Effect of soil bacteria on hyphal growth of the arbuscular mycorrhizal fungus Glomus claroideum

The effect of 46 bacterial strains isolated from tilled and non-tilled soils collected at 3 localities on the growth of intraradical hyphae of the arbuscular mycorrhizal (AM) fungusGlomus claroideum was demonstrated. A larger number of stimulatory bacterial isolates was obtained from tilled soils, but the bacteria showing the strongest stimulation of hyphal growth were isolated from a soil that had not been cultivated. Isolates obtained from hyphae of AM fungi showed no substantial stimulatory effects, but produced more uniform effects on hyphal growth than the isolates of bacteria obtained from soil. Bacterial cenoses present in 3 different soils differ significantly in their effects on AM fungi.     

High abundance and role of antifungal bacteria in compost-treated soils in a wildfire area

Compost has been widely used in order to promote vegetation growth in post-harvested and burned soils. The effects on soil microorganisms were scarcely known, so we performed the microbial analyses in a wildfire area of the Taebaek Mountains, Korea, during field surveys from May to September 2007. Using culture-dependent and -independent methods, we found that compost used in burned soils influenced a greater impact on soil fungi than bacteria. Compost-treated soils contained higher levels of antifungal strains in the genera Bacillus and Burkholderia than non-treated soils. When the antifungal activity of Burkholderia sp. strain O1a_RA002, which had been isolated from a compost-treated soil, was tested for the growth inhibition of bacteria and fungi isolated from burned soils, the membrane-filtered culture supernatant inhibited 19/37 fungal strains including soil fungi, Eupenicillium spp. and Devriesia americana; plant pathogens, Polyschema larviformis and Massaria platani; an animal pathogen, Mortierella verticillata; and an unidentified Ascomycota. However, this organism only inhibited 11/151 bacterial strains tested. These patterns were compatible with the culture-independent DGGE results, suggesting that the compost used in burned soils had a greater impact on soil fungi than bacteria through the promotion of the growth of antifungal bacteria. Our findings indicate that compost used in burned soils is effective in restoring soil conditions to a state closer to those of nearby unburned forest soils at the early stage of secondary succession.     

Effects of zinc-smelter emissions on forest soil microflora.

Within 2 km of a zinc (Zn) smelter in Palmerton, Pennsylvania, near the Lehigh Water Gap, up to 13.5% Zn by weight has been measured in the O2 horizon of the soil, and up to 8% Zn in the A1 horizon. The total numbers of bacteria, actinomycetes, and fungi (measured by dilution plate counts) were greatly reduced in the most severely Zn-contaminated soils compared with control soils. The reduction of microbial populations may be a partial cause of the decreased rate of litter decomposition at Lehigh Gap. Growth of most bacteria from control sites was reduced by 100 to 200 muM Zn, most actinomycetes by 100 muM Zn, and most fungi by 100 to 1000 muM Zn in thin-Pablum extract agar (TPab). All the tested actinomycetes and non-spore-forming bacteria isolated from Zn-contaminated Lehigh Gap soils were Zn-tolerant, growing normally in media containing 600-2000 muM Zn. Most fungi, regardless of source, were capable of at least 50% of normal growth at 700 muM Zn. Zinc-tolerant bacteria, actinomycetes, and fungi were readily isolated from low-Zn soils, suggesting that selection for Zn tolerance may proceed rapidly. Acidophilic Mortierella species have been selectively eliminated near the smelter, apparently because of elevated soil pH. Peryronellaea glomerata (Corda) Goidanich and Coniothyrium spp. were found only in the high-Zn soils.     

内蒙草原不同植物功能群及物种对土壤微生物组成的影响

为了分析不同植物群落组成对内蒙古典型草原土壤微生物群落组成的影响,本研究利用植物功能群剔除处理实验平台,采用荧光定量PCR(real-timePCR)和自动核糖体间隔区基因分析(automated ribosomal intergenic spacer analysis,ARISA)技术,对不同植物功能群组成的非根际土壤和常见物种的根际土壤中细菌和真菌的数量及群落结构进行了分析。结果表明,在非根际土壤中,不同植物功能群组成对细菌数量有显著影响,而对真菌数量及细菌和真菌的群落结构影响不明显;在根际土壤中,不同植物物种对细菌、真菌的数量都有显著影响。此外,聚类分析表明,不同物种的根际土中细菌和真菌的群落结构也有所不同,尤其以细菌的群落结构变化较为明显。研究结果表明不同植物物种可以通过根系影响土壤微生物群落组成。     

