameters of colony formation by heterotrophic soil bacteria were determined. The bacterial community structure and phenotypic diversity were studied using concept of r/K strategies and echophysiological index, respectively. The physiological state of indigenous heterotrophic bacteria and gram-negative group did not change under the influence of the cyanogenic strains introduced. Phenotypic diversity of the soil bacteria also did not change significantly. However, some short-term shifts in community structure of indigenous heterotrophic bacteria were noticed. This study shows that the introduction of great numbers of cyanogenic P. fluorescens strains could be safely used as potential agents in biological control of soil-born pathogens.     

Haemopoiesis in mice genetically lacking granulocyte-macrophage colony stimulating factor during chronic infection with Mycobacterium avium

In order to test the role of granulocyte-macrophage colony stimulating factor (GM-CSF) in haemopoiesis during chronic infection, mice with a targeted disruption of the gene for GM-CSF were infected intraperitoneally with the facultative intracellular pathogen, Mycobacterium avium. The bacteria spread to lungs, liver and spleen and persisted for more than 10 weeks at levels between 105 and 106 CFU. Bacterial numbers did not differ significantly between infected GM-CSF-/- and wild-type mice, making this an excellent model in which to study the effects of GM-CSF deficiency on haemopoietic cells without complications of interpretation relating to differences in bacterial load. Haemopoietic colony forming cells (CFC) in the bone marrow of GM-CSF-/- mice before infection were not different from wild-type. However, whereas CFC in wild-type mice increased 1.5-fold with infection, GM-CSF-/- mice were unable to increase their CFC and numbers were significantly lower than in infected wild-type mice. Cells attracted to the peritoneal cavity of the GM-CSF-/- mice following i.p. injection of bacteria were notably lacking in the large, granular macrophages of activated appearance, which were a feature in wild-type mice. Nitric oxide production by peritoneal cells from GM-CSF-/- mice was deficient. Thus, GM-CSF is not critical for haemopoiesis during chronic infection, but in its absence the mice are unable to increase their output of haemopoietic cells and there are deficiencies in macrophage activation.     

Examination of Bacterial Characteristics of Anaerobic Membrane Bioreactors in Three Pilot-Scale Plants for Treating Low-Strength Wastewater by Application of the Colony-Forming-Curve Analysis Method

Characteristic sludge ecosystems arising in anaerobic membrane bioreactors of three pilot-scale plants treating low-strength (less than 1 g of biological oxygen demand per liter) sewage or soybean-processing wastewater were examined by analysis of the colony-forming-curves (CFC) obtained by counting colonies at suitable intervals. The wastewaters, containing high amounts of suspended solids (SS) (SS/chemical oxygen demand ratio, 0.51 to 0.80), were treated by using two types of bioreactors: (i) a hydrolyzation reactor for solubilization and acidification of SS in wastewater and (ii) a methane fermentation reactor for producing methane. The colony counts for the two sewage treatment plants continued to increase even after 3 weeks of incubation, whereas those for soybean-processing wastewater reached an approximately constant level within 3 weeks of incubation. The CFCs were analyzed by correlating the rate of colony appearance on roll tubes with the physiological types of bacteria present in the bioreactors. It was found that there were large numbers of slow-colony-forming anaerobic bacteria within the bioreactors and that the viable populations consisted of a few groups with different growth rates. It is considered that the slow-growing colonies appearing after 10 days of incubation were the dominant microflora in the sewage treated by hydrolyzation reactors. In particular, highly concentrated sludge (30.0 g of mixed-liquor volatile SS per liter) retained by the membrane separation module contained a large number of such bacteria. Slow-growing colonies of these bacteria could be counted by using a sludge extract medium prepared from only the supernatant of autoclaved sludge. In addition, the highest colony counts were almost always obtained with the sludge extract medium, meaning that most of the anaerobic bacteria in these sludges have complex nutrient requirements for growth. This report also indicates the usefulness of application of the CFC analysis method to the study of bacterial populations of anaerobic treatment systems.     

