Higher Diversity of Rhizobium leguminosarum Biovar viciae Populations in Arable Soils than in Grass Soils

The bacterial genetic diversity after long-term arable cultivation was compared with that under permanent grassland using replicated paired contrasts. Pea-nodulating Rhizobium leguminosarum populations were sampled from pairs of arable and grass sites at four locations in Yorkshire, United Kingdom. Isolates were characterized using both chromosomal (16S-23S ribosomal DNA internal transcribed spacer PCR-restriction fragment length polymorphism) and plasmid (group-specific repC PCR amplification) markers. The diversities of chromosomal types, repC profiles, and combined genotypes were calculated using richness in types (adjusted to equal sample sizes by rarefaction), Shannon-Wiener index, and Simpson's index. The relative differences in diversity within each pair of sites were similar for all three diversity measures. Chromosomal types, repC profiles, and combined genotypes were each more diverse in arable soils than in grass soils at two of the four locations. The other comparisons showed no significant differences. We conclude that rhizobial diversity can be affected by differences between these two management regimens. Multiple regression analyses indicated that lower diversity was associated with high potential nitrogen and phosphate levels or with acidity.     

Biogeography of diazotrophic bacteria in soils

This study evaluated diazotrophic bacterial diversity of soils from four different sites in South and North America. Approximately one hundred and thirty-nine thousand partial sequences of the small subunit of the bacterial ribosomal RNA gene generated for a previous study were used for this work. Sequences that presented at least 90% similarity with known diazotrophic organisms were pulled from the original dataset and a new library containing 14,842 sequences from nitrogen-fixing bacteria were analysed. The number of sequences and the abundance of identifiable/cultivable diazotrophic genera were used for the calculation of the Shannon–Weaver diversity index and Evenness. All soils exhibited similar diazotrophic diversity, illustrating the great amount of similarity found between randomly chosen soils. Out of 81 diazotrophic genera, 45 were found in common in the four soils tested irrespective of the localization or cultivation. The degree of dominance of these common genera within their communties differed widely between soils. Sixteen types were found in only one sample.     

Soil parent material is a key determinant of the bacterial community structure in arable soils

The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes.     

Analysis of unculturable bacterial communities in tea orchard soils based on nested PCR-DGGE

The bacterial communities in the soils from tea orchards and their adjacent wasteland in Anhui Province, China were analysed by nested PCR-DGGE technique combined with sequencing. DGGE profiles revealed that the DGGE patterns of different soils were similar to each other and the most intensely bands appeared in all lanes. The bacterial genetic diversity index of tea orchard soils was lower than that of wasteland. For the tea orchard soils, Shannon’s diversity index decreased in the order: 45-year-old tea orchard >25-year-old tea orchard >7-year-old tea orchard >70-year-old tea orchard. The analysis of 16S rRNA gene sequences indicated that the fragments belong to Proteobacteria, Acidobacteria, TM7, Cyanobacteria and Firmicutes. A comprehensive analysis of the bacterial community structure in the tea orchard soils indicated the bacterial community was dominantly composed of Acidobacteria, followed by Proteobacteria (Gamma and Alpha), Firmicutes, Cyanobacteria and candidate division TM7. The RDA combined with UPGMA clustering analysis showed that the more similar the environmental variables were, the more similar the bacterial community structures in tea orchard soils were.     

Mycobacterium diversity and pyrene mineralization in petroleum-contaminated soils

Degradative strains of fast-growing Mycobacterium spp. are commonly isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soils. Little is known, however, about the ecology and diversity of indigenous populations of these fast-growing mycobacteria in contaminated environments. In the present study 16S rRNA genes were PCR amplified using Mycobacterium-specific primers and separated by temperature gradient gel electrophoresis (TGGE), and prominent bands were sequenced to compare the indigenous Mycobacterium community structures in four pairs of soil samples taken from heavily contaminated and less contaminated areas at four different sites. Overall, TGGE profiles obtained from heavily contaminated soils were less diverse than those from less contaminated soils. This decrease in diversity may be due to toxicity, since significantly fewer Mycobacterium phylotypes were detected in soils determined to be toxic by the Microtox assay than in nontoxic soils. Sequencing and phylogenetic analysis of prominent TGGE bands indicated that novel strains dominated the soil Mycobacterium community. Mineralization studies using [(14)C]pyrene added to four petroleum-contaminated soils, with and without the addition of the known pyrene degrader Mycobacterium sp. strain RJGII-135, indicated that inoculation increased the level of degradation in three of the four soils. Mineralization results obtained from a sterilized soil inoculated with strain RJGII-135 suggested that competition with indigenous microorganisms may be a significant factor affecting biodegradation of PAHs. Pyrene-amended soils, with and without inoculation with strain RJGII-135, experienced both increases and decreases in the population sizes of the inoculated strain and indigenous Mycobacterium populations during incubation.     

