An MRI time course of 512 echo-planar images (EPI) in resting human brain obtained every 250 ms reveals fluctuations in signal intensity in each pixel that have a physiologic origin. Regions of the sensorimotor cortex that were activated secondary to hand movement were identified using functional MRI methodology (FMRI). Time courses of low frequency (< 0.1 Hz) fluctuations in resting brain were observed to have a high degree of temporal correlation (P < 10(-3)) within these regions and also with time courses in several other regions that can be associated with motor function. It is concluded that correlation of low frequency fluctuations, which may arise from fluctuations in blood oxygenation or flow, is a manifestation of functional connectivity of the brain.

Functional connectivity in the motor cortex of resting human brain using echo-planar MRI.

Evolution of Protein Molecules

Gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. Although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. This review summarizes the development in the field since our previous review (H. Nikaido and M. Vaara, Microbiol. Rev. 49:1-32, 1985) was published. With the discovery of protein channels, structural knowledge enables us to understand in molecular detail how porins, specific channels, TonB-linked receptors, and other proteins function. We are now beginning to see how the export of large proteins occurs across the outer membrane. With our knowledge of the lipopolysaccharide-phospholipid asymmetric bilayer of the outer membrane, we are finally beginning to understand how this bilayer can retard the entry of lipophilic compounds, owing to our increasing knowledge about the chemistry of lipopolysaccharide from diverse organisms and the way in which lipopolysaccharide structure is modified by environmental conditions.

Molecular Basis of Bacterial Outer Membrane Permeability Revisited

Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater–freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.

/pdf/transitions-in-bacterial-communities-along-the-2000-km-2cszg1uinl.pdf

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.

https://www.pnas.org/content/pnas/112/8/E911.full.pdf

Structure, variation, and assembly of the root-associated microbiomes of rice.

ing aerobic or facultatively anaerobic endospore-forming bacilli is represented by rRNA group 3 and contains 28 validated species and 2 subspecies. The genus is phenotypically similar to other members of the family Bacillaceae but is difficult to distinguish from the other genera by morphology alone. Recently a highly specific primer set directed to the 16S rDNA of Paenibacillus was described (Shida et al., 1997), which enabled the rapid identification of Paenibacillus to the genus level. However the identification of Paenibacillus below the genus level remains difficult and time-consuming due to the absence of well-defined phenotypes that differentiate species (Reva et al., 2001). In our previous studies, we have demonstrated that a hypervariable (HV) region, corresponding to the 5 end region of 16S rDNA (nucleotide positions 70 to 344; Bacillus subtilis numbering), is a useful marker for the rapid identification and grouping of Alicyclobacillus species (Goto et al., 2002b, c) and Bacillus species (Goto et al., 2000). In this study, 28 type strains and 31 additional strains of Paenibacillus species were subjected to a sequence comparison of the HV regions and the use of this HV region for molecular typing of the various species of the genus Paenibacillus was evaluated. The 59 strains used in this study were obtained from ATCC (American Type Culture Collection, Manassas, VA, USA), DSM (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany), IAM (Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan), IFO (Institute for Fermentation, Osaka, Japan) and NCIMB (National Collection of Industrial and Marine Bacteria, Aberdeen, UK). The Paenibacillus strains were cultivated by the methods recommended in the ATCC, DSM, IAM, IFO and NCIMB strain catalogues, respectively. The two newest species, P. azoreducens (Meehan et al., 2001) and P. jamilae (Aguilera et al., 2001), were not included because these type strains were not available for distribution at the time of this study. Extraction and purification of genomic DNA, sequencing of the 16S rDNA and HV region, and phylogenetic analysis were performed as described in our previous papers (Goto et al., 2000, 2002a, b). Sequences determined during the present work have been deposited in the DNA data bank of Japan (DDBJ) under the accession numbers AB073186 to AB073206 and AB073362 Evaluation of the hypervariable region in the 16S rDNA sequence as an index for rapid species identification in the genus Paenibacillus

Evaluation of the hypervariable region in the 16S rDNA sequence as an index for rapid species identification in the genus Paenibacillus.

