Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils

The extent of microbial community diversity in two similar sandy surface soils from Virginia and Delaware (USA) was analysed with a culture-independent small subunit ribosomal RNA (SSU rRNA) gene-based cloning approach with about 400-700 SSU rDNA clones obtained from each sample. While there were no operational taxonomic units (OTUs) having more than three individuals, about 96-99% of the OTUs had only a single individual. The clones showing less than 85% similarity to the sequences in the current databases were fully sequenced. The majority of the clones (55%) had sequences that were more than 20% different from those in the current databases. About 37% of the clones differed by 15-20% in sequence from the database, 16% of the clones differed by 10-15%, and 5% of the clones differed by only 1-10%. Phylogenetic analysis indicated that these sequences fell into 10 of the 35-40 known phylogenetic divisions. Many of the clones were affiliated with Acidobacterium (35%). While a substantial portion of the clones belong to alpha (24%) and beta (12%) Proteobacteria, a few of them were affiliated with delta (6%) and gamma (3%) Proteobacteria. About 6% of the clones belong to Planctomycetes, and 4% of the clones were related to gram-positive bacteria. About 4% of clones were related to other bacterial divisions, including Cytophaga, Green sulfur bacteria, Nitrospira, OP10, and Verrucomicrobia. Eight sequences had no specific association with any of the known divisions or candidate divisions and were phylogenetically divided into three novel division level groups, named AD1, AD2 and AD3. Candidate division AD1 represented by six clones (4%) was found in both sites and consisted of two subdivisions. The community structures were similar between these two widely separated, sandy, oligotrophic, surface soils under grass vegetation in a temperate, humid climate but somewhat dissimilar to community structures revealed in similar studies in other types of soil habitats.     

Microbial performance under increasing nitrogen availability in a Mediterranean forest soil

In forest ecosystems, the external nitrogen (N) inputs mainly involve wet and dry depositions that potentially alter inorganic N availability in the soil and carbon (C) turnover. This study assesses the effect of a slow increase of inorganic N availability on microbial community activity and functionality in a Mediterranean forest soil. A four-month incubation experiment was performed with soil collected from the organic layer of a forest site and fertilized with a solution of ammonium nitrate. The fertilizer was supplied at an equivalent of 0, 10, 25, 50 and 75 kg N ha⁻¹ (0, 0.3, 0.7, 1.3 and 2 mg N g⁻¹ for control N0 and treatments N1, N2, N3 and N4, respectively). The incubation was carried out under optimal conditions, with the addition of the nutritive solution in small aliquots once a week to mimic the phenomenon of N deposition. In order to isolate the effect of N, the pH of the NH₄NO₃ solutions was adjusted to soil pH, and phosphorus was added in order to prevent any nutrient limitation effect. Inorganic N, C-mineralization, the activity of one oxidative enzyme (o-diphenol oxidase) and 8 hydrolitic enzymes (α-glucosidase, β-glucosidase, N-acetyl-β-d-glucosaminidase, cellulase, leucine amino-peptidase, acid phosphatase, butyric esterase and β-xylosidase) and the community level physiological profile (CLPP) were measured and analyzed during the whole incubation and at the end of the experiment as a proxy for microbial decomposition activity. In the first month, the highest N availability (N4) repressed the microbial respiration activity but stimulated microbial enzymatic activity, suggesting a change of C-pathways from spilling to enzymes and biomass investment. The treatments N1, N2 and N3 had no effect in the same period. Throughout the incubation, a general stress condition affected all the treated soils. As a consequence, treated soils exhibited higher respiration rates than the control. This was accompanied by a loss of functional diversity and an end-detected decline in biomass C. Although at the end of incubation most of the soil features showed a clear correlation with the inorganic N pool, the organic C content was strongly affected by different patterns of microbial activity during the experiment: the highest N treatment (N4) showed a lower C loss than the N3 treatment. Overall, the experiment showed how inorganic N availability can potentially alter the C cycle in a Mediterranean forest soil. The effect is non linear, depending on microbial community dynamics, on the community’s ability to adapt given the time scale of the process, and on N supply amount. Our study also revealed a common pattern in the short-term response to N addition in other, similar ecosystems with different climatic conditions.     