Long-term effects of crop management on Rhizobium leguminosarum biovar viciae populations

Little is known about factors that affect the indigenous populations of rhizobia in soils. We compared the abundance, diversity and genetic structure of Rhizobium leguminosarum biovar viciae populations in soils under different crop managements, i.e., wheat and maize monocultures, crop rotation, and permanent grassland. Rhizobial populations were sampled from nodules of pea- or vetch plants grown in soils collected at three geographically distant sites in France, each site comprising a plot under long-term maize monoculture. Molecular characterization of isolates was performed by PCR-restriction fragment length polymorphism of 16S-23S rDNA intergenic spacer as a neutral marker of the genomic background, and PCR-restriction fragment length 0polymorphism of a nodulation gene region, nodD, as a marker of the symbiotic function. The diversity, estimated by richness in types and Simpson's index, was consistently and remarkably lower in soils under maize monoculture than under the other soil managements at the three sites, except for the permanent grassland. The highest level of diversity was found under wheat monoculture. Nucleotide sequences of the main rDNA intergenic spacer types were determined and sequence analysis showed that the prevalent genotypes in the three maize fields were closely related. These results suggest that long-term maize monoculturing decreased the diversity of R. leguminosarum biovar viciae populations and favored a specific subgroup of genotypes, but the size of these populations was generally preserved. We also observed a shift in the distribution of the symbiotic genotypes within the populations under maize monoculture, but the diversity of the symbiotic genotypes was less affected than that of IGS types. The possible effect of such changes on biological nitrogen fixation remains unknown and this requires further investigation.     

Novel soil lineages of Archaea are present in semi-arid soils of eastern Australia

The diversity of Archaea was studied in vertisolic and loam soils of a semi-arid region in Australia. Sampling was undertaken at an agricultural site, two grassland environments, and a brigalow (Acacia harpophylla) woodland. Archaeal community structure was profiled using amplified ribosomal DNA restriction analysis (ARDRA) combined with rDNA sequencing of an example of each restriction fragment length polymorphism type. Sequence comparison and phylogenetic analysis demonstrated that both crenarchaeotal and euryarchaeotal Archaea were present at oxic depths in the soil at all field sites. Along with previously described soil archaeal lineages, novel soil lineages and the deeply divergent Pendant-33 group of Euryarchaeota were also detected. A novel statistical method for comparing ARDRA derived data was demonstrated and implemented using the archaeal communities from the four field sites. Archaeal diversity, as measured by this method, was significantly higher in the agricultural site than at either of the grassland sites or the brigalow woodland.     

Vegetation effects on phosphorus fractions in set-aside soils

As increasing amounts of arable land are being set aside, it is of importance to study the effect of vegetation on soil fertility. The fractionation of soil P under grassland, beech and spruce vegetation was investigated in sites previously fertilized with P by extracting sequentially with Resin, NaHCO₃, NaOH, HCl and finally NaOH after ultrasonic pretreatment. Under beech a large part of extractable P was found in inorganic fractions which are considered to be available for plants (Resin P₁ and Bicarbonate P₁). Under grass, a large part of the extractable P was found in potentially labile organic forms (Bicarbonate P_o and Fulvic acid P_o). After 25 years of permanent grass vegetation, the extractability of soil P was comparable to that from an adjacent arable plot. On spruce covered soils most of the added fertilizer P was rendered unextractable 20–30 years after application. However the available data does not allow a clear interpretation of this phenomena, as effects of soil parent material as well as vegetation may be taken into consideration. No decrease in P-extractability was found between beech and grass covered soils which had been fertilized for more than 200 years, when compared to less rich soils from the same area. On the basis of the current data it may be concluded that the vegetation affects the distribution of soil phosphorus fractions, and thus soil fertility. In the soils under investigation, grassland and beech vegetation conserved the phosphate availability to a high extent.     

