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In order to investigate temporal variation in the arbuscular mycorrhizal (AM) fungal community in a tropical forest in the Republic of Panama, seedlings of the canopy emergent Tetragastris panamensis were sampled three times over a period of 3 years. We used AM-specific primers to amplify and clone partial small subunit ribosomal RNA gene sequences. Over 550 clones were classified into 18 AM fungal types. As the seedlings matured, the fungal diversity decreased and there was a significant shift so that previously rare types replaced formerly dominant fungal types. Further, seedlings of different ages sampled at the same time point were colonised by significantly different fungal populations. Our results indicate that both time and host age may influence the mycorrhizal population.

• The diversity of arbuscular mycorrhizal (AM) fungi was investigated in an unfertilized limestone grassland soil supporting different synthesized vascular plant assemblages that had developed for 3 yr. • The experimental treatments comprised: bare soil; monocultures of the nonmycotrophic sedge Carex flacca; monocultures of the mycotrophic grass Festuca ovina; and a species-rich mixture of four forbs, four grasses and four sedges. The diversity of AM fungi was analysed in roots of Plantago lanceolata bioassay seedlings using terminal-restriction fragment length polymorphism (T-RFLP). The extent of AM colonization, shoot biomass and nitrogen and phosphorus concentrations were also measured. • The AM diversity was affected significantly by the floristic composition of the microcosms and shoot phosphorus concentration was positively correlated with AM diversity. The diversity of AM fungi in P. lanceolata decreased in the order: bare soil > C. flacca > 12 species > F. ovina. • The unexpectedly high diversity in the bare soil and sedge monoculture likely reflects differences in the modes of colonization and sources of inoculum in these treatments compared with the assemblages containing established AM-compatible plants.

Using newly designed fungal-specific polymerase chain reaction (PRC) primers, Vandenkoornhuyse et al examined total fungal diversity in a relatively mundane habitat, the roots of a plant. In addition to the unexpected breadth of taxa found, the study suggests the existence of previously unknown groups of fungi.

We used differences in small subunit ribosomal RNA genes to identify groups of arbuscular mycorrhizal fungi that are active in the colonisation of plant roots growing in arable fields around North Yorkshire, UK. Root samples were collected from four arable fields and four crop species, fungal sequences were amplified from individual plants by the polymerase chain reaction using primers NS31 and AM1. The products were cloned and 303 clones were classified by their restriction pattern with HinfI or RsaI; 72 were subsequently sequenced. Colonisation was dominated by Glomus species with a preponderance of only two sequence types, which are closely related. There is evidence for seasonal variation in colonisation in terms of both level of colonisation and sequence types present. Fungal diversity was much lower than that previously reported for a nearby woodland.

With the public release of the Populus genome (Tuskan et al., 2006), the United States Department of Energy’s Joint Genome Institute (JGI) embarked on an effort to create a community wide genomics resource for bacterial and fungal associates of Populus (Martin et al., 2004). Included in the list of species were several Populus endophytes (Burkholderia cepacia, Pseudomonas putida, Enterobacter spp., Serratia proteamaculans, Stenotrophomonas maltophilia; http://genome.jgi-psf.org/ draft_microbes/), Laccaria bicolor (Martin et al., 2008), Melampsora laraci-populina (http://www.jgi.doe.gov/sequencing/ why/3088.html) and Glomus intraradices (http://www.jgi. doe.gov/sequencing/DOEmicrobes2004.html). Ideally, the development of genomic tools for these organisms will facilitate the study of Populus and of its microbial associates in experimental and natural environments using whole-genome microarrays, models of predicted metabolite and protein interactions, cross-species promoter analyses and molecular surveys of community diversity. Together these resources will provide the possibility to take a holistic approach in understanding how symbionts and pathogens interact with the host tree in contrasting environments. The production of a completely annotated and assembled G. intraradices genome has proven to be an especially arduous challenge and, after 4 yr of effort, it is not yet at hand. In this context, a workshop was held by the Glomus Genome Consortium (GGC) on September 16–17, 2008, in Nancy, France, to review the progress that has been made to date on the Glomus genome.

