Distinct microbial communities associated with buried soils in the Siberian tundra

Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.     

Microbial communities of frozen soils of the Tuimaada Valley in Central Sakha

This study determined the characteristic features of microbial communities inhabiting frozen soils of Central Sakha. All groups of microorganisms were present in high numbers comparable with the microbial densities in steppe soils of Transbaikalia; their distribution along soil profiles followed a specific pattern with no decrease in abundance with depth. In summer, the dominant groups of the microbial pool were actinomycetes and oligonitrophilic bacteria, while in autumn it was heterotrophic bacteria. A typical feature of the frozen soils of Central Sakha was the gradual penetration of microorganisms into deeper soil horizons during the vegetation season and their accumulation in the suprapermafrost horizon by autumn.     

The microbiology of soils under successive wheat crops in relation to take-all disease

Abstract Thirty-eight wheat fields in southern England were sampled in an attempt to correlate the amount of take-all disease with 35 microbiological and chemical measurements of soil. There was little correlation between field take-all and pot tests to determine soil infectivity. Myxogastrids were important components of the soil population, being up to half of the amoebal population, and most soils contained dictyostelids, reticulate amoebae and myxobacteria. Amoebae, ciliates, bacteria and saprophytic fungi were recorded for all soils. pH was a major determinant of soil populations, being clearly correlated with fungal abundance and with numbers of ciliates, dictyostelids and bacteria. Principal component analysis separated dictyostelids from the other soil amoebae and again showed the importance of pH in determining soil microbial populations. Take-all was negatively correlated with soil fertility and positively related to nematodes and myxobacteria, but this was probably an effect of take-all, and represented saprophytic growth on dead roots rather than being a cause. Reticulate amoebae and dictyostelids were both correlated with low levels of take-all. This study emphasises the large number of interrelated populations of soil microorganisms which could have an effect on the severity of take-all infections.     

Soil Organic Carbon Content Decreases in Both Surface and Subsoil Mineral Horizons by Simulated Future Increases in Labile Carbon Inputs in a Temperate Coniferous Forest

Soils represent important pools of soil organic carbon (SOC) that can be greatly influenced by labile C inputs, which are expected to increase in future due to CO₂ enrichment of atmosphere and a concomitant rise in plant primary productivity. Studying effects of variable labile C inputs on SOC pool helps to understand how soils respond to global change. However, this knowledge is missing for coniferous forest soils despite being widespread throughout the northern temperate zone. We conducted a 7-month field manipulation experiment to study the effects of variable labile C inputs (simulated by additions of C₄ sucrose) on the C content in soil fractions and on microbial abundance in the organic (O), surface mineral (A), and subsoil mineral (B) horizons of a temperate coniferous forest soil. SOC in less-protected soil fractions and total organic C were substantially decreased by labile C additions that simulated future increases in C inputs. The SOC losses were comparable between the A and B horizon (40% vs. 30%). However, because sucrose availability estimated from its incorporation into soil fractions and microbial biomass sharply decreased with soil depth, the loss of C was higher in the B than in the A horizon when related to the amount of sucrose added. Utilization of sucrose was highest by fungi in the O horizon and by bacteria in the mineral soil horizons. The results indicate that future increases in labile C inputs to coniferous forest soils will cause rapid and substantial losses of SOC in both the surface and subsoil mineral horizons.

     

Distribution of bacteria and fungi in the earthworm Libyodrillus violaceous (Annelida: Oligochaeta), a native earthworm from Nigeria