高肥力土壤条件下不同基因型花生对氮素利用的差异

在桶栽条件下,利用¹⁵N示踪技术,选用20个基因型花生为供试材料,研究了高肥力土壤条件下不同基因型花生对氮素利用的差异.结果表明:高肥力土壤条件下花生氮素营养以土壤氮为主,根瘤固氮次之,肥料氮最低.不同基因型间花生对全氮、肥料氮、土壤氮和根瘤固氮的吸收和积累均存在显著差异,基因型间遗传变异以根瘤固氮最大,肥料氮和土壤氮相当.氮素荚果生产效率和氮肥利用率基因型间差异显著,最高值分别为最低值的3.6和2.1倍.全氮、肥料氮、土壤氮和根瘤固氮的氮素收获指数基因型间均存在显著遗传变异,且以根瘤固氮的氮素收获指数基因型间遗传变异最大.花生荚果产量与不同氮源氮素积累量及氮素收获指数、氮素荚果生产效率和氮肥利用率呈显著或极显著正相关.依据花生对不同氮源氮素吸收积累和荚果产量筛选出全氮高积累高产型、肥料氮高积累高产型、土壤氮高积累高产型和根瘤固氮高积累高产型四大类型花生,其中四大类型特征兼有的有4个花生基因型.     

Thiosulfate sulfurtransferase (rhodanese) in forest soils

Concentrations of thiosulfate sulfurtransferase (rhodanese; EC 2.8.1.1) in soils of five types of forest stands (spruce and pine stands without ground vegetation, and mountain ash, birch and pine stands with grass cover) were followed. Soils from grassed stands contained much higher concentrations of the enzyme than soils without ground vegetation. On grassed locations higher enzyme concentrations were found in fermentation horizons, whereas on locations without the ground vegetation they were detected in humus horizons. Urea fertilization and SO₂ pollution did not exhibit any significant effect.     

围栏对青藏高原不同类型草地土壤原核微生物多样性的影响

草地退化是草地植被的倒退演替,导致生物多样性丧失和生态系统功能退化,围栏是恢复退化草地生态系统功能的有效管理措施。微生物是土壤中的重要组成部分,在维持草地生态系统稳定性和功能方面发挥着重要作用。然而,目前尚不清楚围栏如何影响不同类型草地土壤微生物群落。以青藏高原草甸、草原和荒漠草地三种草地类型的退化草地为研究对象,设置围栏和放牧两种处理,采用Illumina HiSeq高通量测序技术研究了围栏对土壤原核微生物群落多样性和群落结构的影响。结果表明：围栏未显著影响草甸土壤原核微生物的丰富度、Shannon多样性和均匀度,但显著增加了草原土壤的原核微生物的丰富度、Shannon多样性和均匀度（P<0.05）,稍降低了荒漠草地土壤原核微生物的丰富度、Shannon多样性和均匀度（P=0.086、0.072和0.099）。在围栏处理的草地中,土壤原核微生物丰富度、Shannon多样性和均匀度与年均温、干旱度和pH显著负相关（P<0.01）,与年平均降水量、溶解性有机碳、地上生物量和植物多样性显著正相关（P<0.01）。在放牧处理的草地中,土壤原核微生物丰富度、Shannon多样性和均匀度与年均温和干旱度显著负相关（P<0.05）,但原核微生物丰富度和Shannon多样性与所有土壤理化和植被因素均无显著相关性。冗余分析（RDA）表明,不同类型草地土壤原核微生物群落结构发生了显著的变化,并沿草甸、草原和荒漠草地的过渡逐渐转变（P<0.001）。方差分解分析（VPA）进一步表明,原核微生物群落结构变化主要受年均温、年平均降水量、干旱度和pH的驱动。围栏显著改变了不同类型草地中部分样点土壤原核微生物群落结构。三种草地类型的主要原核微生物优势门均为放线菌门（Actinobacteria）、变形菌门（Proteobacteria）和酸杆菌门（Acidobacteria）。放线菌门（Actinobacteria）的相对丰度在荒漠草地土壤中最高,而变形菌门（Proteobacteria）和酸杆菌门（Acidobacteria）的相对丰度在草甸土壤中最高。此外,不同类型围栏和放牧草地土壤原核微生物类群的相对丰度均无显著差异。研究表明不同类型草地土壤原核微生物群落对围栏的响应不同,这为因地制宜制定草地管理措施提供了数据支持,为草地退化的防治提供了理论支持。     

Excessive variation in Y chromosomal DNA in Rumex acetosa (Polygonaceae)

