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.     

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 [¹⁴C]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.     

Chemistry and Microbial Functional Diversity Differences in Biofuel Crop and Grassland Soils in Multiple Geographies

We obtained soil samples from geographically diverse switchgrass (Panicum virgatum L.) and sorghum (Sorghum bicolor L.) crop sites and from nearby reference grasslands and compared their edaphic properties, microbial gene diversity and abundance, and active microbial biomass content. We hypothesized that soils under switchgrass, a perennial, would be more similar to reference grassland soils than sorghum, an annual crop. Sorghum crop soils had significantly higher NO₃ ^? -N, NH₄ ⁺ -N, SO₄ ^2? -S, and Cu levels than grassland soils. In contrast, few significant differences in soil chemistry were observed between switchgrass crop and grassland soils. Active bacterial biomass was significantly lower in sorghum soils than switchgrass soils. Using GeoChip 4.0 functional gene arrays, we observed that microbial gene diversity was significantly lower in sorghum soils than grassland soils. Gene diversity at sorghum locations was negatively correlated with NO₃ ^? -N, NH₄ ⁺ -N, and SO₄ ^2? -S in C and N cycling microbial gene categories. Microbial gene diversity at switchgrass sites varied among geographic locations, but crop and grassland sites tended to be similar. Microbial gene abundance did not differ between sorghum crop and grassland soils, but was generally lower in switchgrass crop soils compared to grassland soils. Our results suggest that switchgrass has fewer adverse impacts on microbial soil ecosystem services than cultivation of an annual biofuel crop such as sorghum. Multi-year, multi-disciplinary regional studies comparing these and additional annual and perennial biofuel crop and grassland soils are recommended to help define sustainable crop production and soil ecosystem service practices.     

Community Composition and Functioning of Denitrifying Bacteria from Adjacent Meadow and Forest Soils

We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in α-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.     

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.     

Yeast Communities of the Moscow City Soils

Yeast abundance and diversity were studied in the soils (topsoil) of Moscow city: urban soils under lawn vegetation and close to the areas of household waste disposal, as well as in zonal soddy-podzolic soils (retisols) in parks (Losiny Ostrov and Izmailovo). The numbers of soil yeasts were similar in all studied urban biocenoses (on average ~3.5 × 10³ CFU/g). From all studied soils, 54 yeast species were isolated. The highest yeast diversity was found in the soils adjacent to the areas of household waste storage. Soils from different urban sites were found to have different ratios of ascomycetous and basidiomycetous yeasts: basidiomycetes predominated in urban soils under lawn vegetation, while in the areas close to the waste disposal sites their share was considerably lower. The differences between the studied urban soils were also found in the structure of soil yeast complexes. In urban soils with high anthropogenic impact, the isolation frequency of clinically important yeast species (Candida parapsilosis, C. tropicalis, Diutina catenulata, and Pichia kudriavzevii) was as high as 35% of all studied samples, while its share in the community was 17%. The factors responsible for development of specific features of yeast communities in various urban soils are discussed in the paper.     

Degraded soil increases the performance of a dominant grass, <Emphasis Type="Italic">Andropogon gerardii</Emphasis> (Big bluestem)

Dominant grasses can suppress subordinate species in grassland restorations. Examining factors that influence performance of a dominant grass when interacting with subordinate forbs may provide insights for maintaining plant community diversity. The objective of our study was to determine how soils of different restoration ages and functionally different forbs influence the performance (using biomass and tillering rate as proxies) of a dominant grass: Andropogon gerardii. Sites included a cultivated field and two restored prairies (4 or 16 years after restoration) at Konza Prairie (NE Kansas). We hypothesized A. gerardii performance would be greater in more degraded soils and when interacting with legumes. Soil structure, nutrient status, and microbial biomass were measured in soil that was used to conduct the plant interaction study. Andropogon gerardii performance was measured during an 18-week greenhouse experiment using the relative yield index calculated from net absolute tillering rate and final biomass measurements in three soil restoration age treatments combined with four interacting forb treatments. Restoration improved soil structure, reduced plant-available nutrients, and increased microbial biomass. Relative yield index values of A. gerardii were greater with non-legumes than legumes. Andropogon gerardii performed best in degraded soils, which may explain the difficulty in restoring tallgrass prairie diversity in long-term cultivated soil. Results from this study suggest practices that promote soil aggregation and fungal biomass, coupled with including a high abundance of legumes in seed mixes could reduce dominance of A. gerardii and likely increase plant diversity in tallgrass prairie restorations.     