茶树根际微生物研究

利用选择性培养基,对土壤肥力肥沃、中等、贫瘠茶园的茶树根际细菌、真菌和放线菌进行了分离。根据菌体形态及培养特征、生理生化指标、DNA的G Cmol％值等,对根际细菌进行了鉴定和分类。研究了不同肥力、不同茶龄的茶园根际细菌的数量和类群的变化;根际真菌的数量变化;根际放线菌的数量变化。主要结果为：土壤肥沃的茶园根际细菌的数量最多,土壤贫瘠的茶园数量最少;相同土壤肥力的茶园,10年生茶园根际细菌的数量最多,4年生的次之,20年生的最少。根际真菌的数量,土壤肥沃茶园的较少,中等和贫瘠茶园的较多。根际放线菌的数量,20年生茶园的明显高于4年生和10年生茶园的,而且,土壤贫瘠茶园的数量较多。从9种不同类型茶园中分离获得的纯化细菌经鉴定分别属于20个属,中等肥力的茶园最适于多数细菌的生长与繁殖,类群最为丰富,但类群的优势度低于另外两种土壤;不同茶龄的茶园随着茶龄的增加,肥沃茶园和中等茶园的根际中有较多的细菌类群定殖,但20a茶龄的类群较少;贫瘠茶园类群的优势度最大。     

Ecology of nematophagous fungi: Effect of the soil nutrients N,P and K,and seven major metals on distribution

The effects of the major soil nutrients and seven common metals on the distribution of nematophagous fungi were evaluated by comparing the concentration of the elements in soils with and without nematophagous fungi. Mineral nutrients, which were all positively correlated with nematode density, were the most important elements determining the presence of such fungi. Endoparasites producing adhesive conidia were independent of all the elements tested, while those species forming ingested conidia were isolated from soils high in nutrients, indicating a strong dependence on nematode density. Knob forming predators which rely on their ability to spontaneously produce traps to obtain nutrients were isolated from soils with low concentrations of mineral nutrients, while species with constricting rings were isolated from richer soils containing a greater density of nematodes. Net-forming species were largely independent of soil fertility, although generally they were isolated from soils with limited nutrientsd, especially K. Like other fungi, nematophagous fungi are generally not found in soils containing elevated concentrations of heavy metals. The results indicate that even concentrations of heavy metals which naturally occur in Irish soils can restrict the distribution of this fungal group. However the endoparasiteMeria coniospora is tolerant to all metals and to Cu in particular.     

中国盐碱土壤中AM菌的生态分布

对我国盐碱土壤中丛枝菌根（Ａｒｂｕｓｃｕｌａｒ Ｍｙｃｏｒｒｈｉｚａ,ＡＭ） 菌的种属构成、生态分布状况进行了研究．结果表明,不同地区ＡＭ 菌种属构成不同,其种属组成、分布与土壤类型、碱化度和土壤有机质含量有关．盐渍化砂土、壤土和粘土中,Ｇｌｏｍｕｓ 属的真菌数量最多,Ａｃａｕｌｏｓｐｏｒａ 属次之,而Ｇｌｏｍｕｓ 属中的Ｇ．ｍｏｓｓｅａｅ 则是分布最为广泛的菌种．随土壤碱化度的增加,Ｇｌｏｍｕｓ ｍｏｓｓｅａｅ 出现频率随之相对增加．在一定范围内有机质含量越高,土壤中ＡＭ 菌种和属的种类就越多．ＡＭ 菌的种属组成因不同寄主植物而异,其中豆科植物根围中ＡＭ 菌分布的种属数量最多．     

Soil mycoflora from trufflè native areas of Saudi Arabia

Soil fungi of areas in the North-Eastern region of Saudi Arabia where truffles are native were surveyed. Forty-three species of fungi belonging to twenty genera were isolated. Most were recovered from soils underneath or around truffle ascocarps: thirty species from soil under the surface of Tirmania nivea ascocarps, twenty-four from Terfezia boudieri soil and twenty species each from Tirmania pinoyi and Terfezia claveryi soils. Rhizosphere soil of Helianthemum lippi, on the other hand, yielded twenty-four fungal species while only fourteen fungal species were found in soil without vegetation. The total counts of fungi/g soil were highest in soils from the under surface of truffles, followed by rhizosphere soil, with the lowest in soils without vegetation.     