Twelve Rhizobium leguminosarum isolates from France, Germany and the UK, each carrying between four and seven plasmids, were screened by PCR using primers designed to amplify partial traA and traC genes and the intergenic spacer (igs) between them, which is expected to contain oriT (the nick site for conjugal transfer). Five strains, 1062, RES-2, RES-6, RES-7 and RES-9, generated oriT-containing PCR fragments. Sequencing identified three types that are related to but different from other rhizobial plasmid oriT sequences in the database. Sequence comparisons revealed conserved motifs in the igs, including a 14-bp putative nic site, a stem-loop and a tra box. The RES-2, RES-6 and RES-9 PCR products were used as probes in Southern hybridisation studies to screen the 12 strains for related sequences. Eleven strains contain at least one homologous sequence, but of the 64 plasmids present among the 12 strains only 17 hybridised to the oriT probes. Four sequence variants of the repC plasmid replication initiation gene have previously been described in these strains, but there is no correlation between repC and oriT sequence distributions, and there is evidence for recombination to generate different repC-oriT combinations. Three plasmids, pYK32, pYK36 and pYK39, containing the oriT amplified from RES-2, RES-6 and RES-9, respectively, were constructed for functional analysis of the oriT sequence variation. Each plasmid was transformed into R. leguminosarum strains 1062, RES-2 and RES-9 to generate nine donor-plasmid combinations, and their mobilisation frequencies into Escherichia coli and agrobacterium tumefaciens measured following biparental matings. All three plasmid constructs were mobilised at a similar frequency (10(-7) to 10(-8) per recipient) by each donor strain, suggesting that there is no discrimination by the transfer proteins between the different oriT sequences.

A Biolog™ (sole carbon source utilisation) user database of tropical and temperature rhizobial strains was created and used in conjunction with the partial 16S rRNA sequencing method to characterise 12 rhizobial isolates from African acacias and other tropical woody legumes. There was close agreement between the two methods but also some significant discrepancies. A high degree of diversity was shown in the relatively small sample of isolates, with 4 out of 5 of the currently proposed rhizobial genera represented. This is the first time Biolog has shown congruence with genotypic fingerprinting using a wide selection of rhizobial reference and test strains.

We used differences in small subunit ribosomal RNA genes to identify groups of arbuscular mycorrhizal fungi that are active in the colonisation of plant roots growing in arable fields around North Yorkshire, UK. Root samples were collected from four arable fields and four crop species, fungal sequences were amplified from individual plants by the polymerase chain reaction using primers NS31 and AM1. The products were cloned and 303 clones were classified by their restriction pattern with HinfI or RsaI; 72 were subsequently sequenced. Colonisation was dominated by Glomus species with a preponderance of only two sequence types, which are closely related. There is evidence for seasonal variation in colonisation in terms of both level of colonisation and sequence types present. Fungal diversity was much lower than that previously reported for a nearby woodland.

Rhizobia are the bacteria that form nitrogen-fixing nodules on legumes. The current list of four rhizobium genera and 17 species is reviewed, with some comments on likely future developments in the taxonomy. Sequences of the small subunit ribosomal RNA (SSU or 16S rRNA) support the well-established subdivision of rhizobia into three genera: Rhizobium, Bradyrhizobium and Azorhizobium. These all lie within the alpha subdivision of the Proteobacteria, but on quite distinct branches, each of which also includes many bacterial species that are not rhizobia. Rhizobium, by this definition, is still broad and polyphyletic, so there have recently been suggestions that this genus should be split into four genera. SSU sequences may be the best phylogenetic tool we have, but they are not an infallible guide to evolutionary relationships, particularly among closely related species: slow evolution, recombination, intraspecific variation and even intragenomic heterogeneity are all limitations that can be illustrated by examples from the rhizobia It seems likely that the ability to form legume nodules was not present in the common ancestor of all rhizobia but that the nodulation genes were transferred between phylogenetically distinct bacteria, so that the phylogeny of nodulation genes will probably differ from that of the bacteria that carry them. Nitrogen fixation genes are often linked to nodulation genes, but they need not have the same evolutionary history.

The arbuscular mycorrhizal (AM) fungi have been elevated to the phylum Glomeromycota based on a ribosomal gene phylogeny. In order to test this phylogeny, we amplified and sequenced small subunit ribosomal RNA (SSUrRNA), actin and elongation factor 1 (EF1)-alpha gene fragments from single spores of Acaulospora laevis, Glomus caledonium, Gigaspora margarita, and Scutellospora dipurpurescens. Sequence variation within and among spores of an isolate was low except for SSUrRNA in S. dipurpurescens, and the actin amino acid sequence was more conserved than that of EF1-alpha. The AM fungal sequences were more similar to one another than to any other fungal group. Joint phylogenetic analysis of the actin and EF1-alpha sequences suggested that the sister group to the AM fungi was a Zygomycete order, the Mortierellales.