贵州烟草根围AM真菌多样性的初步研究

从贵州省内烟区不同土壤生态环境下采集烟草根际土样,湿筛离心法分离丛枝菌根（AM）真菌孢子,鉴定出烟草AM真菌4属20种,其中球囊霉属9种,无梗囊霉属7种,巨孢囊霉属3种,盾巨孢囊霉属1种。从土壤样品DNA中扩增AM真菌特异性片段并采用DGGE技术对AM真菌多样性进行分析。测序结果显示烟草根际土壤中菌根真菌主要菌群为球囊霉属,与湿筛离心法的鉴定结果一致。为进一步研究贵州地区AM真菌多样性以及开发应用提供了依据。     

Molecular analysis of arbuscular mycorrhizal fungi colonising a semi-natural grassland along a fertilisation gradient

The community of arbuscular mycorrhizal fungi (AMF) colonizing the roots of Festuca pratensis and Achillea millefolium was characterized in a Swedish pasture at different times, along a gradient of fertilization. The small subunit ribosomal RNA gene was subjected to PCR and denaturing gradient gel electrophoresis (DGGE), sequencing and phylogenetic analysis. The sequences found in this study clustered in 10 discrete sequence groups, seven belonging to Glomus, two to Scutellospora and one to Diversispora. A negative correlation was observed between soil mineral nitrogen and the number of AMF sequence groups in the roots. The frequency of occurrence of AMF in roots decreased dramatically between June and September. No plant-host specificity could be detected.     

High diversity of arbuscular mycorrhizal fungi in a boreal herb-rich coniferous forest

* Here, the diversity of arbuscular mycorrhizal (AM) fungi was determined in a boreal herb-rich coniferous forest in relation to environmental variables. * Root samples of five plant species (Fragaria vesca, Galeobdolon luteum, Hepatica nobilis, Oxalis acetosella and Trifolium pratense) were analysed from stands differing in age and forest management intensity. * Thirty-four Glomeromycota taxa (small-subunit ribosomal RNA gene (SSU rDNA) sequence groups) were detected from 90 root samples (911 clones), including eight new taxa. Sequence groups related to Glomus intraradices were most common (MO-G3 and MO-G13). Samples of H. nobilis were colonized by more AM fungal taxa (3.68 +/- 0.31) than those of O. acetosella (2.69 +/- 0.34), but did not differ significantly in this respect from those of F. vesca (3.15 +/- 0.38). Effects of forest management, host plant species (except above) or season on the number or composition of fungal taxa in root samples were not detected, and neither were they explained by environmental variables (vegetation, soil and light conditions). * This is the most taxon-rich habitat described to date in terms of root-colonizing Glomeromycota. The data demonstrate the importance of temperate coniferous forests as habitats for AM fungi and plants. Lack of obvious fungal community patterns suggests more complex effects of biotic and abiotic factors, and possibly no adverse effect of common forest management practices on AM fungal diversity.     

Changes in arbuscular mycorrhizal fungal communities during invasion by an exotic invasive plant

Exotic invasive plants can show strong plant–soil feedback responses, but little is known about time scales for significant changes in soil microbial communities to occur after invasion. Previous work has suggested that plant invasions can modify arbuscular mycorrhizal (AM) fungal community structure. However, there is a lack of understanding about how long it takes for these changes to develop. To test this we investigated temporal changes in AM fungal communities colonising the invasive plant Vincetoxicum rossicum (Apocynaceae). We hypothesised that AM fungal community structure would change in a particular direction during the invasion process. We collected soil from two sites with a long history of invasion by this plant, with each site having paired invaded and uninvaded plots. Soil from these plots was used in a glasshouse experiment to characterise AM fungal community structure in the roots of V. rossicum at different times throughout a simulated growing season. AM fungal community structure differed between invaded and uninvaded plots. However, contrasting with our hypothesis, AM fungal communities colonising V. rossicum growing in soil from uninvaded plots did not change towards those in plants growing in previously invaded soil. Our data suggest that changes to AM fungal communities in the presence of V. rossicum require longer than the first growing season after establishment to develop.     