Bacterial and fungal taxon changes in soil microbial community composition induced by short-term biochar amendment in red oxidized loam soil

To take full advantage of biochar as a soil amendment, the objective of this study was to investigate the effects of biochar addition on soil bacterial and fungal diversity and community composition. Incubation experiments with a forest soil (a red oxidized loam soil) with and without biochar amendment were conducted for 96 days. The culture-independent molecular method was utilized to analyze soil bacterial and fungal species after the incubation experiments. Results showed that bacteria and fungi responded differently to the biochar addition during the short-term soil incubation. Twenty four and 18 bacterial genara were observed in the biochar amended and unamended soils, respectively, whereas 11 and 8 fungal genera were observed in the biochar amended and unamended soils, respectively. Microbial taxa analysis indicated that the biochar amendment resulted in significant shifts in both bacterial and fungal taxa during the incubation period. The shift for bacteria occurred at the genus and phylum levels, while for fungi only at the genus level. Specific taxa, such as Actinobacteria of bacteria and Trichoderma and Paecilomyces of fungi, were enriched in the biochar amended soil. The results reveal a pronounced impact of biochar on soil microbial community composition and an enrichment of key bacterial and fungal taxa in the soil during the short time period.     

Keratinophilic fungi of school playgrounds in the Nablus area,West Bank of Jordan

The distribution of keratinophilic fungi in the soil of 57 school playgrounds in the Nablus area was studied with relation to human presence. A total number of 73 species was recovered. Thirteen of these species were dermatophytes and closely related fungi. The most common and frequent species of the latter fungi were: Arthroderma cuniculi (found in 32.1% of school playgrounds), Chrysosporium keratinophilum (32.1%), Microsporum gypseum (10.7%), T. terrestre (7.1%), and C. asperatum (7.1%). Twenty eight of the isolated species had been reported to be pathogenic; these comprised 64.3% of the keratinophilic mycoflora of school playgrounds.     

A method for the preferential isolation of actinomycetes from soils

A successful plate-method for the preferential isolation of actinomycetes from soils is described. The principles underlying it are: (1) the inhibition of growth of non-sporulating bacteria by pre-incubation at a high temperature (110 C) for 10 min, and (2) limiting the spreading growth of sporeforming bacteria and fungi by the use of dried plates.The majority of the 191 species isolated by this method from 82 soil samples were shown to be pectinolytic.     

Populations of Dalapon-decomposing Bacteria in Soil as Influenced by Additions of Dalapon or Other Carbon Sources

The numbers of bacteria capable of decomposing the herbicide dalapon were determined for five soils by the most-probable-number method. Before treatment of the soils with dalapon, the numbers varied from 1,000 to 10,000 cells per g of soil. Incubation of the soils with dalapon resulted in large increases (100-fold) in two of three soils in which dalapon was decomposed rapidly. Lack of increase in numbers in spite of rapid decomposition in the other soil probably indicated breakdown by a chemical process or decomposition by fungi. In the remaining two soils, in which decomposition was slow in one and did not occur in the other, the initial numbers were at the low end of the range and the increase was small on incubation with dalapon. Addition of ground alfalfa or ground corn plant material to a soil did not result in significant increases in the numbers of dalapon-decomposing bacteria, either during or after decomposition of the plant material. Glucose depressed the rate of breakdown of dalapon in the soil and increased dalapon-decomposing Bacillus species rather than Arthrobacter and Agrobacterium species, which were found to increase on incubation with dalapon itself. The most-probable-number method appears to be a valuable tool for pesticide-ecology studies.     

Volatile-mediated antagonism of soil bacterial communities against fungi

Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.     

Actinomycetes-antagonists isolated from bulgarian soils

A total of 1257 Actinomycetes strains, the majority of which of the albus, griseus and globisporus series, were isolated from 345 samples from the rhizosphere of various plants and soils. According to these observations the cultivation of the soil is not of paramount importance for the quantitative and species composition of the Actinomycetes. The determination of the antibacterial spectrum shows that 45% of the isolated strains have antagonistic properties with respect to Gram positive, Gram negative, acid fast bacteria, yeastlike fungi and moulds.     