Genetic control of lipopolysaccharide induced generation of serum colony stimulating factor and proliferation of splenic granulocyte/macrophage precursor cells.

Administration of bacterial lipopolysaccharides (LPS) to mice causes a rise in tissue and serum colony stimulating factor (CSF) levels and in bone marrow and splenic colony forming cells (CFC). Two inbred strains of mice differing in their response to LPS were used to study the genetic control of LPS induced granulopoietic responses: a high responder strain (C3H/eB) which reacts to LPS by an elevation in serum CSF and by an increase in splenic CFC levels, and a low responder strain (C3H/HeJ) which fails to show these responses. The ability to generate serum CSF after administration of LPS is controlled by a single autosomal dominant gene, while the splenic CFC response to LPS follows the characteristic patterns of a polygenic inheritance control. The associated relationships of CSF and CFC responsiveness have been investigated in backcross (F1 X C3H/Hej) and F2 mice. Most mice which generated high levels of CSF showed a high or intermediate CFC response and most mice which did not generate any detectable levels of serum CSF showed a low splenic CFC response. The results suggest that CSF may play a physiologic role in vivo as a granulopoietin. In addition it was shown that the genetic control mechanisms governing the CSF/CFC responses are determined by the lipid A-KDO portion of the LPS molecule, suggesting that lipid A is the active part of the LPS molecule in stimulating granulopoiesis.     

The effect of endotoxin on murine stem cells

Previous studies showed that after 5 μg of Salmonella typhosa endotoxin there was an increase in colony stimulating factor temporally related to a fall in murine marrow in vitro colony forming cells (CFC). This was followed by differentiation along the marrow granulocytic pathway. The present studies showed that after 5 μg of endotoxin the peripheral blood CFC fell by approximately 50% at one hour, rose to a level ten fold that of control at six hours and then returned to control values by 48 hours. There was a progressive increase in the number of splenic CFC to ten fold that of control from 24 to 72 hours after endotoxin. These data imply a migration of CFC from the marrow to the spleen along with an in-situ increase in splenic CFC. Thus, either migration or differentiation may explain the fall in marrow CFC after endotoxin. Spleen colony forming units (CFU) in the marrow were measured by a transplantation technique and the transplantation fraction (f Fx) determined. A decrease in marrow CFU at 24 hours after endotoxin was secondary to a change in the f Fx. from 11.1% to 7.6%. There was however, an increased percentage of CFU in DNA synthesis in the interval of 6–48 hours after endotoxin, as judged by the hydroxyurea technique. As the marrow CFC fell within 20 minutes of endotoxin administration, the data suggest the CFC may be affected initially and that changes in the generative cycle of the CFU may be of a secondary nature.     

Enrichment culture and isolation of slow-growing bacteria

 Enrichment containing large numbers of slow-growing bacteria was developed by repeated batch culture under high biomass concentrations (more than 10 000 mg biomass/l). The characteristics of slow-growing bacterial populations were elucidated by application of colony-forming-curve (CFC) analysis. The CFC were obtained by counting the number of visible colonies on agar plates at successive intervals. The enrichment consisted of several groups with different colony-forming rates and the slow-growing bacteria appeared on cell extract/agar plates after 7 days of incubation. It was found that large numbers of slow-growing bacteria survived under starvation conditions. One of the slow colony-forming bacteria, strain TI-X7, was tentatively identified as being of the genus Micrococcus. The enrichment contained a large amount of Micrococcus-like tetrad cells. The dialysate fractions in excess cell extract, permeable through dialysis tubing, were extremely effective for growth of strain TI-X7. Received: 15 December 1995/Accepted: 20 February 1996     