Earthworms are soil invertebrates that play a key role in recycling organic matter in soils. In Nigeria, earthworms include Libyodrillus violaceous. Aerobic and anaerobic bacterial counts, as well as fungal counts of viable microorganisms in soils and gut sections, were made on twenty L. violaceous collected from different sites on the campus of the University of Agriculture, Abeokuta, Nigeria. The samples were collected between April and November, 2002. Numbers of microorganisms were higher in castings and gut sections than in un-ingested soil samples. The guts and their contents also had higher moisture and total nitrogen contents than the un-ingested soils. Bacteria and fungi isolated from the samples were identified by standard microbiological procedures on the bases of their morphological and biochemical characteristics. Isolated bacteria were identified as Staphylococcus, Bacillus spp., Pseudomonas aeruginosa, Streptococcus mutans, Clostridium, Spirocheata spp., Azotobacter spp., Micrococcus lylae, Acinetobacter spp., Halobacterium for bacteria. Yeast isolates were identified as Candida spp., Zygosaccharomyces spp., Pichia spp., and Saccharomyces spp while molds were identified as, Aspergillus spp., Pytium spp., Penicillium spp., Fusarium spp and Rhizopus spp. Of the five locations examined, the refuse dump area had the highest numbers of both aerobic and anaerobic organisms, followed by the arboretum while the cultivated land area recorded the lowest counts. The higher numbers of microorganisms observed in the gut sections and casts of the earthworms examined in this work reinforce the general concept that the gut and casts of earthworms show higher microbial diversity and activity than the surrounding soil.     

除草剂二氯喹啉酸对水稻田土壤中微生物种群的影响

对好氧微生物采用平板稀释法,厌氧微生物采用最大或然计数法和滚管法研究土壤中施入0．33、0．67、1．00、1．33、2．00μg·g^-1干土除草剂二氯喹啉酸后对土壤可培养微生物种群数量的影响。结果表明,各种微生物对二氯喹啉酸的反应随其施加浓度的不同而有差异．二氯喹啉酸对水稻田土壤中好氧性细菌、水解发酵细菌、反硝化细菌数量的影响都是短暂的,第33d时均能恢复至接近对照水平,浓度在1．33μg·g^-1干土以下时二氯喹啉酸促进真菌数量增加,高于该浓度时则具有抑制作用．施用各浓度二氯喹啉酸初期,对土壤中放线菌和产甲烷菌有一定程度的抑制效应,但低浓度时抑制效应在培养后期消失．正常土壤施用量的二氯喹啉酸(即0．67μg·g^-1干土)对水田土壤微生物各种群无实质危害级农药。     

微生物溶解磷矿粉能力与pH及分泌有机酸的关系

从玉米根际和非根际土壤中分离得到的 74株溶解磷矿粉的微生物 ,发现它们的溶磷能力差异很大 ,主要决定于菌株本身的特性 ,与其来源无关 ,真菌普遍比细菌要强。真菌的溶磷能力与其培养介质的 pH之间呈显著的负相关 ,但细菌的这种关系非常弱。二者都产生多种有机酸 ,真菌主要分泌草酸、丙二酸和乳酸 ,而细菌主要分泌草酸、酒石酸、丙二酸、乳酸和乙酸 ,不同菌株分泌有机酸的数量和种类差异很大 ,但溶磷量与有机酸总量或单个有机酸浓度之间 ,没有发现显著的相关性 ,唯独柠檬酸与真菌的溶磷量之间存在显著的相关性。说明不同菌株有完全不同的溶磷机理 ,可能多种机理并存。     

Airborne microbial flora in a cattle feedlot

A total of 1,408 cattle held in eight commercial feedlot pens were used to examine the quantity and diversity of microorganisms in cattle feedlot air. The effect of two feeding patterns on the generation of airborne dust and the total numbers of microorganisms was also examined (four feedlot pens/treatment). Microbial samples were collected, and dust particles that were 2.5 microm or less in diameter were measured with a Dustrak monitor during the evening dust peak for 4 days at sites both upwind and downwind of the feedlot pens. An Andersen biological cascade sampler was employed with different medium and incubation combinations for the capture and identification of bacteria and fungi. The results showed that when bacteria were considered, only nonpathogenic gram-positive organisms were recovered. However, gram-negative bacteria may have been present in a viable but nonculturable state. Fungi were recovered in smaller numbers than bacteria, and none of the fungi were pathogenic. The Dustrak results showed that one feeding pattern resulted in cattle behavior that generated levels of downwind dust lower (P = 0.04) than the levels generated by the behavior resulting from the other feeding pattern. However, the Andersen sampler results showed that there were no differences between feeding patterns with regard to the total number or diversity of microorganisms. The disparity may have been due to the different operating principles of the two systems. The overall numbers of microorganisms recovered were lower than those reported in studies of intensively housed farm animals in which similar recovery techniques were used.     