内蒙古草原典型植物对土壤微生物群落的影响

为了分析内蒙古草原不同植物物种对土壤微生物群落的影响, 采用实时荧光定量PCR (real-time PCR)以及末端限制性片段长度多态性分析(terminal restriction fragment length polymorphism, T-RFLP)等分子生物学技术, 测定了退化-恢复样地上几种典型植物的根际土壤和非根际土壤中细菌和真菌的数量及群落结构。结果表明, 不同植物物种对根际和非根际细菌及根际真菌数量均有显著影响。根际土壤中的细菌和真菌数量普遍高于非根际土壤, 尤其以真菌更为明显。对T-RFLP数据进行多响应置换过程(multi-response permutation procedures, MRPP)分析和主成分分析(principal component analysis, PCA), 结果表明, 大多数物种的根际细菌及真菌的群落结构与非根际有明显差异, 并且所有物种的真菌群落可以按根际和非根际明显分为两大类群。此外, 细菌和真菌群落结构在一定程度上存在按物种聚类的现象, 以细菌较为明显。这些结果揭示了不同植物对土壤微生物群落的影响特征, 对理解内蒙古草原地区退化及恢复过程中植被演替引起的土壤性质和功能的变化有一定的帮助。     

Degradation of polycyclic aromatic hydrocarbons with three to seven aromatic rings by higher fungi in sterile and unsterile soils

Seven commercial 3- to 7-ring (R) polycyclic aromatic hydrocarbons (PAH) as well as PAH derived from lignite tar were spiked into 3 soils (0.8 to 9.7% of organic carbon). The disappearance of the original PAH was determined for the freshly spiked soils, for soils incubated for up to 287 d with their indigenous microflora, and for autoclaved, unsterile and pasteurized soils inoculated with basidiomycetous and ascomycetous fungi. Three to 12 d after spiking, 22 to 38% of the PAH could no longer be recovered from the soils. At 287 d, 88.5 to 92.7%, 83.4 to 87.4%, and 22.0 to 42.1% of the 3-, 4-, and 5- to 7-R PAH, respectively, had disappeared from the unsterile, uninoculated soils. In 2 organic-rich sterile soils, the groups of wood- and straw-degrading, terricolous, and ectomycorrhizal fungi reduced the concentration of 5 PAH by 12.6, 37.9, and 9.4% in 287 d. Five- to 7-R PAH were degraded as efficiently as most of the 3- to 4-R PAH. In organic-rich unsterile soils inoculated with wood- and straw-degrading fungi, the degradation of 3- to 4-R PAH was not accelerated by the presence of fungi.The 5- to 7-R PAH, which were not attacked by bacteria, were degraded by fungi to 29 to 42% in optimum combinations of fungal species and soil type. In organic-poor unsterile soil, these same fungi delayed the net degradation of PAH possibly for 2 reasons. Mycelia of Pleurotus killed most of the indigenous soil bacteria expected to take part in the degradation of PAH, whereas those of Hypholoma and Stropharia promoted the development of opportunistic bacteria in the soil, which must not necessarily be PAH degraders. Contemporarily, the contribution of the fungi themselves to PAH degradation may be negligible in the absence of soil organic matter due to the lower production of ligninolytic enzymes. It is concluded that fungi degrade PAH irrespective of their molecular size in organic-rich and wood chip-amended soils which promote fungal oxidative enzyme production.     

Diversity of mesophilic clostridia in Costa Rican soils

Costa Rica is located in the Tropic, one of the most biologically diverse regions of the world; its soil is an important epicenter of biodiversity and Clostridium spp. are among the most frequent bacteria. The diversity of clostridia in Costa Rican soils and its possible association with geographic zone, pH or type of soil was studied in 117 soil samples: 18 from the Atlantic Zone, 30 from the Central Plateau, 30 from the Dry Pacific, 13 from the North Zone, and 26 from the South Pacific. The pH and the mesophilic clostridia species were determined for each sample. For bacterial isolation, a selective methodology for spores and pre-reduced anaerobically sterilized media were used. A total of 1945 strains of clostridia were isolated, 98% were identified and corresponded to 54 species; the most frequent species were C. subterminale (56%), C. oceanicum (51%), C. bifermentans and C. glycolicum (50%, each), C. sporogenes (49%), and C. sordellii (42%). An average of 7.1 species per sample was obtained; the Atlantic Zone showed the greatest diversity: 8.6 species per sample and a total of 45 species. Except for C. chauvoei, all described toxigenic clostridia species were isolated; C. sordellii (42%) and C. perfringens (38%) were the most frequent. No statistical relation could be established between geographic zone or type of soil and any species, showing that clostridia had a high adaptation capability to grow in different soil conditions; only some clostridia were isolated from very acidic samples while others from soils with a wide range of pH. In general, a uniform distribution of most species and a high variety of clostridia in Costa Rican soils were observed, in agreement with the high biodiversity described for other living beings in this country.     