Genetic diversity of Metarhizium anisopliae var. anisopliae in southwestern British Columbia

The abundance and genetic diversity of the entomopathogenic fungus, Metarhizium anisopliae var. anisopliae, in southwestern British Columbia (BC) and southern Alberta was examined. The fungus was found to be widespread in soil throughout southwestern BC, and was recovered from 56% of 85 sample sites. In contrast to southwestern BC, no M. anisopliae isolates were recovered in southern Alberta. An automated fluorescent amplified fragment length polymorphism (AFLP) method was used to examine genetic diversity. In excess of 200 isolates were characterized. The method identified 211 polymorphic amplicons, ranging in size from ≈92 to 400 base pairs, and it was found to be reproducible with a resolution limit of 86.2% similarity. The AFLP method distinguished Metarhizium from other entomopathogenic fungal genera, and demonstrated considerable genetic diversity (25 genotypes) among the reference strains of M. anisopliae isolates examined (i.e. recovered from various substrates and geographical locations). Although 13 genotypes of M. anisopliae var. anisopliae were recovered from southwestern BC soils, the vast majority of isolates (91%) belonged to one of two closely-related genotypes. Furthermore, these two genotypes predominated in urban, agricultural and forest soils. The reasons for the limited diversity of M. anisopliae var. anisopliae in southwestern BC are uncertain. However, findings of this study are consistent with island biogeography theory, and have significant implications for the development of this fungus for microbial control of pest insects.     

Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons

Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 10⁴ CFU g of soil⁻¹. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.     

Nitrous Oxide Reductase (nosZ) Gene Fragments Differ between Native and Cultivated Michigan Soils

The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are α-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in γ-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (D_mean = 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (D_mean = 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community.     

Allozyme and RAPD polymorphism in Tylophora indica (Burm.f.) Merr.

Tylophora indica (Burm.f.) Merr (syn. T. asthmatica), is being indiscriminately collected for medicinal use which is not sustainable. Conservation of the species requires information on existing genetic content and its distribution in different populations. In the present study, polymorphism in allozyme and RAPD profiles of five populations were analysed using six enzyme systems and ten random primers. Genetic content in terms of allozymes and RAPDs as revealed by Shannon-Weiner index was more or less same in all the populations. Evenness as calculated from observed diversity (Shannon-Weiner index, H’) and the maximum expected diversity (H^max) for the allozymes and RAPDs was high for individual populations indicating that the distribution of genetic content was fairly uniform. From the results, it was concluded that collection of few genotypes from geographically distinct locations rather than intensive collection within one or two locations would be representative of the genetic variability present in this species.     

Diversity of amoA and pmoA Genes in Extremely Saline Alkaline Soils of the Former Lake Texcoco

Abstract

Ammonia-oxidizing bacteria (AOB) and aerobic methane oxidizing-bacteria (MOB) were studied in three extreme soils of the former Lake Texcoco, Mexico, with pH ranging from 8.5 to 10.5 and electrolytic conductivity (EC) from 0.67 to 84.76 dS m^?1, and in two arable soils. Soil DNA was extracted with three different methods and total DNA was used as a template to amplify the pmoA and amoA functional genes and subsequently sequenced by pyrosequencing. The amoA gene sequences clustered as uncultured AOB dominated in the Texcoco soils, while Nitrosospira was dominant in the arable soils. Sequences of MOB associated with Nitrosococcus-rel (Type I) dominated (>85%) in the Texcoco soils, but they were more diverse in the arable soils, for example, JR2, JR3, Methylocaldum USC-g (Type I), USC-a (Type II) and gp23 (pxmA). Aerobic methane oxidizing-bacteria and AOB microbial diversity were significantly related to EC and pH (p?<?0.05). As such, the lower MOB and AOB microbial diversity in the Texcoco soil compared to the arable soil was determined by its higher EC and pH.     