Effects of Nematophagous Fungi on Numbers and Death Rates of Bacterivorous Nematodes in Arable Soil

In a series of microcosm experiments with an arable, sandy loam soil amended with sugarbeet leaf, the short-term (8 weeks) dynamics of numbers of nematodes were measured in untreated soil and in γ-irradiated soil inoculated with either a field population of soil microorganisms and nematodes or a mixed population of laboratory-propagated bacterivorous nematode species. Sugarbeet leaf stimulated an increase in bacterivorous Rhabditidae, Cephalobidae, and a lab-cultivated Panagrolaimus sp. Differences were observed between the growth rates of the nematode population in untreated and γ-irradiated soils, which were caused by two nematophagous fungi, Arthrobotrys oligospora and Dactylaria sp. These fungi lowered the increase in nematode numbers due to the organic enrichment in the untreated soil. We estimated the annually produced bacterivous nematodes to consume 50 kg carbon and 10 kg nitrogen per ha, per year, in the upper, plowed 25 cm of arable soil.     

Methanotrophic Bacteria in the Rhizosphere of Trichloroethylene-Degrading Plants

The presence and density of methanotrophic bacteria has been shown to play an important role in the bioremediation of trichloroethylene (TCE). This article describes the methanotrophic bacterial densities in rhizosphere soils from two areas of the Department of Energy's Savannah River Site in Aiken, South Carolina. A direct fluorescent antibody (DFA) technique was evaluated to determine the presence of methanotrophic bacteria in roots and rhizospheres from vascular plants. The first site, the Miscellaneous Chemical Basin (MCB), was contaminated with a mixture of chemicals, including chlorinated solvents. The second site will be potentially affected by outcropping of TCE-contaminated groundwater. Significantly higher numbers of methanotrophic bacteria were observed with DFA in rhizosphere soils and on roots of Lespedeza cuneata and Pinus taeda (that previously showed higher rates of ¹⁴C-TCE mineralization) compared with nonvegetated soils. In addition, viable and heterotrophic microbial counts were consistently higher in rhizosphere soils and on plant roots compared with nonvegetated soils. Therefore, the presence of these plant species may enhance ¹⁴C-TCE mineralization by selectively increasing the microbial population in the root zone. Methanotrophic bacteria were directly observed by DFA in soils, on the surface of root hairs, within plant roots, and in higher densities associated with mycorrhizal fungi. These experiments provide further evidence that specific types of bacterial interactions with vegetation in the rhizosphere may play an important role in remediation of TCE-contaminated soils and groundwater.     

Airborne Microbial Flora in a Cattle Feedlot

A total of 1,408 cattle held in eight commercial feedlot pens were used to examine the quantity and diversity of microorganisms in cattle feedlot air. The effect of two feeding patterns on the generation of airborne dust and the total numbers of microorganisms was also examined (four feedlot pens/treatment). Microbial samples were collected, and dust particles that were 2.5 μm or less in diameter were measured with a Dustrak monitor during the evening dust peak for 4 days at sites both upwind and downwind of the feedlot pens. An Andersen biological cascade sampler was employed with different medium and incubation combinations for the capture and identification of bacteria and fungi. The results showed that when bacteria were considered, only nonpathogenic gram-positive organisms were recovered. However, gram-negative bacteria may have been present in a viable but nonculturable state. Fungi were recovered in smaller numbers than bacteria, and none of the fungi were pathogenic. The Dustrak results showed that one feeding pattern resulted in cattle behavior that generated levels of downwind dust lower (P = 0.04) than the levels generated by the behavior resulting from the other feeding pattern. However, the Andersen sampler results showed that there were no differences between feeding patterns with regard to the total number or diversity of microorganisms. The disparity may have been due to the different operating principles of the two systems. The overall numbers of microorganisms recovered were lower than those reported in studies of intensively housed farm animals in which similar recovery techniques were used.     