Molecular biodiversity of arbuscular mycorrhizal fungi in trace metal-polluted soils

We assessed the indigenous arbuscular mycorrhizal fungi (AMF) community structure from the roots and associated soil of Plantago major (plantain) plants growing on sites polluted with trace metals (TM) and on unpolluted sites. Uncontaminated and TM-contaminated sites containing As, Cd, Cu, Pb, Sn and Zn were selected based on a survey of the TM concentration in soils of community gardens in the City of Montréal. Total genomic DNA was extracted directly from these samples. PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE), augmented by cloning and sequencing, as well as direct sequencing techniques, was all used to investigate AMF community structure. We found a decreased diversity of native AMF (assessed by the number of AMF ribotypes) in soils and plant roots harvested from TM-polluted soils compared with unpolluted soils. We also found that community structure was modified by TM contamination. Various species of Glomus, Scutellospora aurigloba and S. calospora were the most abundant ribotypes detected in unpolluted soil; ribotypes of G. etunicatum, G. irregulare/G. intraradices and G. viscosum were found in both polluted and unpolluted soils, while ribotypes of G. mosseae and Glomus spp. (B9 and B13) were dominant in TM-polluted soils. The predominance of G. mosseae in metal-polluted sites suggests the tolerance of this species to TM stress, as well as its potential use for phytoremediation. These data are relevant for our understanding of how AMF microbial communities respond to natural environments that contain a broad variety of toxic inorganic compounds and will substantially expand our knowledge of AMF ecology and biodiversity.     

Medicago species affect the community composition of arbuscular mycorrhizal fungi associated with roots

Sequencing of the 5' end of the large ribosomal subunit (LSU rDNA) and quantitative polymerase chain reaction (qPCR) were combined to assess the impact of four annual Medicago species (Medicago laciniata, Medicago murex, Medicago polymorpha and Medicago truncatula) on the genetic diversity of arbuscular mycorrhizal (AM) fungi, and on the relative abundance of representative AM fungal genotypes, in a silty-thin clay soil (Mas d'Imbert, France). Two hundred and forty-six Glomeromycete LSU rDNA sequences from the four plant species and the bulk soil were analysed. The high bootstrap values of the phylogenetic tree obtained allowed the delineation of 12 operational taxonomic units (OTUs), all belonging to Glomus. Specific primers targeting Glomeromycetes and major OTUs were applied to quantify their abundance by qPCR. Glomeromycetes and targeted OTUs were significantly more abundant in the root tissues than in the bulk soil, and the frequencies of three of them differed significantly in the root tissues of the different plant species. These differences indicate that, despite the absence of strict host specificity in mycorrhizal symbiosis, there was a preferential association between some AM fungal and plant genotypes.     

Fine roots, arbuscular mycorrhizal hyphae and soil nutrients in four neotropical rain forests: patterns across large geographic distances

* It is commonly hypothesized that stand-level fine root biomass increases as soil fertility decreases both within and among tropical forests, but few data exist to test this prediction across broad geographic scales. This study investigated the relationships among fine roots, arbuscular mycorrhizal (AM) fungi and soil nutrients in four lowland, neotropical rainforests. * Within each forest, samples were collected from plots that differed in fertility and above-ground biomass, and fine roots, AM hyphae and total soil nutrients were measured. * Among sites, total fine root mass varied by a factor of three, from 237+/-19 g m-2 in Costa Rica to 800+/-116 g m-2 in Brazil (0-40 cm depth). Both root mass and length were negatively correlated to soil nitrogen and phosphorus, but AM hyphae were not related to nutrients, root properties or above-ground biomass. * These results suggest that understanding how soil fertility affects fine roots is an additional factor that may improve the representation of root functions in global biogeochemical models or biome-wide averages of root properties in tropical forests.     

The northward shifting neophyte Tragopogon dubius is just as effective in forming mycorrhizal associations as the native T. pratensis

Background: As a consequence of climate warming, many organisms are shifting their range towards higher latitudes and altitudes. As not all do so at the same speed, this may disrupt biotic interaction. Release from natural enemies through range expansion can result in invasiveness, whereas loss of mutualists can reduce plant vigour and fitness. One of the most important groups of plant symbiotic mutualists is the arbuscular mycorrhizal fungi (AMF).

Aims: We used greenhouse experiments to test whether Tragopogon dubius, a species that has recently expanded its range northward and colonised the Netherlands, is able to associate with the same AMF as the native congener T. pratensis.

Methods: In soils collected from four locations in the new range of T. dubius we compared the density of infective AMF propagules associating with both plant species, as well as AMF colonisation of the roots. The AMF community structure in the roots of these species was also analysed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE).

Results: Tragopogon dubius and T. pratensis did not differ in any of these characteristics.

Conclusions: We therefore conclude that the range-shifting T. dubius is as effective in the formation of mycorrhiza as the native congener.     