Rumex acetosa is one of the few angiosperms that possesses sex chromosomes. The same types of abundant repetitive sequences cover both heterochromatic Y chromosomes present in males. The aim of this study was to investigate genetic variation in paternally inherited Y chromosomal DNA and in maternally inherited cpDNA, and to find out whether the examined genomic regions are suited to a phylogeographic study in R. acetosa. DNA sequence polymorphisms present in the 850-bp heterochromatic segment on the Y chromosomes were compared to variation in the 409-bp long chloroplast section (trnL- trnF spacer) in R. acetosa originating from several European locations and from the Altai mountains in Russia. A great amount of genetic variation was detected within the Y chromosomal region while only four chloroplast genotypes were detected. Although the chloroplast haplotypes possessed some geographic pattern, no clear phylogeographic pattern was detected based on the variable Y chromosomes. The mean Y chromosomal nucleotide diversity among all samples equaled 6.6 %, and the mean proportion of polymorphic sites per individual equaled 8.2 % among SNP sites and 1.7 % among all sites investigated. The high number of substitutions detected in the Y chromosomal DNA shows that this heterochromatic sequence has a high mutation rate. The diversity pattern indicates that gene flow via pollen is extensive and it blurs any geographical pattern in the Y chromosomal variation. The high number of repeats and uncertainty concerning the extent of recombination between the two Y chromosomes impair the usability of the Y chromosomal segment for phylogeographic or population genetic studies.     

Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens

The diversity of soil microbial communities can be key to the capacity of soils tosuppress soil-borne plant diseases. As agricultural practice, as well as directedagronomical measures, are known to be able to affect soil microbial diversity, it isplausible that the soil microflora can be geared towards a greater suppressivity ofsoil-borne diseases as a result of the selection of suitable soil management regimes.In the context of a programme aimed at investigating the microbial diversity of soilsunder different agricultural regimes, including permanent grassland versus arableland under agricultural rotation, we assessed how soil microbial diversity is affectedin relation to the suppression of the soil-borne potato pathogen Rhizoctoniasolani AG3. The diversity in the microbial communities over about a growingseason was described by using cultivation-based – plating on different media – and cultivation-independent – soil DNA-based PCR followed by denaturing gradient gel electrophoresis (DGGE) community fingerprinting – methods. The results showed great diversity in the soil microbiota at both the culturable and cultivation-independent detection levels. Using cultivation methods, various differences between treatments with respect to sizes of bacterial and fungal populations were detected, with highest population sizes generally found in rhizospheres. In addition, the evenness of eco-physiologically differing bacterial types was higher in grassland than in arable land under rotation. At the cultivation-independent level, clear differences in the diversities of several microbial groups between permanent grassland and arable land under rotation were apparent. Bio-assays that assessed the growth of R. solani AG3 hyphae through soil indicated a greater growth suppression in grassland than in arable land soils. Similarly, an experiment performed in the glasshouse showed clear differences in both microbial diversities and suppressiveness of R. solani growth in soil, depending on the presence of either maizeor oats as the crop. The significance of these findings for designing soil managementstrategies is discussed.     

Vegetation and soils of the Meikle Kilrannoch ultramafic sites

Summary

The vegetation of two ultramafic sites (MK1 and MK2) at Meikle Kilrannoch are described. MK1 is dome shaped and has much weathering bedrock whilst MK2 is flatter, lacks weathering bedrock and has probably been entirely peat covered. Six vegetation Groups were recognized: I, high-level blanket bog; II and III, grass heath (with II more sedge-rich); IV, dwarf shrub heath; V and VI, debris (an open vegetation on stony skeletal soils). Vegetation maps were produced which had five mapping units: Group I, Groups II and IH combined, Group IV, Groups V and VI combined, and non-vegetated eroding peat. Three main soil types occur: peat, which underlies Group I; a complex of freely draining magnesian brown soils and imperfectly drained magnesian gleys which bear Groups II–IV; and skeletal soils, derived either from weathering bedrock (MK1 only) or ultramafic drift, which bear vegetation in Groups V or VI. The rare plants are commonest in, but not restricted to, debris vegetation on skeletal soils. The likely plant toxicity of soil magnesium at the sites is reaffirmed but it is suggested that the low plant cover in the debris is more likely to result from low nutrients or intensive frost action or both. Floristic differences between MK1 and MK2 are discussed and quantified for Lychnis alpina (which had 68000individuals on the former site and 46 on the latter) but the causes of the differences remain unexplained.     