Consequences of Melaleuca quinquenervia Invasion on Soil Nematodes in the Florida Everglades

The tree Melaleuca quinquenervia invades all types of habitats of South Florida leading to up to 80% loss of aboveground diversity. To examine impacts on the belowground ecosystem, we investigated the composition and diversity of nematodes from soils dominated by the invasive tree and compared them with soils supporting native plant communities at six locations across the Florida Everglades over three years. Despite the significant differences in soil type, hydrology, and native plant composition of the sites, there were consistent differences in nematode communities between soil environments under the native and invaded plant communities. The total abundance and diversity of nematodes in soils dominated by M. quinquenervia was 60% and 80% of adjacent soils under native plants. Fungal-feeding and plant-parasitic nematodes were twice as abundant under native plants as under M. quinquenervia. Nematode communities under M. quinquenervia were bacterivore-dominated, while under native vegetation plant-parasite dominated. The overall diversity of nematodes was 20% lower under the exotic than under native plants, with plant parasites being 36% and fungivores being 30% less diverse. Soil moisture, % of Ca, Mg, and clay particles and total soil C and N were greater in M. quinquenervia soils, but plant-available concentrations of P, K, Ca, and Mg as well as CEC were reduced. Overall, data suggests that the invasion process may modify soil biotic and abiotic conditions that in turn promote the advancement of the exotic M. quinquenervia and displacement of the native plants.     

Abundance and Diversity of Viruses in Six Delaware Soils

The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 × 10⁹ to 4.17 × 10⁹ g⁻¹ dry weight) than in agricultural soils (8.7 × 10⁸ to 1.1 × 10⁹ g⁻¹ dry weight). Soil VLP abundance was significantly correlated to moisture content (r = 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r = 0.885) and viral (r = 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.     

Temporal analyses of the distribution and diversity of Salmonella in natural biofilms

The diversity and distribution of salmonellae in freshwater biofilms were analyzed at a fine scale (i.e. in 20 locations from a 324 cm² area) for two sites in San Marcos, TX. A concrete storm water overflow channel (City Park) was sampled 4 times and a concrete surface in the spring-fed headwaters of the San Marcos River (Spring Lake) 5 times between April and September 2009, and each biofilm sample analyzed by a combination of traditional enrichment methods and molecular techniques. PCR detection of the invA gene, that encodes a protein of a type III secretion system present in salmonellae, after semi-selective enrichment of salmonellae was achieved in biofilms from all 20 locations at the City Park site, with locations generally being positive 2-3 times out of 4 sampling times for a total of 59% positive samples. InvA gene fragment detection in biofilms was less frequent for the 5 sampling times and 20 locations from the Spring Lake site (18% of all samples), with 1 sampling time being entirely negative and 8 locations remaining negative throughout the study. Rep-PCR fingerprinting of 491 Salmonella isolates obtained from both sites resulted in 30 distinct profiles, with 26 and 7 profiles retrieved from City Park and Spring Lake samples, respectively, and thus with 3 profiles present at both sites, and multiple strains frequently obtained from single locations at both sites. The composition of Salmonella strains in the area analyzed changed in time with large differences between early (April, June) and late sampling times (September) within and among sites, except for one strain (S12) that was present at almost all sampling times at both sites, though often at different locations within the area analyzed. These results demonstrate the presence of salmonellae in natural biofilms and a significant micro-heterogeneity with differences in diversity and persistence of salmonellae.     

Influence of Inorganic Nitrogen Management Regime on the Diversity of Nitrite-Oxidizing Bacteria in Agricultural Grassland Soils

To assess links between the diversity of nitrite-oxidizing bacteria (NOB) in agricultural grassland soils and inorganic N fertilizer management, NOB communities in fertilized and unfertilized soils were characterized by analysis of clone libraries and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Previously uncharacterized Nitrospira-like sequences were isolated from both long-term-fertilized and unfertilized soils, but DGGE migration patterns indicated the presence of additional sequence types in the fertilized soils. Detailed phylogenetic analysis of Nitrospira-like sequences suggests the existence of one newly described evolutionary group and of subclusters within previously described sublineages, potentially representing different ecotypes; the new group may represent a lineage of noncharacterized Nitrospira species. Clone libraries of Nitrobacter-like sequences generated from soils under different long-term N management regimes were dominated by sequences with high similarity to the rhizoplane isolate Nitrobacter sp. strain PJN1. However, the diversity of Nitrobacter communities did not differ significantly between the two soil types. This is the first cultivation-independent study of nitrite-oxidizing bacteria in soil demonstrating that nitrogen management practices influence the diversity of this bacterial functional group.     