Podzol formation in sandy soils of Finland

Podzolization occurs quickly in acidic parent materials with addition of acidic litter from coniferous trees. This study was conducted to evaluate Podzol formation and estimate lengths of time required to meet morphological and chemical criteria of podzolic B horizon and spodic horizon in Finland. Soil color, organic C, ODOE, and extractable Al and Fe were measured in a seven-pedon chronosequence (230–1800 years) and four older pedons (8300–11,300 years). The bulk mineralogical composition of the BC and C horizons was uniform with quartz, plagioclase and K-feldspar as main components and amphibole, illite and chlorite as minor components. The fine (<5 μm) fraction of selected samples was primarily amorphous allophone-like material with some mixed-layered illite–vermiculite. All pedons in the study met the criteria for albic horizons according to the FAO–Unesco, World Reference Base (WRB) and Soil Taxonomy systems. According to the FAO–Unesco system, all pedons had spodic B horizons and were classified as Podzols. According to the WRB system, none of pedons of the chronosequence had spodic horizons, whereas the older pedons met the criteria for a spodic horizon. About 4780 years were required to form a spodic horizon according to the WRB system. The oldest pedon of the chronosequence and the older pedons had spodic horizons according to Soil Taxonomy, but the younger pedons failed to meet the spodic horizon criteria. About 1520 years were required to form a spodic horizon that met the color and organic C criteria of Soil Taxonomy, whereas it took about 4780 years to meet the required accumulation of Fe and Al. This study points out the discrepancy between the color criteria and the criteria reflecting the accumulation of Al, Fe and organic matter in the B horizon.     

Substrate utilization patterns of desert soil microbial communities in response to xeric and mesic conditions

The Negev Desert is characterized by low soil moisture and organic matter content and an unpredictable rainfall amount, dispersion, and intensity. Water and nutrient availability are, therefore, the major limiting factors of biological activity in arid and semi-arid ecosystems. Plants have developed different ecophysiological adaptations in order to cope with the harsh conditions in this xeric environment, e.g., excretion of salt (Reaumuria negevensis) and chemical compounds (Artemisia sieberi) through the leaves. Microorganisms constitute a major part of these ecosystems' total biomass, and are diverse members of the soil food web, being primarily responsible for breaking down complex organic compounds, which are then recycled. They are also known to be very sensitive to abiotic changes and can time their activity to the environmental conditions.Soil samples were collected monthly from a 0 to 10 cm depth, under the canopies of A. sieberi, Noaea mucronata, and R. negevensis. Samples collected from inter-shrub spaces served as control. CO₂ evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community, were determined by MicroResp™ analysis. A significant difference was found between the two dry periods in most of the examined parameters. The values of water, organic matter content, and total soluble nitrogen were higher in soil samples collected in the vicinity of R. negevensis than in samples collected in the vicinity of N. mucronata, A. sieberi, and the open area. A similar trend was found in CO₂ evolution, microbial biomass, and H' values, in which soil samples collected beneath the canopies of N. mucronata and R. negevensis and from open area had higher values during the wet periods (which were characterized by a mesic environment) and in samples collected beneath the A. sieberi in the wet 2006 and dry 2007 periods.     

Effect of intercropping on crop yield and chemical and microbiological properties in rhizosphere of wheat (Triticum aestivum L.), maize (Zea mays L.), and faba bean (Vicia faba L.)

In this study, we investigated crop yield and various chemical and microbiological properties in rhizosphere of wheat, maize, and faba bean grown in the field solely and intercropped (wheat/faba bean, wheat/maize, and maize/faba bean) in the second and third year after establishment of the cropping systems. In both years, intercropping increased crop yield, changed N and P availability, and affected the microbiological properties in rhizosphere of the three species compared to sole cropping. Generally, intercropping increased microbial biomass C, N, and P availability, whereas it reduced microbial biomass N in rhizosphere of wheat. The rhizosphere bacterial community composition was studied by denaturing gradient gel electrophoresis of 16S rRNA. In the third year of different cropping systems, intercropping significantly changed bacterial community composition in rhizosphere compared with sole cropping, and the effects were most pronounced in the wheat/faba bean intercropping system. The effects were less pronounced in the second year. The results show that intercropping has significant effects on microbiological and chemical properties in the rhizosphere, which may contribute to the yield enhancement by intercropping.     