Distribution of sulphur forms in soils from beech and spruce forests of Mont Lozère (France)

From a quantitative inventory of sulphur forms and sulphur budget, the relation between the distribution of the various sulphur forms and the sulphate fluxes in three soil profiles has been addressed. These profiles are located in two forested watersheds at Mont Lozère. One has been sampled in a beech forest and the other two in a spruce forest and in a harvested plot of this spruce forest, respectively. The mean annual input-output budgets showed a sulphur immobilization in the soil cover of the three plots. In the preserved spruce forest plot, because of larger dry depositions, the sulphur immobilization is much greater than in other plots and occurs essentially in the B horizons. In the other two profiles, the dominant immobilization occurs in the parent material.The total sulphur content is very high in the forest floor reaching 2065 g S g^-1 in the litter of one of the soils under spruce. In the organo-mineral horizons of soils under spruce, the total sulphur content decreases with depth and ranges from 310 to 520 g S g^-1 in the A horizons to 100–200 g S g^-1 in the parent material. In the profile under beech, the total sulphur content is lower except in the parent material. In all cases, the organic sulphur is the major part of sulphur often representing more than 90% of total sulphur. In organo-mineral soil horizons of the spruce forest, the part of the sulphateesters is more important than in the soil of the beech forest, probably related to the different nature of the microbial activity in the spruce forest. In contrast, the humification processes are more efficient in the soil under beech, which can be due to the greater input of organic sulphur by litterfall. It appears that the dominant organic sulphur form varies as a function of microbial ecology and sulphate flux. The maximum of the inorganic sulphate is located at the base of the B horizons in the soil of the spruce forest and in the parent material of the soil under beech. In these horizons, the high content of inorganic sulphate can be related to the higher amounts of amorphous Fe and Al phases.     

Determination of low bacterial concentrations in hyperarid Atacama soils: comparison of biochemical and microscopy methods with real-time quantitative PCR

Hyperarid Atacama soils are reported to contain significantly reduced numbers of microbes per gram of soil relative to soils from other environments. Molecular methods have been used to evaluate microbial populations in hyperarid Atacama soils; however, conflicting results across the various studies, possibly caused by this low number of microorganisms and consequent biomass, suggest that knowledge of expected DNA concentrations in these soils becomes important to interpreting data from any method regarding microbial concentrations and diversity. In this paper we compare the number of bacteria per gram of Atacama Desert soils determined by real-time quantitative polymerase chain reaction with the number of bacteria estimated by the standard methods of phospholipids fatty acid analysis, adenine composition (determined by liquid chromatography - time-of-flight mass spectrometry), and SYBR-green microscopy. The number determined by real-time quantitative polymerase chain reaction as implemented in this study was several orders of magnitude lower than that determined by the other three methods and probably underestimates the concentrations of soil bacteria, most likely because of soil binding during the DNA extraction methods. However, the other methods very possibly overestimate the bacteria concentrations owing to desiccated, intact organisms, which would stain positive in microscopy and preserve both adenine and phospholipid fatty acid for the other methods.     