COLONY FORMATION IN AGAR: IN VITRO ASSAY FOR HAEMOPOIETIC STEM CELLS

Using a method in which embryo fibroblasts were used as feeder layers, the colony forming capacity in agar of a variety of mouse haemopoietic suspensions was compared with their CFU s content. A striking parallelism between the results of the two assays was found. In addition, under certain conditions higher numbers of CFU s could be retrieved from 5-day-old agar colonies than were originally plated, indicating that the CFC a (Colony Forming Cell agar) may fulfil the requirements of pluripotency as well as of self-renewal, both prerequisites for any haemopoietic stem cell candidate. Although our data by no means provide direct proof that the CFC s and the CFC a are identical, they certainly support such a concept. the contradictory findings by others that CFU s and CFU c (Colony Forming Unit culture) can be separated on a velocity gradient is attributed to different culture conditions, in other words, that their CFU cè are not identical with our CFU a .
Our findings also indicate that for mouse cells our soft agar colony assay meets the criteria of a quantitative assay for haemopoietic stem cells and that extension of this technique to bone marrow of primates including humans seems to be justified.     

Alginate Beads as Synthetic Inoculant Carriers for Slow Release of Bacteria That Affect Plant Growth

Uniform synthetic beads were developed as carriers for the bacterial inoculation of plants. The beads are made of sodium alginate and skim milk and contain a large reservoir of bacterial culture which releases the bacteria at a slow and constant rate. The beads are biodegradable and produce no environmental pollution. The strength of the beads, the rate of bacterial release, and the time of their survival in the soil can be controlled by several hardening treatments. The final product, lyophilized beads, is simple to use and is applied to the seeds concomitantly with sowing. The released bacteria are available for root colonization immediately at seed germination. Dry beads containing bacteria can be stored at ambient temperature over a long period without loss of bacterial content; storage requires a limited space, and the quality control of a number of bacteria in the bead is simple. The level of plant inoculation with beads was similar to that with previously used peat inoculants, but the former method yielded more consistent results, as the frequency of inoculated plants was much higher. The former method provides a different approach for inoculation of plants with beneficial rhizosphere bacteria.     

Influence of PCBs on the predator-prey relation between bacteria and protozoa in soil

Abstract This work deals with the impact of a possible accidental pollutant, pyralene (Prodelec, France; PCBs in trichlorobenzene), intoduced into the soil. Its influence on the predator-prey relation between bacteria and amoebae was studied by comparing the population dynamics of (i) an inoculated bacterial population ( A. lipoferum ) chosen as a biological tracer, (ii) the indigenous bacterial microflora, (iii) the infigenous amoebae. In the absence of pyralene the inoculated bacterial population decreased from 10⁷ to 10⁴ bacteria g⁻¹ soil (dw), grazed by the infigenous amoebae whose numbers increased 3-fold. In contrast, in presence of 2500 ppm of pyralene the introduced bacteria survived at a higher level (3·10⁶ bacteria g⁻¹ soil (dw)) while the number of amoebae diminished slightly. No predation occurred with PCB contamination. The indigenous bacterial microflora was not affected quantitatively by pyralene. In pure liquid culture with 500 ppm of pyralene added, bacterial growth was inhibited and an amoebal strain isolated from an inoculated uncontaminated soil was killed. We conclude that the active form of the amoebae were killed, and encystement was inhibited by pyralene in the soil. Hence the protozoa were unable to regulate the introduced A. lipoferum strain as they did in the absence of the pollutant.     

A method for quantifying pulmonary Legionella pneumophila infection in mouse lungs by flow cytometry

ABSTRACT: BACKGROUND: Pulmonary load of Legionella pneumophila in mice is normally determined by counting serial dilutions of bacterial colony forming units (CFU) on agar plates. This process is often tedious and time consuming. We describe a novel, rapid and versatile flow cytometric method that detects bacteria phagocytosed by neutrophils. FINDINGS: Mice were infected with L. pneumophila via intratracheal or intranasal administration. At various times after bacteria inoculation, mouse lungs were harvested and analysed concurrently for bacterial load by colony counting and flow cytometry analysis. The number of L. pneumophila-containing neutrophils correlated strongly with CFU obtained by bacteriological culture. CONCLUSIONS: This technique can be utilised to determine pulmonary bacterial load and may be used in conjunction with other flow cytometric based analyses of the resulting immune response.     