The effects of earthworm functional group diversity on nitrogen dynamics in soils

A novel experimental design, based on the simplex model, was used to study the effects of earthworm functional group diversity on nitrogen dynamics in soils. This mesocosm experiment was carried out at two densities of earthworm and at two levels of food supply. Leachate was collected and analysed over a 20-week period. Soil nitrogen content was measured when the soil columns were destructively sampled on week 30.Results showed the presence of variation among the functional groups in their effects on N dynamics and that both population densities and levels of resource availability were significant. Ammonium concentrations in leachate were generally higher with anéciques and endogées; the opposite was true for nitrate-N, which under certain circumstances was higher with epigées. A significant synergy between the endogées and anéciques was shown in terms of nitrate in soil. Earthworm biomass was important in some instances. For example, larger amounts of soil nitrate were present at higher densities of endogées. A varying effect of food supply was seen for the three functional groups. For example, there were reduced concentrations of nitrate-N in the leachate from the anecic monocultures at low levels of food supply, while increased amounts were leached from the epigées at low food supply. Greater concentrations of ammonium-N were leached from anéciques monocultures at low levels of food supply. Increased food supply resulted in increased amounts of soil nitrate-N in monocultures of both epigées and endogées. It was apparent that nitrogen transformations and amounts available in soil water are dependant on the composition of the earthworm community.     

Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments

The prevalence of antibiotic production loci in soil is a key issue of current research aimed to unravel the mechanisms underlying the suppressiveness of soil to plant pathogens. Pyrrolnitrin (PRN) is a key antibiotic involved in the suppression of a range of phytopathogenic fungi. Therefore, field soils from different agricultural regimes, including permanent grassland, arable land under common agricultural rotation and arable land under maize monoculture, were investigated in respect of the prevalence of pyrrolnitrin biosynthetic loci. Primers for detection of the prnD gene were used for initial PCR/hybridisation-based assessments. By this method, evidence was obtained for the contention that PRN production loci were most prevalent in grasslands, however, robust quantitative data were not achieved.To quantify the prevalence of PRN biosynthetic loci, we designed a TaqMan PCR system based on the prnD gene for the real-time quantitative detection of this production locus in soil. The system was found to be specific for prnD sequences from Pseudomonas, Serratia and Burkholderia species. Using pure culture DNA, the prnD gene was detectable down to a level of 60 fg, or approximately 10 gene copies, per amplification reaction. Application of the system to soil DNA spiked with different levels of the target DNA indicated that, in a soil DNA background, specific amplification could be obtained to about the same level of sensitivity.Field soil samples obtained from the different agricultural regimes were then screened for the prevalence of prnD with the real-time PCR system. The quantitative data obtained suggested a strongly enhanced presence of prnD genes in grassland or grassland-derived plots, as compared to the prevalence of this biosynthetic locus in the arable land plots. The implications of these findings are placed in the context of the suppressiveness of soil to phytopathogens, notably Rhizoctonia solani AG3.     

Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Denitrification is an important part of the nitrogen cycle in the environment, and diverse bacteria, archaea, and fungi are known to have denitrifying ability. Rice paddy field soils have been known to have strong denitrifying activity, but the microbes responsible for denitrification in rice paddy field soils are not well known. Present study analyzed the diversity and quantity of the nitrite reductase genes (nirS and nirK) in a rice paddy field soil, sampled four times in one rice-growing season. Clone library analyses suggested that the denitrifier community composition varied over sampling time. Although many clones were distantly related to the known NirS or NirK, some clones were related to the NirS from Burkholderiales and Rhodocyclales bacteria, and some were related to the NirK from Rhizobiales bacteria. These denitrifiers may play an important role in denitrification in the rice paddy field soil. The quantitative PCR results showed that nirK was more abundant than nirS in all soil samples, but the nirK/nirS ratio decreased after water logging. These results suggest that both diversity and quantity changed over time in the rice paddy field soil, in response to the soil condition.     

Diet-related composition of the gut microbiota of Lumbricus rubellus as revealed by a molecular fingerprinting technique and cloning

Interactions between earthworms and microorganisms are essential for the functioning of soil ecosystems as they affect organic matter degradation and nutrient cycling. This is also true for the alpine region, where socio-economic changes lead to the increasing abandonment of pastures, which in turn, causes a considerable shift in the diet of saprotrophic invertebrates and thus impacts food web and decomposition processes. To enhance our understanding of how this diet shift influences earthworms and associated microorganisms, we studied the gut content and cast microbiota of Lumbricus rubellus (Lumbricidae, Oligochaeta), a key macrodecomposer on alpine pastureland in the Central Alps. A feeding experiment with L. rubellus and three different food sources that represent the vegetation shift from an alpine pasture to an abandoned site was set up. Earthworms were collected in the field, transferred to a climate chamber and fed with cow manure, dwarf shrub or grass litter for six weeks. PCR-DGGE (Polymerase chain reaction-denaturing gradient gel electrophoresis) analysis of the DNA extracted from the substrates, the earthworms' gut contents and casts revealed that the gut and cast microbiota was strongly influenced by the food source ingested. Cloning of bacterial 16S rRNA gene fragments demonstrated that the intestinal content was dominated by Proteobacteria, especially from the Gamma-subclass, followed by members of the phyla Bacteroidetes, Actinobacteria and Firmicutes. In contrast, Actinobacteria were detected abundantly in all samples types when a cultivation approach was used. In conclusion, the gut microbiota of L. rubellus was shown to be substantially affected by the food source ingested, suggesting that this essential macrodecomposer is exposed to the diet shift resulting from a land-use change in the alpine area.     