长期定位施肥对石灰性紫色水稻土AMF多样性的影响

为了解长期定位施肥对石灰性紫色水稻土丛枝菌根真菌（AMF）物种多样性的影响,从稻麦轮作下连续26年定位施农家肥（M）、氮肥+农家肥（NM）、氮磷肥+农家肥（NPM）、氮磷钾肥+农家肥（NPKM）、不施肥（CK）、氮肥（N）、氮磷肥（NP）、氮磷钾肥（NPK）等不同施肥处理小区采集根区土样,分离鉴定AMF、测定多样性特征。共鉴定出17种AMF,其中球囊霉属Glomus 12种,占已分离总数的70.5%,为优势属;无梗囊霉属Acaulospora 3种,占17.6%;原囊霉属Archaeospora和内养囊霉属Entrophospora各1种,各占5.9%。无论是石灰性紫色土种植水稻还是小麦,AMF侵染率最高的施肥处理均为无肥处理（CK）,施肥特别是磷肥,降低AMF侵染率、孢子密度、相对多度和种丰度。变性梯度凝胶电泳（denaturing gradient gel electrophoresis,DGGE）分析结果表明,不施肥对照（CK）的AMF多样性最丰富,多样性指数最高,水稻和小麦种植下的多样性指数分别为2.68和3.02;与无机肥处理相比,农家肥配施无机肥提高了AMF多样性指数。农家肥配施无机肥更有利于AMF发育。     

Arbuscular mycorrhizal dynamics in a chronosequence of Caragana korshinskii plantations

Arbuscular mycorrhizal (AM) fungi in a chronosequence of 5–42-year-old Caragana korshinskii plantations in the semi-arid Loess Plateau region of northwestern China were investigated. AM fungi colonization, spore diversity and PCR-denatured gradient gel electrophoresis-based AM fungal SSU rRNA gene sequences were analyzed. AM fungi colonization [measured as the percent of root length (%RLC), vesicular (%VC) and arbuscular (%AC) colonization] and spore density were significantly correlated with sampling month, but not with plant age, except for %RLC. The percent of vesicular colonization was negatively correlated with soil total nitrogen and organic carbon, and spore density was negatively correlated with soil moisture and available phosphorus. Ten distinguishable AM fungal spore morphotypes, nine Glomus and one Scutellospora species, were found. Nine AM fungal Glomus phylotypes were identified by sequencing, but at each sampling time only four to six AM fungal phylotypes were detected. The AM fungal community was significantly seasonal, whereas the AM fungal species richness did not increase with plantation age. A significant change in AM fungal colonization and community composition over an annual cycle was observed in this study, and our results suggest that the changes of AM are the product of the interaction between host phenology, soil characteristics and habitat. Understanding these interactions is essential if habitat restoration is to be effective.     

Phylogenetic relatedness explains highly interconnected and nested symbiotic networks of woody plants and arbuscular mycorrhizal fungi in a Chinese subtropical forest

Elucidating symbiotic relationships between arbuscular mycorrhizal fungi (AMF) and plants contributes to a better understanding of their reciprocally dependent coexistence and community assembly. However, the main drivers of plant and AMF community assembly remain unclear. In this study, we examined AMF communities from 166 root samples of 17 woody plant species from 10 quadrats in a Chinese subtropical forest using 454 pyrosequencing of 18S rRNA gene to describe symbiotic AMF–plant association. Our results show the woody plant–AMF networks to be highly interconnected and nested, but in antimodular and antispecialized manners. The nonrandom pattern in the woody plant–AMF network was explained by plant and AMF phylogenies, with a tendency for a stronger phylogenetic signal by plant than AMF phylogeny. This study suggests that the phylogenetic niche conservatism in woody plants and their AMF symbionts could contribute to interdependent AMF and plant community assembly in this subtropical forest ecosystem.     

The role of in vitro cultivation on symbiotic trait and function variation in a single species of arbuscular mycorrhizal fungus

In vitro propagation of AM fungi using transformed root cultures (TRC) is commonly used to obtain pure AM fungal propagules for use in research and industry. Early observations indicate that such an artificial environment can alter traits and function of AM fungi over time. We hypothesized that increased in vitro cultivation may promote ruderal strategies in fungi by enhancing propagule production and reducing mutualistic quality. To examine the effect of in vitro cultivation on the trait and function of AM fungi, we inoculated plants with 11 Rhizoglomus irregulare isolates which fell along a cultivation gradient spanning 80 generations. We harvested plants at 10, 20 and 30 d post inoculation to observe differences in fungal and plant traits post infection. In vitro cultivation led to increased spore production but reduced plant shoot phosphorus. Our results indicate that in vitro propagation may indirectly select for traits that affect symbiotic quality.     

The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis

Aims:  To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure.
Methods and results:  Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47·2% of total clones), Bacteroides (35·4%) and Spirochaetes (13·2%). Methanoculleus bourgensis (29·0%), Methanosarcina barkeri (27·4%) and Methanospirillum hungatei (10·8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of ≥97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs.
Conclusions:  In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes , Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota.
Significance and Impact of the Study:  This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota.