Estudio de las rizobacterias del suelo de la taiga de Chernevaya en Siberia occidental y su posible efecto sobre el crecimiento de las plantas

El aislamiento de bacterias del suelo de varios ambientes con tasas de fertilidad excepcionalmente altas representa una oportunidad para identificar agentes prometedores para promover la producción agrícola. El objetivo del artículo es estudiar las densidades de bacterias cultivables y aislar bacterias de la rizosfera del rábano y el trigo de primavera. Las plantas se cultivaron en el experimento en maceta con suelo Chernevaya virgen, que poseía una productividad extraordinaria, y suelo forestal zonal que no demostró características similares. Se purificaron cincuenta y nueve aislados bacterianos y se evaluaron sus efectos beneficiosos sobre el crecimiento temprano del trigo. Los aislados pertenecían a los filos Proteobacteria, Actinobacteria y Firmicutes, y los géneros más representados fueron Pseudomonas , Streptomyces , Paenibacillus y Methylobacterium . Estas bacterias dominantes se utilizaron en estudios de inoculación de plantas. Las cepas promovieron un aumento significativo en la longitud y biomasa de los brotes y las raíces, por lo que pueden considerarse rizobacterias promotoras del crecimiento de las plantas [PGPR]. En cuanto a los ensayos de biotest, se seleccionaron cepas que mostraron altas capacidades de promoción del crecimiento de las plantas [PGP] para una mayor investigación. Este estudio contribuyó a aislar bacterias de un entorno natural único con potencial biotecnológico para mejorar el crecimiento de las plantas y mostró potencia para ser explotadas como bioinoculantes

Physical properties as a key factor in the soil functioning in Chernevaya Taiga (Western Siberia)

On the barrier-rain slopes of the low mountains of Western Siberia, there are tall-grass forests dominated by fir and aspen. Their regional name is Chernevaya taiga (from the word "chernyj" – black). Chernevaya taiga is a unique representative of the highly productive and fertile ecosystems of Western Siberia. The key features of the development of these ecosystems in the mountains of Southern Siberia are still poorly investigated. The soil physical properties play a crucial role in forming the functioning of the Chernevaya taiga ecosystem. The thermal regime, particle size distribution (profile differentiation and texture class) and hydrophysical constants of soils in Chernevaya taiga are studied. It is shown that the soil profiles of Chernevaya taiga are differentiated by the content of fine particles, which indicates the development of eluvial-illuvial hydrological and biogeochemical regimes. The favourable thermic regime is caused by a thick layer of snow existence during the winter period, when the soils of Chernevaya taiga are not frozen during the winter period. This is one of the key factors of high productivity of this ecosystem. Soils of Chernevaya taiga are characterized by increased values of key hydrological constants in comparison with sandy textured soils of oligotrophic environments

Elemental and molecular composition of humic acids isolated from soils of tallgrass temperate rainforests (Chernevaya taiga) by 1H-13C HECTCOR NMR spectroscopy

The soils of Chernevaya taiga (tallgrass fir-aspen hemiboreal rainforest) have high fertility in comparison with oligotrophic analogs formed in boreal taiga. We have studied humic acids isolated from the soils of Chernevaya and oligotrophic taiga in the Novosibirsk, Tomsk, Kemerovo and the Altai regions of Russia and for the first time the structural and molecular composition of humic acids was determined using13C CP/MAS and1H-13C HETCOR NMR spectroscopy. According to data obtained in this study, up to 48% of aromatic compounds accumulate in the soils of Chernevaya taiga, which is higher than in the oligotrophic taiga and comparable with this rate of steppe Chernozems. In the course of active processes of transformation of organic matter, a significant number of aromatic fragments accumulates in the middle horizons of soil profiles. Using13C CP/MAS spectroscopy, it was possible to identify the main structural fragments (aliphatic and aromatic) that formed in humic acids of the Chernevaya taiga. The HETCOR experiment made it possible to accurately determine the boundaries of chemical shifts of the main groups of structural fragments of humic acids. Our results demonstrate that the stabilization of organic compounds occurs in the soil of the Chernevaya taiga, which leads to the resistance of organic matter to biodegradation that is not typical for benchmark soils of boreal environments

The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

BACKGROUND: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. RESULTS: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. CONCLUSION: The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae

MetaGT : A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a microbiome. RNA-Seq data provides the possibility to determine active genes in the community and how their expression levels depend on external conditions. Although the field of metatranscriptomics is relatively young, the number of projects related to metatranscriptome analysis increases every year and the scope of its applications expands. However, there are several problems that complicate metatranscriptome analysis: complexity of microbial communities, wide dynamic range of transcriptome expression and importantly, the lack of high-quality computational methods for assembling meta-RNA sequencing data. These factors deteriorate the contiguity and completeness of metatranscriptome assemblies, therefore affecting further downstream analysis. Here we present MetaGT, a pipeline for de novo assembly of metatranscriptomes, which is based on the idea of combining both metatranscriptomic and metagenomic data sequenced from the same sample. MetaGT assembles metatranscriptomic contigs and fills in missing regions based on their alignments to metagenome assembly. This approach allows to overcome described complexities and obtain complete RNA sequences, and additionally estimate their abundances. Using various publicly available real and simulated datasets, we demonstrate that MetaGT yields significant improvement in coverage and completeness of metatranscriptome assemblies compared to existing methods that do not exploit metagenomic data. The pipeline is implemented in NextFlow and is freely available fromhttps://github.com/ablab/metaGT.Peer reviewe

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild

Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

<p>Abstract</p> <p>Background</p> <p>Initial interest in <it>Dechloromonas aromatica </it>strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism.</p> <p>Results</p> <p>The <it>a priori </it>prediction that the <it>D. aromatica </it>genome would contain previously characterized "central" enzymes to support anaerobic aromatic degradation of benzene proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzylsuccinate synthase (<it>bss</it>ABC) genes (responsible for fumarate addition to toluene) and the central benzoyl-CoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of <it>de novo </it>HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex and exosortase (epsH) are also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (<it>sox</it>FCDYZAXB) gene cluster, Calvin cycle enzymes, and proteins involved in nitrogen fixation in other species (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively).</p> <p>Conclusion</p> <p>Analysis of the <it>D. aromatica </it>genome indicates there is much to be learned regarding the metabolic capabilities, and life-style, for this microbial species. Examples of recent gene duplication events in signaling as well as dioxygenase clusters are present, indicating selective gene family expansion as a relatively recent event in <it>D. aromatica</it>'s evolutionary history. Gene families that constitute metabolic cycles presumed to create <it>D. aromatica'</it>s environmental 'foot-print' indicate a high level of diversification between its predicted capabilities and those of its close relatives, <it>A. aromaticum </it>str EbN1 and <it>Azoarcus </it>BH72.</p

Draft Genome Sequence of Mn(II)-Oxidizing Bacterium Oxalobacteraceae sp. Strain AB_14.

Biological Mn(II) oxidation produces reactive manganese oxides that help to mitigate metal contamination in the environment. Here, we present the genome of Oxalobacteraceae sp. strain AB_14, a species of Mn(II)-oxidizing bacteria (MOB) that is notable for its ability to catalyze Mn oxidation at low pH (5.5)