四种牧草植物替代控制对黄顶菊入侵土壤细菌多样性的影响

土壤微生物群落与植物的生长发育密切相关, 入侵植物可以改变入侵地土壤微生物类群, 使土壤理化性质发生变化, 从而促进其入侵过程。该文通过比较高丹草(Sorghum bicolor × S. sudanense)、向日葵(Helianthus annuus)、紫花苜蓿(Medi- cago sativa)和多年生黑麦草(Lolium perenne)4种替代植物与黄顶菊(Flaveria bidentis)混合种植(以下简称混种)后不同时期的土壤细菌多样性的变化, 揭示土壤细菌群落对黄顶菊入侵及替代管理措施的响应规律。结果表明, 单独种植(以下简称单种)黄顶菊的土壤细菌多样性下降, 并且在整个生长期多样性指数多数情况下低于高丹草、向日葵、紫花苜蓿和多年生黑麦草单种或与黄顶菊混种的土壤。当4种替代植物与黄顶菊混种后, 土壤细菌16S rRNA的变性梯度凝胶电泳(DGGE)图谱与它们分别种植时存在明显差异, 且不同生长期各个混种土壤都有特征细菌群落。4种替代植物单种或与黄顶菊混种的土壤细菌Shannon多样性指数变化规律与植物生长发育趋势相同, 7月份达到高峰, 8月份开始降低。总之, 黄顶菊入侵降低了土壤细菌群落多样性, 4种替代植物与黄顶菊混种后, 又可提高土壤细菌群落多样性, 这种变化对黄顶菊成功入侵和替代防控具有重要作用。     

Evaluation of abundance of aerobic bacteria in the rhizosphere of transgenic and non-transgenic alfalfa lines

Fourteen genetically modified lines of alfalfa (Medicago sativa) containing the gene Ov from Japanese quail, coding for a methionine-rich protein ovalbumin, were evaluated for nodulation ability and concentration of aerobic bacteria in the rhizosphere. The transgenic lines were derived from a highly regenerable genotype Rg9/I-14-22, selected from cv. Lucia. On selective media, a higher concentration of ammonifying bacteria, bacterial spores, denitrifying and nitrifying bacteria were observed in the rhizosphere of transgenic clonesand, on the other hand, lower concentration of cellulolytic bacteria and Azotobacter spp. compared with the rhizosphere of non-transgenic clone SE/22-GT2. A statistically significant difference in the concentration of all the bacterial types was found between samples taken from two types of substrates (i.e. sterile vs. nonsterile). Higher bacterial concentration (measured as colony forming units per g soil dry mass) were observed for all tested groups of culturable bacteria in the non-sterile substrate. The presence of Azotobacter spp. was found only in the rhizosphere of plants grown in non-sterile soil in which the highest number of fertile soil particles (97 %) was observed in transgenic clones SE/22-9-1-12 and SE/22-11-1-1S.1. Concentration of bacteria involved in the N cycle in the soil was increased in the rhizosphere of transgenic clones and decreased in the rhizosphere of non-transgenic plants compared with the average value. In spite of some differences in colony numbers in samples isolated from the root rhizosphere of transgenic and nontransgenic alfalfa plants, we could not detect any statistically significant difference between individual lines.     