Characterization of Astragalus sinicus Rhizobia by Restriction Fragment Length Polymorphism Analysis of Chromosomal and Nodulation Genes Regions

Two hundred and four isolates of rhizobia were sampled from root nodules of Astragalus sinicus grown in rice fields of six southern provinces of China. Genotypic diversity was determined by Southern hybridization using nodDBC genes as a probe, restriction fragment length polymorphism (RFLP) analysis of PCR-amplified 16S-23S rDNA intergenic spacers (IGS), and plasmid profile. Our results show that rhizobia associated with A. sinicus were very diverse, and 10 genotypes were resolved within the previously identified dominant 16S rDNA type. Diversity levels varied greatly between different geographical locations. The same nod gene genotypes were harbored by distinct chromosomal types, suggesting that lateral plasmid transfer occurred during the evolution process. Received: 14 June 1999 / Accepted: 20 July 1999     

Identification and Specific Detection of a Novel Pseudomonadaceae Cluster Associated with Soils from Winter Wheat Plots of a Long-Term Agricultural Field Experiment

The genus Pseudomonas (sensu stricto) represents a group of microorganisms directly involved in functions conferring plant health. We performed a study in the DOK long-term agricultural field experiment on the basis of previously published Pseudomonas-selective PCR primers in order to investigate the community structure of the microbial groups defined by the target range of these primers. Three different agricultural management systems, i.e., conventional, biodynamic, and bio-organic, along with mineral and unfertilized controls were investigated, with each system planted with either winter wheat or a grass-clover ley. Amplified small-subunit rRNA gene fragments were analyzed using the genetic profiling techniques restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE), revealing distinct differences between soils planted with winter wheat and grass clover but only minor differences between the management systems. Phylogenetic analyses of 59 clone sequences retrieved from bio-organic and unfertilized systems identified sequences related to Pseudomonas fluorescens and a novel cluster termed Cellvibrio-related Pseudomonadaceae (CRP). The CRP clones were exclusively isolated from winter wheat soil samples and were responsible for the crop-specific differences observed in RFLP and DGGE profiles. New primers were designed for the amplification of CRP targets directly from soil DNA, yielding strong signals exclusively for winter wheat soils. We concluded that crop-associated CRP exist in agricultural soils and that genetic profiling followed by specific probe design represents a valuable approach for identification as well as sensitive and rapid monitoring of novel microbial groups in the environment.     

Terminal Restriction Fragment Length Polymorphism Analysis of Soil Bacterial Communities under Different Vegetation Types in Subtropical Area

Soil microbes are active players in energy flow and material exchange of the forest ecosystems, but the research on the relationship between the microbial diversity and the vegetation types is less conducted, especially in the subtropical area of China. In this present study, the rhizosphere soils of evergreen broad-leaf forest (EBF), coniferous forest (CF), subalpine dwarf forest (SDF) and alpine meadow (AM) were chosen as test sites. Terminal-restriction fragment length polymorphisms (T-RFLP) analysis was used to detect the composition and diversity of soil bacterial communities under different vegetation types in the National Natural Reserve of Wuyi Mountains. Our results revealed distinct differences in soil microbial composition under different vegetation types. Total 73 microbes were identified in soil samples of the four vegetation types, and 56, 49, 46 and 36 clones were obtained from the soils of EBF, CF, SDF and AM, respectively, and subsequently sequenced. The Actinobacteria, Fusobacterium, Bacteroidetes and Proteobacteria were the most predominant in all soil samples. The order of Shannon-Wiener index (H) of all soil samples was in the order of EBF>CF>SDF>AM, whereas bacterial species richness as estimated by four restriction enzymes indicated no significant difference. Principal component analysis (PCA) revealed that the soil bacterial communities’ structures of EBF, CF, SDF and AM were clearly separated along the first and second principal components, which explained 62.17% and 31.58% of the total variance, respectively. The soil physical-chemical properties such as total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP) and total potassium (TK) were positively correlated with the diversity of bacterial communities.     

Spatial and Resource Factors Influencing High Microbial Diversity in Soil

To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson’s index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.