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite’s impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C₃ perennial grasses, C₄ midgrasses, C₄ shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.     

Molecular diversity of bacterial chitinases in arable soils and the effects of environmental factors on the chitinolytic bacterial community

The molecular diversity of bacterial chitinases in the bulk soils of arable land was investigated using culture-independent methods. The results demonstrate that bacterial chitinases in arable soils are highly diverse and comprise unique groups when their sequences were compared to those in public databases. The diversity of bacterial chitinases in arable soil was further evaluated using conventional phylogenetic analysis, the UniFrac analysis of the phylogenetic data, and the multidimensional scaling (MDS) analysis of T-RFLP profiles to elucidate the relationship between the diversity of bacterial chitinases and soil characteristics. These analyses indicate that environmental factors such as soil type and pH are responsible for shaping the composition of bacterial chitinases.     

Long-term erosion of tree reproductive trait diversity in edge-dominated Atlantic forest fragments

Habitat loss and fragmentation promote relatively predicable shifts in the functional signature of tropical forest tree assemblages, but the full extent of cascading effects to biodiversity persistence remains poorly understood. Here we test the hypotheses that habitat fragmentation (a) alters the relative contribution of tree species exhibiting different reproductive traits; (b) reduces the diversity of pollination systems; and (c) facilitates the functional convergence of reproductive traits between edge-affected and early-secondary forest habitats (5-32 years old). This study was carried out in a severely fragmented 670-km² forest landscape of the Atlantic forest of northeastern Brazil. We assigned 35 categories of reproductive traits to 3552 trees (DBH ? 10 cm) belonging to 179 species, which described their pollination system, floral biology, and sexual system. Trait abundance was calculated for 55 plots of 0.1 ha across four habitats: forest edges, small forest fragments (3.4-83.6 ha), second-growth patches, and core tracts of forest interior within the largest available primary forest fragment (3500 ha) in the region. Edge-affected and secondary habitats showed a species-poor assemblage of trees exhibiting particular pollination systems, a reduced diversity of pollination systems, a higher abundance of reproductive traits associated with pollination by generalist diurnal vectors, and an elevated abundance of hermaphroditic trees. As expected, the reproductive signature of tree assemblages in forest edges and small fragments (edge-affected habitats), which was very similar to that of early second-growth patches, was greatly affected by both habitat type and plot distance to the nearest forest edge. In hyper-fragmented Atlantic forest landscapes, we predict that narrow forest corridors and small fragments will become increasingly dominated by edge-affected habitats that can no longer retain the full complement of tree life-history diversity and its attendant mutualists.     

Soil niche effect on species diversity and catabolic activities in an ectomycorrhizal fungal community

The species of an ectomycorrhizal (ECM) community were investigated in a temperate oak forest by morphotyping and ITS rDNA sequencing. Thirty-six ECM morphotypes were found at the site. The niche effect (as organic soil, mineral soil or dead woody debris artificially introduced in the soil) on the ECM community structure and on the potential catabolic activities of the most abundant morphotypes was studied. The morphotypes in each niche were subjected to enzymatic tests developed for hydrolytic and oxidative enzymes involved in the decomposition of organic compounds. The ECM community structure varied widely depending on the soil horizon or habitat patch. The species richness was higher in the A1 horizon than in the other niches. Different ECM species had different activity patterns for the eight enzymatic tests while co-occurring in the same niche. Catabolic activities also changed within species between niches. Dead woody debris were extensively colonized by two saprotrophic fungi (Megacollybia platyphylla and Armillaria sp.) and, in this particular niche, ECM morphotypes predominantly belonged to the genera Lactarius and Tomentella. These morphotypes showed high chitinase activities. This study suggested also that some ECM fungi could obtain nutrients via the chitin degradation of dead or live saprobes.     

Genetic diversity within Aspergillus flavus strains isolated from peanut-cropped soils in Argentina

The genetic diversity of Aspergillus flavus populations isolated from the peanut-cropped soils in the peanut-growing region at Cordoba Province was evaluated by analysis of vegetative compatibility group (VCG). VCG_s were determined through complementation assays between nitrate-nonutilizing (NNO) mutants. Fifty-six VCG_s were identified from 100 isolates. Twenty-five VCG_s contained two or more isolates and 31 VCG_s contained only a single isolate. In general, there were significant differences among VCG_s in aflatoxin and CPA production. One VCG group included a single atoxigenic strain since it was neither aflatoxin nor cyclopiazonic acid producer. This isolate could be useful as a biological control agent, since it was unable to form a stable heterokaryon in the complementation test with the other isolates. Seven A. flavus isolated from soil were atypical because they simultaneously produced aflatoxins B, G and CPA.     

滦河水库系统浮游植物时空变化特征研究

2009年对滦河水库系统潘家口-大黑汀水库的浮游植物时空变化特征进行研究,结果表明,潘家口-大黑汀水库共监测到浮游植物8门34科62属,其中本次研究共发现库区新记录藻类11属;种类最多的为绿藻门和硅藻门,分别有27属和14属,分别占32.4%和23.5%;其中优势种类为8属,常见种类为17属,次常见或稀有种类为37属。藻密度在春末和夏初较小,在秋季的8、9月生长量达到最大,在冬季又开始降低,以潘家口坝上样点为例,5月藻密度为160.9万个.L-1,9月藻密度1 721.27万个.L-1;春季主要的优势类群为硅甲藻,夏季为隐硅藻,秋季为蓝绿藻,夏秋季节的优势属为假鱼腥藻（蓝藻门）。藻类分布存在空间性差异,种类最多的样点（下池）共发现43属,种类最少的样点（大黑汀库区）仅发现20属。与20世纪80年代的调查结果相比,47属为共有浮游植物,相似性系数为64.8%,浮游植物群落结构由硅藻型向蓝-绿藻型转变,其中变化最大的样点为潘家口坝上,相似性系数仅为29.4%,藻类密度增加了近20倍,总磷和总氮浓度分别增加1.41倍和3.63倍,潘家口-大黑汀水库富营养化程度呈加剧趋势。     

Compositional and functional features of humic acids from organic amendments and amended soils in Minnesota, USA

The use of organic amendments requires an adequate control of the chemical quality of their humic acid (HA)-like fractions and of the effects that these materials may have on the status, quality, chemistry and functions of native soil HAs. In this work, the compositional, functional and structural properties of the HA-like fractions isolated from a liquid swine manure (LSM), a municipal sewage sludge (SS), and two municipal solid waste composts (MSWCs) were evaluated in comparison to those of HAs isolated from three unamended soils and from the corresponding soils amended with LSW, SS, and MSWC at various rates in three field plot experiments conducted in Minnesota, USA. With respect to the unamended soil HAs, the HA-like fractions of the three amendments featured a greater aliphatic character, a marked presence of proteinaceous, S-containing and polysaccharides-like structures, an extended molecular heterogeneity, small organic free radical contents and a small degree of humification. The MSWC-HAs featured a larger degree of humification than LSM-HA and SS-HA. The three amendments affected in different ways and by various extents the compositional, structural and functional properties of soil HAs depending upon the nature, origin and application rate of the amendment. In general, the data obtained suggested that proteinaceous, S-containing and aliphatic structures contained in HA-like fractions of organic amendments were partially incorporated into native soil HAs.     

Microbial and soil parameters in relation to N mineralization in soils of diverse genesis under differing management systems

 Oregon soils from various management and genetic histories were used in a greenhouse study to determine the relationships between soil chemical and biological parameters and the uptake of soil mineralized nitrogen (N) by ryegrass (Lolium perenne L.). The soils were tested for asparaginase, amidase, urease, β-glucosidase, and dipeptidase activities and fluorescein diacetate hydrolysis. Microbial biomass carbon (C) and N as well as metabolic diversity using Biolog GN plates were measured, as were total soil N and C, pH, and absorbance of soil extracts at 270 nm and 210 nm. Potentially mineralizable N (N₀) and the mineralization rate constant (k) were calculated using a first order nonlinear regression model and these coefficients were used to calculate the initial potential rate of N mineralization (N₀ k). Except for Biolog GN plates, the other parameters were highly correlated to mineralized N uptake and each other. A model using total soil N and β-glucosidase as parameters provided the best predictor of mineralized N uptake by ryegrass (R ² =0.83). Chemical and biological parameters of soils with the same history of formation but under different management systems differed significantly from each other in most cases. The calculated values of the initial potential rate of mineralization in some cases revealed management differences within the same soil types. The results showed that management of soils is readily reflected in certain soil chemical and biological indicators and that some biological tests may be useful in predicting N mineralization in soils. Received: 31 January 1997