日本弓背蚁颊下囊内含物中细菌的组成研究

【目的】颊下囊是蚂蚁口前腔中一个特殊的袋状结构,在蚂蚁取食过程中,固体食物和其它颗粒在进入食道前被过滤在颊下囊中,稍后被蚂蚁从口前腔排出,这种过滤机制保证了主要利用液体食物的蚂蚁整个消化道的畅通。本文旨在揭示蚂蚁颊下囊结构及其内含物中存在的细菌类群及其可能在蚂蚁的消化、清洁以及其它方面发挥的潜在作用。【方法】利用扫描电镜确定了日本弓背蚁颊下囊在蚂蚁头部的位置及其形状,然后采用传统的细菌分离培养与细菌16S r RNA基因序列分析相结合的方法进行了颊下囊内含物以及蚁巢内土壤样品细菌的分离培养研究。【结果】(1)颊下囊位于蚂蚁口腔的后侧,呈袋状结构,内部含有大量的固体颗粒物质;(2)3个蚁巢工蚁颊下囊内含物每克样品中可培养细菌的菌落总数(cfu/g)数量差异较大,并且显著大于同巢土壤样品的细菌cfu/g数量;(3)从3个蚁巢的工蚁颊下囊内含物中共分离到11属的细菌,分别隶属于厚壁菌门(Firmicutes)、放线菌门(Actinobacteria)和γ-变形菌纲(γ-Proteobacteria)三大类群,其中放线菌门细菌为优势类群;在属级水平上,巢1和巢2工蚁颊下囊内含物中的优势菌群为微杆菌属,分别占47.83%和49.73%,巢3优势菌群为不动杆菌属和微杆菌属,分别占37.27%和30%;3个蚁巢土壤样品优势菌均为芽孢杆菌属,分别占各自分离总菌落数的49.69%、56.22%和44.79%。(4)蚁巢土壤中所分离出的细菌均能在同巢工蚁的颊下囊内含物中分离得到,但同一蚁巢蚂蚁颊下囊内含物与其巢内土壤的细菌组成存在明显差异;不同蚁巢蚂蚁颊下囊内含物的细菌组成也存在明显差异。【结论】蚂蚁的颊下囊中存在丰富的细菌种类,在蚁巢土壤中分离到的细菌均能在颊下囊中发现,而在颊下囊中分离到的部分细菌并没有在相应的蚁巢土壤样品中分离到。     

Survival Studies with the Fire Blight Pathogen Erwinia amylovora in Soil and in a Soil-inhabiting Insect

The survival of Erwinia amylovora in soil and in the soil-inhabiting insect Folsomia candida was investigated. Although E. amylovora is an air-borne pathogen, it may reach the soil with rain and other dissemination events. The pathogen was selected on agar plates with two antibiotics and identified by its characteristic colony morphology on minimal agar with copper ions and confirmed by polymerase chain reaction assays. Rates of bacterial decline were much higher in non-sterile than in sterile soil, where the number of living bacteria was stable over 11 weeks. It declined rapidly in untreated soil from a field, and the pathogen was no longer detected 5 weeks after inoculation. Soil-living microarthropods such as F. candida (Collembola) contain large amounts of bacteria in their gut. When fed with gfp -labelled E. amylovora , the pathogen was digested in the gut within a few days, contributing to the decrease of the bacterial population in the soil and thus preventing bacterial distribution by insects.     

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.     

不同培养基组合提高土壤细菌可培养性的研究

为选择性采用多培养基组合以提高土壤细菌可培养性,利用变性梯度凝胶电泳(DGGE)技术研究了贫营养、富营养和自然营养培养基在3种培养方式下获得细菌种群的差异。结果表明:平板培养条件下,细菌在贫营养培养基上生长较慢,菌落连续稳定形成。培养5d后,富营养的LB培养基和贫营养的R2A培养基获得菌落数最多,分别是贫营养的0.1×LB培养基获得菌落数的5.1倍和5.3倍。7种培养基中,LB培养基获得细菌种群数目最多,营养成分适当稀释后,培养物中有新的种群出现。贫营养培养基和富营养培养基培养物DGGE图谱相似性低,条带互补性强。三角瓶静置培养时,R2A和LB培养基获得细菌种群数目较多,其它几种培养基获得的细菌类群都能在这2种培养基中找到。试管静置培养条件下,LB培养基获得细菌种群数目最多,某些种群也只出现在R2A培养基和TSB培养基上,R2A及LB培养基与TSB培养基获得的细菌种群差异较为明显。研究结果为特殊培养基设计及选用合适培养基分离土壤细菌提供参考。     

