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Illumina amplicon sequencing of soil in a temperate pine forest in the southeastern United States detected an abundant, nitrogen (N)-responsive fungal genotype of unknown phylogenetic affiliation. Two isolates with ribosomal sequences consistent with that genotype were subsequently obtained. Examination of records in GenBank revealed that a genetically similar fungus had been isolated previously as an endophyte of moss in a pine forest in the southwestern United States. The three isolates were characterized using morphological, genomic, and multilocus molecular data (18S, internal transcribed spacer [ITS], and 28S rRNA sequences). Phylogenetic and maximum likelihood phylogenomic reconstructions revealed that the taxon represents a novel lineage in Mucoromycotina, only preceded by Calcarisporiella, the earliest diverging lineage in the subphylum. Sequences for the novel taxon are frequently detected in environmental sequencing studies, and it is currently part of UNITE's dynamic list of most wanted fungi. The fungus is dimorphic, grows best at room temperature, and is associated with a wide variety of bacteria. Here, a new monotypic genus, Bifiguratus, is proposed, typified by Bifiguratus adelaidae.

Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.

A large circular plasmid detected in Francisella novicida-like strain PA10-7858, designated pFNPA10, was sequenced completely and analyzed. This 41013-bp plasmid showed no homology to any of the previously sequenced Francisella plasmids and was 8-10 times larger in size than them. A total of 57 ORFs were identified within pFNPA10 and at least 9 of them encoded putative proteins with homology to different conjugal transfer proteins. The presence of iteron-like direct repeats and an ORF encoding a putative replication protein within pFNPA10 suggested that it replicated by the theta mode. Phylogenetic analyses indicated that pFNPA10 had no near neighbors in the databases and that it may have originated within an environmental Francisella lineage. Based on its features, pFNPA10 appears to be a novel extra-chromosomal genetic element within the genus Francisella. The suitability of pFNPA10 as a vector for transformation of species of Francisella by conjugation remains to be explored. Key words: Francisella, plasmid, conjugal transfer proteins, theta replication. Un grand plasmide circulaire detecte au sein de la souche PA10-7858 d'une bacterie de type Francisella novicida, designee pFNPA10, a ete completement sequence et analyse. Ce plasmide de 41013 pb ne presente aucune homologie avec les plasmides sequences precedemment chez Francisella et il est 8 a 10 fois plus grand que ces derniers. Au total, 57 ORF ont ete identifies au sein de pFNPA10 et au moins 9 d'entre eux codent pour des proteines putatives qui presentent une homologie avec differentes proteines de transfert par conjugaison. La presence de repetitions directes, semblables a des iterons, et d'un ORF codant pour une possible proteine de replication au sein de pFNPA10 suggerent que ce plasmide est sujet a une replication de type theta. Les analyses phylogenetiques ont indique que pFNPA10 n'a pas de proches voisins au sein des bases de donnees et qu'il pourrait tirer son origine au sein d'un lignage environnemental du Francisella. Sur la base de ses caracteristiques, le pFNPA10 semble representer un nouvel element genetique extra-chromosomique au sein du genre Francisella. Il reste a explorer le potentiel d'utilisation du pFNPA10 comme vecteur de transformation des especes de Francisella par conjugaison. [Traduit par la Redaction] Mots-cles: Francisella, plasmide, proteines de transfert par conjugaison, replication de type theta., Introduction The bacterial family Francisellaceae consists of a single genus and three well-recognized species: Francisella tularensis, Francisella novicida, and Francisella philomiragia, which differ greatly in their pathogenic interactions with humans [...]

The abundance and composition of bacteria of the phylum Acidobacteria surveyed in subsurface sediments from uranium-contaminated sites using amplification of 16S rRNA genes followed by clones/sequence analysis produced a revised and greatly expanded phylogeny of the Acidobacteria phylum consisting of 26 subgroups.

A study was conducted to characterize the community structure and activity of N2 fixing microorganisms in soil crusts from Chihuahua desert as well as from the Colorado plateau. It was found that functionally biological soil crusts play important roles in soil stability, water retention and flow.

Research has been conducted on the biodiversity in microbial communities. The structure of soil bacterial community has been investigated and the results are presented.

Research has been conducted on the soil bacteria and their populations. The effect of the environmental condition changes on the bacteria and their populations has been investigated and the differences in the soil bacterial communities which inhibit various locations in the arid grassland soil have been analyzed and reported.

Research demonstrates a substantial conservation of nucleotide sequences between the Bacillus anthracis virulence plasmid pXO1 and the DNA from other Bacillus species. Data indicate a sequence homology of 80 and 98% as shown by polymerase chain reaction analysis.

An analytical procedure is presented for improving outcomes from replicate terminal restriction fragment profiles used in DNA testing of microbial communities. The procedure involves sample size standardization, which, although it has many practical applications, may be inappropriate for samples that are disparately low in DNA quantities compared to other samples in the set.

Research has been conducted on the complex microbial communities. The relationship between the microbial communities in environmental samples has been investigated.

Researchers have created a Pseudomonas strain that can be used as a biosensor for phenols. This is done by placing a reporter gene under the control of a promoter that is induced by phenol or any other pollutant.

Members of the bacterial kingdom Acidobacterium exhibit genetic and metabolic diversity as well as wide environmental distribution. To test this observation, members of Acidobacterium found in 43 environmental samples were analyzed by polymerase chain reaction amplification. Results show that Acidobacterium members are very widespread in terrestrial environments, particularly in neutral soils and sediments. The wide distribution and diversity of the members of Acidobacterium are comparable to those of Proteobacteria and gram-positive bacterial kingdoms.

Levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree soil samples have been compared using methods based on amplification of 16S rRNA genes. To this end, 179 cultivated bacterial isolates and 801 16S rRNA genes amplified from extracted soil DNA were analyzed. Results show a total of 34 phylotypes identified among the cultivated isolates while 498 phylotypes occurred among the 16S ribosomal DNA clones. The levels of phylotype similarity between bacterial communities were uniformly low.

The construction of a small-scale, non-selective procedure for DNA sample preparation supporting rapid-in-the-field polymerase chain reaction analysis for detection of microbial spores and cells is described. Three methods capable of releasing genomic DNA from three microorganisms were chosen for cell and spore disruption techniques. The reagents and buffers used in the three methods were changed and the techniques are miniaturized to provide maximum DNA yields.

Microbiological research shows that the microorganisms found in northern Arizona soil vary widely in their genetic makeup. Genetic sequencing analysis using PCR amplification with primers specific for bacterial 16S ribosomal ribonucleic acid gene sequences was performed. Five groups of microorganisms, representing 64% of the sequence samples, have not been classified before. Further research is continuing to establish more about the newly-identified microorganisms.