Communities of arbuscular mycorrhizal fungi in arable soils are not necessarily low in diversity

Communities of arbuscular mycorrhizal fungi (AMF) in five agricultural field sites of different management intensities were studied. Variable regions of the ribosomal RNA genes were used to detect and identify AMF directly within colonized roots. Roots from a continuous maize monoculture showed low AMF diversity, in agreement with previous reports on molecular diversity of AMF in agricultural soils. In contrast, a substantially higher diversity of AMF was found throughout the long term 'DOK' field experiment, where organic and conventional agricultural practices have been compared side by side since 1978. In this experiment, a 7-year crop rotation is performed under lower levels of inorganic fertilizer input and chemical pest control. These results are in good agreement with analyses of the spore community previously conducted in these field sites. In a third site, an organically managed leek field with soil of very high phosphate content reflecting the highly intensive conventional field history and intensive tillage, we detected a low-diversity community comparable to the maize monoculture. In addition to fungi from Glomus group A, which have previously been reported to dominate arable soils, we regularly found members of the genera Scutellospora, Paraglomus and Acaulospora. The genus Acaulospora was shown to occur more frequently early in the growing season, suggesting that the life history strategy of AMF may influence the active community at a given time. These data show that the diversity of AMF is not always low in arable soils. Furthermore, low-input agriculture involving crop rotation may provide better conditions to preserve AMF diversity, by preventing the selection for the few AMF taxa tolerating high nutrient levels.     

衡阳紫色土丘陵坡地植被恢复对土壤微生物功能多样性的影响

以典型湖南省衡阳紫色土丘陵坡地不同植被恢复阶段为研究对象,采用空间代替时间序列的方法,选用立地条件基本相似的草本(狗尾草,GS)、灌草(紫薇-狗尾草,FG)、灌丛(牡荆+剌槐,FX)和乔灌(枫香+苦楝-牡荆,AF)群落阶段,运用Biolog-ECO微平板技术,对4个不同恢复阶段0～10和10～20 cm土层的土壤微生物功能多样性进行研究,探讨植被恢复对土壤微生物功能多样性的影响.结果表明: 植被恢复后土壤微生物群落代谢活性显著升高,同一土层不同恢复阶段AWCD值的大小顺序为乔灌群落＞灌丛群落＞灌草群落＞草本群落,相同恢复阶段不同土层的AWCD值的大小顺序为0～10 cm＞10～20 cm;主成分分析(PCA)表明,灌草群落与灌丛群落具有相似的土壤微生物C源利用方式及代谢功能,而草本群落、乔灌群落具有不同的C源利用方式及代谢功能,在主成分分离中起主要贡献作用的C源是糖类、氨基酸类以及代谢中间产物和次生代谢物;土壤微生物的Shannon物种丰富度指数(H)、Shannon均匀度指数(E)、Simpson优势度指数(D)和McIntosh指数(U)均以乔灌群落最高,灌草群落和灌丛群落次之,草本群落最低;相关分析表明,土壤含水量(SWC)、土壤总有机碳(STOC)、全氮(TN)、全磷(TP)和速效磷(AP)对土壤微生物代谢功能及功能多样性指数有重要影响,脲酶(URE)、磷酸酶(APE)、蔗糖酶(INV)和过氧化氢酶(CAT)活性与土壤微生物代谢功能及功能多样性指数存在显著相关关系.表明植被恢复可使土壤微生物代谢功能增强,土壤微生物繁殖加快、数量增大,从而促进土壤微生物对土壤C源的利用强度.     

Genotypic and phenotypic diversity of phlD-containing Pseudomonas strains isolated from the rhizosphere of wheat

Production of 2,4-diacetylphloroglucinol (2,4-DAPG) in the rhizosphere by strains of fluorescent Pseudomonas spp. results in the suppression of root diseases caused by certain fungal plant pathogens. In this study, fluorescent Pseudomonas strains containing phlD, which is directly involved in the biosynthesis of 2,4-DAPG, were isolated from the rhizosphere of wheat grown in soils from wheat-growing regions of the United States and The Netherlands. To assess the genotypic and phenotypic diversity present in this collection, 138 isolates were compared to 4 previously described 2, 4-DAPG producers. Thirteen distinct genotypes, one of which represented over 30% of the isolates, were differentiated by whole-cell BOX-PCR. Representatives of this group were isolated from eight different soils taken from four different geographic locations. ERIC-PCR gave similar results overall, differentiating 15 distinct genotypes among all of the isolates. In most cases, a single genotype predominated among isolates obtained from each soil. Thirty isolates, representing all of the distinct genotypes and geographic locations, were further characterized. Restriction analysis of amplified 16S rRNA gene sequences revealed only three distinct phylogenetic groups, one of which accounted for 87% of the isolates. Phenotypic analyses based on carbon source utilization profiles revealed that all of the strains utilized 49 substrates and were unable to grow on 12 others. Individually, strains could utilize about two-thirds of the 95 substrates present in Biolog SF-N plates. Multivariate analyses of utilization profiles revealed phenotypic groupings consistent with those defined by the genotypic analyses.     