The influence of tree species on canopy soil nutrient status in a tropical lowland wet forest in Costa Rica

The canopy is host to a large percentage of the flora and fauna in tropical wet forests and is distinct from the forest floor in plant richness, soil type and microclimate. In this study, we examined the influence of tree species and season on soil nutrient cycling processes in canopy soils of four tree species common to Costa Rican wet forests. We also compared the canopy soils to the associated forest floor mineral soils. Both tree species and season had strong effects on canopy soil nutrients and processes. Canopy soils from trees with high litter lignin concentrations had higher net N-mineralization rates and higher dissolved inorganic N concentrations than those with low lignin concentrations. During the dry season, net N-immobilization occurred and dissolved organic and inorganic N and available P concentrations were significantly higher than during the wet season. Overall, canopy soils had higher N levels and higher fungi + bacteria richness than forest floor mineral soils. The differences in canopy soil properties observed among tree species indicates that these species have distinct N cycles that reflect differences in both soil origin and biological controls.     

Studies on microbial antagonism in the establishment of clover pasture

Summary Fungi inhabiting soil recently cleared of the native vegetation have been isolated and compared with those isolated from under established clover pastures, Three methods of isolation of the fungi were used in each situation, and profoundly influenced the population obtained.In newly cleared soils the composite fungal population pattern deduced all three isolation methods comprised species of Mortierella, Phoma, Trichoderma, Penicillium, Fusarium, Sclerotium and non-sporing mycelia. In soil supporting established clover pastures the main rhizosphere fungi were species of Fusarium, Aspergillus, Phoma, Curvularia, Macrophomina, Sclerotium and one Ascomycete.Fusarium oxysporum was the most frequently isolated fungus.Conventional plating techniques suggested that the dominant fungi in the rhizosphere of clover wereFusarium oxysporum andAspergillus versicolor, whereas isolation of fungi from hyphae adhering to the clover roots indicated that species of Macrophomina, Curvularia and an Ascomycete were the most abundantly occurring organisms. In the case of the root residues of the native vegetation in newly cleared soils plating techniques resulted in species of the freely sporing Mortierella, Trichoderma, Aspergillus, Fusarium and Penicillium occurring most frequently, whereas the isolation of fungi from hyphal strands on the residues gave a population pattern dominated by species of Mortierella, Phoma, Sclerotium, and non-sporing mycelia.The study indicated a marked succession of fungal species during the decomposition of the root debris in newly cleared soils, and also that some early members of this changing population might exert an adverse effect on the establishment of clover.     

小蓬竹根际土壤微生物及内生真菌多样性分析

为了解喀斯特典型物种-小蓬竹根际土壤微生物及不同部位内生真菌多样性,采用沿等高线等距离取样法采集小蓬竹根际土壤及健康植株,通过可培养对根际土微生物及内生菌进行分离,利用分子技术对其进行鉴定,根据鉴定结果构建系统发育树,并计算小蓬竹根际土壤微生物和根茎叶内生真菌多样性。结果如下：（1）共从根际土壤、根、茎、叶分离得到139个真菌菌株,隶属于27属,其中根际土壤分离得到34个真菌菌株隶属于12属,根部分离得到的63个内生真菌菌株隶属于17个属,茎部分离得到的14个内生真菌菌株隶属于8个属,叶部分离得到28个内生真菌菌株隶属于9个属;（2）根际土壤共分离得到41株细菌菌株,隶属于7个属26个种,20株放线菌菌株,隶属于1属15种;从Shannon-Wiener多样性指数、均匀度指数、Simpson指数排序来看,真菌主要表现为根 > 根际土壤 > 茎 > 叶,细菌和放线菌多样性均较低。（3）按层次聚类分析可分别将真菌、细菌、放线菌聚为3支。小蓬竹根际土壤、根、茎和叶具有丰富的微生物多样性,不同部位菌群组成存在差异性（P<0.05）,且存在以假单胞菌属、芽孢杆菌属等为优势属的抗盐耐旱菌群,这有助于揭示小蓬竹对喀斯特生境的适应性,以及为微生物-植物群落之间相互关系提供一定基础数据,为后期寻找小蓬竹相关耐性功能菌奠定基础。