Aminoadipate reductase (Lys2) is a fungal-specific protein. This enzyme contains an adenylating domain. A similar primary structure can be found in some bacterial antibiotic/peptide synthetases. In this study, we aimed to determine which bacterial adenylating domain is most closely related to Lys2. In addition, we analyzed the substitution rate of the adenylating domain-encoding region. Some bacterial proteins contain more than two similar sequences to that of the adenylating domain of Lys2. We compared 67 amino acid sequences from 37 bacterial and 10 fungal proteins. Phylogenetic trees revealed that the lys2 genes are monophyletic; on the other hand, bacterial antibiotic/peptide synthase genes were not found to be monophyletic. Comparative phylogenetic studies among closely related fungal lys2 genes showed that the rate of insertion/deletion in these genes was lower and the nucleotide substitution rate was higher than that in the internal transcribed spacer (ITS) regions. The lys2 gene is one of the most useful tools for revealing the phylogenetic relationships among fungi, due to its low insertion/deletion rate and its high substitution rate. Lys2 is most closely related to certain bacterial antibiotic/peptide synthetases, but a common ancestor of Lys2 and these synthetases evolutionarily branched off in the distant past.

/pdf/molecular-evolution-of-adenylating-domain-of-aminoadipate-1kdqwrvxcz.pdf

Molecular evolution of adenylating domain of aminoadipate reductase

The origins of fungal group I introns within nuclear small-subunit (nSSU) rDNA are enigmatic. This is partly because they have never been reported in basal fungal phyla (Zygomycota and Chytridiomycota), which are hypothesized to be ancestral to derived phyla (Ascomycota and Basidiomycota). Here we report group I introns from the nSSU rDNA of two zygomycete fungi, Zoophagus insidians (Zoopagales) and Coemansia mojavensis (Kickxellales). Secondary structure analyses predicted that both introns belong to the IC1 subgroup and that they are distantly related to each other, which is also suggested by different insertion sites. Molecular phylogenetic analyses indicated that the IC1 intron of Z. insidians is closely related to the IC1 intron inserted in the LSU rDNA of the basidiomycete fungus Clavicorona taxophila, which strongly suggests interphylum horizontal transfer. The IC1 intron of C. mojavensis has a low phylogenetic affinity to other fungal IC1 introns inserted into site 943 of nSSU rDNA (relative to E. coli 16S rDNA). It is noteworthy that this intron contains a putative ORF containing a His–Cys box motif in the antisense strand, a hallmark for nuclear-encoded homing endonucleases. Overall, molecular phylogenetic analyses do not support the placement of these two introns in basal fungal IC1 intron lineages. This result leads to the suggestion that fungal IC1 introns might have invaded or been transferred laterally after the divergence of the four major fungal phyla.

Group I introns from Zygomycota: evolutionary implications for the fungal IC1 intron subgroup.

Utilisation des techniques de chromatographie HPLC dans la chimiosystematique des Actinomycetes: mise en evidence du Madurose, un sucre tres proche du D-mannose

The analysis of madurose, an actinomycete whole-cell sugar, by hplc after enzymatic treatment

A thermophilic, Gram-positive bacterium that formed a branched vegetative mycelium was isolated from compost. The strain, designated I3T, grew at temperatures between 35 and 62 °C, with optimum growth at 50–55 °C. No growth was observed below 29 °C or above 65 °C. The pH range for growth was 5.7–10.0, the pH for optimum growth was 7.0 and no growth was observed below pH 5.6 or above pH 10.8. The DNA G+C content of strain I3T was 69.2 mol%. The major fatty acids found were C15 : 0 iso (14.2 %), C15 : 0 anteiso (12.1 %), C17 : 0 iso (16.3 %) and C17 : 0 anteiso (21.7 %). The major menaquinones were MK-9(H4), MK-10(H4) and MK-11(H4). The cell wall contained glutamic acid, glycine, alanine and ll-diaminopimelic acid in a molar ratio of 1.0 : 3.9 : 0.6 : 0.5. The polar lipids consisted of ninhydrin-positive phosphoglycolipids, phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The cell-wall sugars were rhamnose and arabinose. 16S rRNA gene sequence analysis assigned this actinomycete to the family Nocardioidaceae, but its 16S rRNA gene sequence shared no more than 95.5 % similarity with those of other members of the family. The chemotaxonomic and phenotypic characteristics of strain I3T differed in some respects from those of members of the genus Actinopolymorpha, the most closely related genus. Therefore, strain I3T represents a novel species in a new genus of the family Nocardioidaceae, for which the name Thermasporomyces composti gen. nov., sp. nov. is proposed. The type strain of the type species is I3T (=JCM 16421T=DSM 22891T).

Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost.

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