Large genotypic variation but small variation in N2 fixation among rhizobia nodulating red clover in soils of northern Scandinavia

AIMS: To analyse the symbiotic variations within indigenous populations of rhizobia nodulating red clover (Trifolium pratense L.) in soils of northern Norway and Sweden at different times of the growing season. METHODS AND RESULTS: A total of 431 nodule isolates sampled under field conditions in summer and autumn, were characterized genetically by targeting both chromosomal and symbiotic genes. The Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction (PCR) fingerprinting of chromosomal DNA revealed considerable variation within the isolated populations that was more influenced by geographical origin than sampling time. Analysis of PCR amplified nodEF gene on the symbiotic plasmid by restriction fragment length polymorphism revealed a high proportion of nod types common to the two studied sites. The symbiotic efficiency of the isolates, representing both dominating and rare nodEF genotypes, showed high N(2) fixation rates in symbiosis with the host plant in a greenhouse experiment using the (15)N isotope dilution method. CONCLUSIONS: Effective N(2)-fixing strains of Rhizobium leguminosarum bv. trifolii nodulating red clover are common and genetically diverse in these northern Scandinavia soils. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides information on the variability, stability and dynamics of resident populations of rhizobia nodulating red clover in Scandinavian soils which has practical implications for applying biological nitrogen fixation in subarctic plant production.     

Environmental influences on bacterial diversity of soils on Signy Island,maritime Antarctic

Soil bacterial diversity at environmentally distinct locations on Signy Island, South Orkney Islands was examined using the denaturing gradient gel profiling approach. A range of chemical variables in soils at each site was determined in order to describe variation between locations. No apparent differences in Shannon Diversity Index (H′) were observed. However, as revealed in an analysis of similarity (ANOSIM), the dominant bacterial communities of all eight studied locations were significantly different. Within this, higher levels of similarity were observed between penguin rookeries, seal wallows and vegetated soils, all of which share varying levels of impact from vertebrate activity, in contrast with more barren soil. In addition, the lowest H′ value was detected from the latter soil which also has the most extreme environmental conditions, and its bacterial community has the greatest genetic distance from the other locations. DGGE analyses indicated that the majority of the excised and sequenced bands were attributable to the Bacteroidetes. Across a range of ten environmental variables, multivariate correlation analysis suggested that a combination of pH, conductivity, copper and lead content potentially contributed explanatory value to the measured soil bacterial diversity.     

The structure and interrelationship of fungal populations in native and cultivated soils

Mitochondrial DNA haplotypes have been characterized for 120 isolates of the asexual fungus Fusarium oxysporum. Sixty of these isolates were obtained from soil in a native grassland in the San Joaquin Valley of California, including 20 isolates from each of six different sampling locations. The same sampling strategy was used to obtain 60 additional isolates from an agricultural field of the same soil type directly adjacent to the native soil. Twenty-three different mitochondrial DNA haplotypes were identified among the 120 isolates, including 11 haplotypes represented by two or more isolates and 12 that were unique. The five most common mitochondrial DNA haplotypes accounted for 93 (78%) of the 120 isolates. Isolates representing each of these five mitochondrial DNA haplotypes were found both in the cultivated and in the native soil. Seventy-two per cent of the isolates found in the cultivated soil were associated with the same mitochondrial DNA haplotype as one or more isolates in the native soil. The remaining isolates in the cultivated soil were associated with comparatively rare mitochondrial DNA haplotypes, most of which showed a close relationship to one of the haplotypes found in the native soil. Hierarchial gene diversity analysis indicated that a significant proportion of the mitochondrial DNA haplotype diversity was attributable to differences between sampling sites in the native soil but not in the cultivated soil. This may reflect significant spatial structuring of genetic diversity in populations of F. oxysporum in a native soil. The proportion of mtDNA haplotype diversity attributable to differences between populations in the native and cultivated soils was not significant. This suggests that our entire collection, encompassing strains from both native and cultivated soils, is representative of a single population of F. oxysporum.