锂对小鼠高增殖潜能集落形成细胞和粒巨噬系祖细胞体外增殖的影响

本文观察了锂对ＢＡＬＢ／Ｃ小鼠骨髓高增殖潜能集落形成细胞（ＨＰＰ－ＣＦＣ）和粒巨噬系祖细胞ＣＦＵ－ＧＭ体外增殖的影响。ＨＰＰ－ＣＦＣ集落由ＩＬ－１、ＩＬ－６、ＷＥＨＩ３条件培养液（ＷＥＨＩ３－ＣＭ,含有ＩＬ－３）及Ｌ９２９条件培养液（Ｌ９２９－ＣＭ,含有Ｍ－ＣＳＦ）所支持,而ＣＦＵ－ＧＭ由ＷＥＨＩ３－ＣＭ所支持。结果显示,ＬｉＣｌ浓度在０．４－２ｍｍｏｌ／Ｌ时呈现剂量依赖性抑制ＨＰＰ－ＣＦＣ增殖;而在０．４－１ｍｍｏｌ／Ｌ的浓度范围内,则对ＣＦＵ－ＧＭ的增殖起剂量依赖性促进作用。这些结果提示ＬｉＣｌ对ＨＰＰ－ＣＦＣ和ＣＦＵ－ＧＭ的作用不同,可能锂有诱导ＨＰＰ－ＣＦＣ向成熟细胞分化的作用     

The novel and efficient method for isolating potassium solubilizing bacteria from rhizosphere soil

Potassium (K) is the third major essential macronutrient for plant growth and more than 90% of potassium in the soil exists in the form of insoluble rocks and silicate minerals. 150 potassium solubilizing bacterial (KSB) strains were isolated from rhizosphere soil using Aleksandrov medium containing insoluble mica powder. Ten efficient KSB strains were selected and quantification studies showed that higher K solubilization (50.6?mg L^?1) was observed in the strain HMP27 followed by strain WHP47 (46.4?mg L^?1) in liquid medium. Potassium solubilization by the bacterial strains is determined by measuring zone of clearance around the bacterial colony. This procedure requires 10–15?days incubation. Therefore, a simple, rapid, and user-friendly method has been developed for screening of potassium solubilizing bacteria using the bromothymol blue dye in modified Aleksandrov medium. Microorganisms possessing potassium solubilization property developed a clear zone around bacterial colony and changed the colour of dye from greenish blue to yellow after two days incubation. High-performance liquid chromatography analysis of the filtrates showed the presence of oxalic, tartaric, citric, and succinic acid, which could be responsible for solubilization of potassium. This method will allow researchers to readily isolate new potassium solubilizing strains adapted to specific environments.     

Cultivation-Dependent and -Independent Approaches for Determining Bacterial Diversity in Heavy-Metal-Contaminated Soil

In recent years, culture-independent methods have been used in preference to traditional isolation techniques for microbial community analysis. However, it is questionable whether uncultured organisms from a given sample are important for determining the impact of anthropogenic stress on indigenous communities. To investigate this, soil samples were taken from a site with patchy metal contamination, and the bacterial community structure was assessed with a variety of approaches. There were small differences in microscopic epifluorescence bacterial counts. Denaturing gradient gel electrophoresis (DGGE) profiles of 16S rRNA gene fragments (16S-DGGE) amplified directly from soil samples were highly similar. A clone library generated from the most contaminated sample revealed a diverse bacterial community, which showed similarities to pristine soil communities from other studies. However, the proportion of bacteria from the soil samples that were culturable on standard plate-counting media varied between 0.08 and 2.2%, and these values correlated negatively with metal concentrations. The culturable communities from each sample were compared by 16S-DGGE of plate washes and by fatty acid profiling of individual isolates. Each approach indicated that there were considerable differences between the compositions of the culturable communities from each sample. DGGE bands from both culture-based and culture-independent approaches were sequenced and compared. These data indicated that metal contamination did not have a significant effect on the total genetic diversity present but affected physiological status, so that the number of bacteria capable of responding to laboratory culture and their taxonomic distribution were altered. Thus, it appears that plate counts may be a more appropriate method for determining the effect of heavy metals on soil bacteria than culture-independent approaches.