Phenotypic characterization of microbes in the rhizosphere of Alyssum murale

Metal hyperaccumulator plants like Alyssum murale are used for phytoremediation of Ni contaminated soils. Soil microorganisms are known to play an important role in nutrient acquisition for plants, however, little is known about the rhizosphere microorganisms of hyperaccumulators. Fresh and dry weight, and Ni and Fe concentrations in plant shoots were higher when A. murale was grown in non-sterilized compared to sterilized soils. The analysis of microbial populations in the rhizosphere of A. murale and in bulk soils demonstrated that microbial numbers were affected by the presence of the plant. Significantly higher numbers of culturable actinomycetes, bacteria and fungi were found in the rhizosphere compared to bulk soil. A higher percent of Ni-resistant bacteria were also found in the rhizosphere compared to bulk soil. Percentage of acid producing bacteria was higher among the rhizosphere isolates compared to isolates from bulk soil. However, proportions of siderophore producing and phosphate solubilizing bacteria were not affected by the presence of the plant. We hypothesize that microbes in the rhizosphere of A. murale were capable of reducing soil pH leading to an increase in metal uptake by this hyperaccumulator.     

根际圈在污染土壤修复中的作用与机理分析

根际圈以植物根系为中心聚集了大量的生命物质及其分泌物,构成了极为独特的“生态修复单元”。本文叙述了根在根际圈污染土壤修复中的生理生态作用,富集、固定重金属,吸收、降解有机污染物等功能;菌根真菌对根际圈内重金属的吸收、屏障及螯合作用,对有机污染物的降解作用;根际圈内细菌对重金属的吸附与固定,对有机污染物的降解作用以及根际圈真菌和细菌的联合修复作用等,同时对可能存在的机理进行了分析,认为根际圈对污染土壤的修复作用是植物修复的重要组成部分和主要理论基础之一,并指出利用重金属超富集植物修复重金属污染土壤具有广阔的应用前景;筛选对水溶性有机污染物高吸收富集及其根 发泌能力强的特异植物,同时接种利于有机污染物降解的专性或非专性真菌和细菌可能会成为有机污染土壤植物修复研究的重要方向之一。     

Enumeration of petroleum-degrading microorganisms.

A variety of factors, including concentration of oil, antibiotics, dyes, and inoculum washes, were examined to determine their effect on the total counts of microorganisms on oil-containing media. The media found to be best for enumerating petroleum-degrading microorganisms contained 0.5% (vol/vol) oil and 0.003% phenol red, with Fungizone added for isolating bacteria and streptomycin and tetracycline added for isolating yeasts and fungi. Washing the inoculum did not improve recovery of petroleum degraders. Specifically, silica gel-oil medium and a yeast medium are recommended for enumeration of petroleum-degrading bacteria and yeasts and fungi, respectively. It is suggested that counts of petroleum degraders be expressed as percentage of the total population rather than total numbers of petroleum degraders per se. Incubation temperature and presence of oil was found to influence the numbers of petroleum-degrading microorganisms at a given sampling site.     

Quantification of the geocarposphere and rhizosphere effect of peanut (Arachis hypogaea L.)

Roots and pods of field-grown peanut (groundnut) (Arachis hypogaea L.) were sampled at the R3, R5, and R7 developmental stages and examined in comparison to root- and pod-free soil for microbial population densities to assess the geocarposphere and rhizosphere effects. G/ S (no. geocarposphere microorganisms/no. soil microorganisms) and R/S (no. rhizosphere microorganisms/no. soil microorganisms) ratios were calculated for total fungi,Asperigillus flavus, spore-forming bacilli, coryneform bacteria, fluorescent pseudomonads, and total bacteria isolated on low- and high-nutrient media. A clear geocarposphere effect was evidenced by increased population densities of bacteria and fungi associated with developing pods compared to soil. G/S and R/S ratios were generally greater than 1.0 for all groups of microorganisms except bacilli. G/S ratios were greater for total bacteria than for total fungi at two of the three sample times, suggesting that bacteria were stimulated more than fungi in the zone around developing pods. In contrast, R/S ratios, were higher for total fungi than for total bacteria at two of three sample times. The preferential association of fungi and bacteria with early developmental stages of the pod indicates that some microorganisms are particularly well adapted for colonization of the peanut geocarposphere. These microorganisms are logical candidates for evaluation as biological control candiates forA. flavus.     

