Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent.

Arbuscular mycorrhizal (AM) fungi are known to exhibit high intra-organism genetic variation. However, information about intra- vs. interspecific variation among the genes commonly used in diversity surveys is limited. Here, the nuclear small subunit (SSU) rRNA gene, internal transcribed spacer (ITS) region and large subunit (LSU) rRNA gene portions were sequenced from 3 to 5 individual spores from each of two isolates of Rhizophagus irregularis and Gigaspora margarita. A total of 1482 Sanger sequences (0.5 Mb) from 239 clones were obtained, spanning ~4370 bp of the ribosomal operon when concatenated. Intrasporal and intra-isolate sequence variation was high for all three regions even though variant numbers were not exhausted by sequencing 12-40 clones per isolate. Intra-isolate nucleotide variation levels followed the expected order of ITS > LSU > SSU, but the values were strongly dependent on isolate identity. Single nucleotide polymorphism (SNP) densities over 4 SNP/kb in the ribosomal operon were detected in all four isolates. Automated operational taxonomic unit picking within the sequence set of known identity overestimated species richness with almost all cut-off levels, markers and isolates. Average intraspecific sequence similarity values were 99%, 96% and 94% for amplicons in SSU, LSU and ITS, respectively. The suitability of the central part of the SSU as a marker for AM fungal community surveys was further supported by its level of nucleotide variation, which is similar to that of the ITS region; its alignability across the entire phylum; its appropriate length for next-generation sequencing; and its ease of amplification in single-step PCR.

The composition of arbuscular mycorrhizal fungal communities in the roots of a ruderal forb is not related to the forest fragmentation process.

Land-use changes and forest fragmentation have strong impact on biodiversity. However, little is known about the influence of new landscape configurations on arbuscular mycorrhizal fungal (AMF) community composition. We used 454 pyrosequencing to assess AMF diversity in plant roots from a fragmented forest. We detected 59 virtual taxa (VT; phylogenetically defined operational taxonomic units) of AMF - including 10 new VT - in the roots of Euphorbia acerensis. AMF communities were mainly composed of members of family Glomeraceae and were similar throughout the fragmented landscape, despite variation in forest fragment size (i.e. small, medium and large) and isolation (i.e. varying pairwise distances). AMF communities in forest fragments were phylogenetically clustered compared with the global, but not regional and local AMF taxon pools. This indicates that non-random community assembly processes possibly related to dispersal limitation at a large scale, rather than habitat filtering or biotic interactions, may be important in structuring the AMF communities. In this system, forest fragmentation did not appear to influence AMF community composition in the roots of the ruderal plant. Whether this is true for AMF communities in soil and the roots of other ecological groups of host plants or in other habitats deserves further study.

Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi.

We aimed to enhance understanding of the molecular diversity of arbuscular mycorrhizal fungi (AMF) by building a new global dataset targeting previously unstudied geographical areas. In total, we sampled 96 plant species from 25 sites that encompassed all continents except Antarctica. AMF in plant roots were detected by sequencing the nuclear SSU rRNA gene fragment using either cloning followed by Sanger sequencing or 454-sequencing. A total of 204 AMF phylogroups (virtual taxa, VT) were recorded, increasing the described number of Glomeromycota VT from 308 to 341 globally. Novel VT were detected from 21 sites; three novel but nevertheless widespread VT (Glomus spp. MO-G52, MO-G53, MO-G57) were recorded from six continents. The largest increases in regional VT number were recorded in previously little-studied Oceania and in the boreal and polar climatic zones - this study providing the first molecular data from the latter. Ordination revealed differences in AM fungal communities between different continents and climatic zones, suggesting that both biogeographic history and environmental conditions underlie the global variation of those communities. Our results show that a considerable proportion of Glomeromycota diversity has been recorded in many regions, though further large increases in richness can be expected in remaining unstudied areas.

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.

Soil nutrient content influences the abundance of soil microbes but not plant biomass at the small-scale.

Small-scale heterogeneity of abiotic and biotic factors is expected to play a crucial role in species coexistence. It is known that plants are able to concentrate their root biomass into areas with high nutrient content and also acquire nutrients via symbiotic microorganisms such as arbuscular mycorrhizal (AM) fungi. At the same time, little is known about the small-scale distribution of soil nutrients, microbes and plant biomass occurring in the same area. We examined small-scale temporal and spatial variation as well as covariation of soil nutrients, microbial biomass (using soil fatty acid biomarker content) and above- and belowground biomass of herbaceous plants in a natural herb-rich boreonemoral spruce forest. The abundance of AM fungi and bacteria decreased during the plant growing season while soil nutrient content rather increased. The abundance of all microbes studied also varied in space and was affected by soil nutrient content. In particular, the abundance of AM fungi was negatively related to soil phosphorus and positively influenced by soil nitrogen content. Neither shoot nor root biomass of herbaceous plants showed any significant relationship with variation in soil nutrient content or the abundance of soil microbes. Our study suggests that plants can compensate for low soil phosphorus concentration via interactions with soil microbes, most probably due to a more efficient symbiosis with AM fungi. This compensation results in relatively constant plant biomass despite variation in soil phosphorous content and in the abundance of AM fungi. Hence, it is crucial to consider both soil nutrient content and the abundance of soil microbes when exploring the mechanisms driving vegetation patterns.

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status.

Study of factors which negatively affect expression of the phenol degradation operon pheBA in Pseudomonas putida.

Transcription of the plasmid-borne phenol catabolic operon pheBA in Pseudomonas putida is activated by the LysR-family regulator CatR in the presence of the effector molecule cis,cis-muconate (CCM), which is an intermediate of the phenol degradation pathway. In addition to the positive control of the operon, several factors negatively affect transcription initiation from the pheBA promoter. First, the activation of the pheBA operon depends on the extracellular concentration of phenol. The pheBA promoter is rapidly activated in the presence of micromolar concentrations of phenol in minimal growth medium, but the initiation of transcription from this promoter is severely delayed after sudden exposure of bacteria to 2.5 mM phenol. Second, the transcriptional activation from this promoter is impeded when the growth medium of bacteria contains amino acids. The negative effects of amino acids can be suppressed either by overproducing CatR or by increasing, the intracellular amount of CCM. However, the intracellular amount of CCM is a major limiting factor for the transcriptional activation of the pheBA operon, as accumulation of CCM in a P. putida catB-defective strain, unable to metabolize CCM (but expressing CatR at a natural level), almost completely relieves the negative effects of amino acids. The intracellular amount of CCM is negatively affected by the catabolite repression control protein via downregulating at the post-transcriptional level the expression of the pheBA-encoded catechol 1,2-dioxygenase and the phenol monooxygenase, the enzymes needed for CCM production.