Microflora of soils under pine forests area affected by gradation of leaf-eating insects

Soils of pine forests in the Bytnica Forestry District, Poland, are poor in nutrients readily accessible to plants. The excessively acidic reaction of the soils, typical for soils under pine forests, unfavourably affects the growth of microorganisms whose numbers are lower than in soils under deciduous and mixed forests. In the pine forests of the studied forestry there were outbreaks of a defoliating insect - pine beauty moth (Panolis flammea L.), which resulted in over 60% defoliation of the trees. The studies were carried out on the area of tree stands subjected to gradation by leaf-eating insects (sprayed and not sprayed) and healthy stand of the same age class (age 60 to 70 years). The studies revealed increased number of soil microorganisms in samples taken from the area affected by pine beauty moth gradation in the case of both unsprayed areas and those sprayed with the pesticide. The occurrence in these soils of larger numbers of ammonifying and denitrifying bacteria points to the presence of conditions favouring the growth of heterotrophic organisms. Changes in the number of actinomycetes and fungi in soils under tree stands subjected to gradation by insects, compared to healthy stands, can be a consequence of a change of environmental conditions (e.g. % content of organic carbon). Soils under defoliated tree stands show higher biochemical activity related to nitrogen cycling in the pine forest ecosystem. This leads to higher availability of organic nitrogen for conversion to inorganic forms of nitrogen, which are utilised by trees. Further changes occurring in soils under forest stands affected by gradation by leaf-eating insects would allow to gain knowledge on the ecological consequences of the use of insecticides in the protection of pine stands against harmful insects, with particular stress on those situations in which pine stands not threatened by complete defoliation are sprayed.     

Distribution and activity of microorganisms in the deep repository for liquid radioactive waste at the Siberian Chemical Combine

The physicochemical conditions, composition of microbial communities, and the rates of anaerobic processes in the deep sandy horizons used as a repository for liquid radioactive wastes (LRW) at the Siberian Chemical Combine (Seversk, Tomsk oblast), were studied. Formation waters from the observation wells drilled into the production horizons of the radioactive waste disposal site were found to be inhabited by microorganisms of different physiological groups, including aerobic organotrophs, anaerobic fermentative, denitrifying, sulfate-reducing, and methanogenic bacteria. The density of microbial population, as determined by cultural methods, was low and usually did not exceed 10(4) cells/ml. Enrichment cultures of microorganisms producing gases (hydrogen, methane, carbon dioxide, and hydrogen sulfide) and capable of participation in the precipitation of metal sulfides were obtained from the waters of production horizons. The contemporary processes of sulfate reduction and methanogenesis were assayed; the rates of these terminal processes of organic matter destruction were found to be low. The denitrifying bacteria from the underground repository were capable of reducing the nitrates contained in the wastes, provided sources of energy and biogenic elements were available. Biosorption of radionuclides by the biomass of aerobic bacteria isolated from groundwater was demonstrated. The results obtained give us insight into the functional structure of the microbial community inhabiting the waters of repository production horizons. This study indicates that the numbers and activity of microbial cells are low both inside and outside the zone of radioactive waste dispersion, in spite of the long period of waste discharge.     

The effect of agricultural utilization on the composition and yield of phenolic acids in low peat soils

Summary Levels of benzoic and cinnamic acids in low peat soils, maintained for 25 years under four different cropping systems, were studied in field experiments. The soil samples were obtained from four horizons of thirteen selected profiles. Seven phenolic acids were identified by high performance liquid chromatographic (HPLC) techniques and their amounts were determined quantitatively. The concentration of phenolic acids in the soils depended on the cropping system and the depth of the soil profiles. Permanent grassland had the highest yield of phenolic compounds in peat soils. Much smaller amounts were found in the order forest, alternate and field utilization. Thus, phenolic compounds may be useful markers with which to follow the decomposition in peat soils. The content of phenolic acids decreased with the depth of the profiles, but in some cases the 25–30 cm soil layers contained higher amounts of phenols than the 5–10 cm layers. Compared with the surface layers the deeper horizons (55–60 cm and 95–100 cm) were low in phenolic acids.