DataSheet1_Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions.docx

Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.</p

Restrikční endonukleázy a genetické testy

This bachelor thesis Restriction endonucleases and genetic tests engages in the issue of restriction enzymes. In the literary review I describe the character of restriction endonucleases, their classification and mechanism of operation. The thesis furthermore touches a topic concerning the effect of the restriction reaction conditions and discusses techniques of utilization of these enzymes, where for example DNA cloning, analysis of variability or genome mapping belong. The practical part of the thesis includes some work with a software for an automatic search for restriction sites and for restriction DNA evaluation

Comparison of the physical organization of <i>nif</i>, <i>fix</i>, and associated genes from fosmid DX-1A-14 with those from three closest organisms.

<p>Organisms: <i>Azoarcus sp.</i>, <i>Herbaspirillum seropedicae</i>, <i>Acetobacter diazotrophicus</i>. The <i>nif</i> genes are highlighted in bold. <i>nrf</i>, <i>nif</i> associated genes; <i>orf</i>, hypothetical protein. The structure of <i>nif</i> gene cluster differs greatly from those of unknown microorganisms. The <i>nif</i> gene cluster does not contain <i>modABC</i> genes occurring in <i>H. seropedicae</i>, and RubisCO gene cluster can not be identified in the <i>nif</i> gene cluster region of <i>H. seropedicae</i>. <i>nifQ</i> gene is clustered together with <i>nifENX</i> and <i>fdxB</i> genes in <i>A. diazotrophicus</i>, while <i>nifV</i>, <i>nifW</i>, <i>fixABCX</i>, and <i>nifQ</i> genes constitute a single operon in fosmid DX-1A-14.</p

Phylogenetic tree of <i>nifK</i> genes.

<p>The phylogenetic tree was constructed by the neighbor-joining method using MEGA, version 4.0 with 1000 bootstrap repetitions. The sequences obtained from metagenomic sequencing of acid mine drainage are designated DX_SY_, followed by their number in library. These sequences are shown in bold. Only some representatives of 93 <i>nifK</i> sequences are shown here. The scale represents the number of amino acid substitutions per site.</p

Additional file 2: Figure S1. of Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination

Detrended correspondence analysis (DCA) of all functional genes in three sites. (PDF 8 kb

Gene products in the <i>nif-fix</i> cluster of fosmid DX-1A-14.

a<p>Organism in which the gene products most similar to that of the nif-fix cluster was found. Organism: <i>Herbaspirillum seropedicae, Burkholderia vietnamiensis, Beijerinckia indica, Rubrivivax benzoatilyticus, Candidatus Accumulibacter phosphatis clade IIA, Ralstonia eutropha, Methylococcus capsulatus, Methylovorus sp., Nitrosomonas europaea, Rhodopseudomonas palustris, Acidovorax delafieldii.</i></p>b<p>Identity of the deduced anomic acid sequence of gene product to the gene product of the organism to which it is most related.</p

List of ORFs from fosmid DX-1A-14, gene length, and similar genes in GenBank.

a<p>Nucleotide identity of fosmid DX-1A-14 gene to the gene of the organism to which it is most related.</p

Reverse transcription PCR of <i>fixX</i> and <i>nifQ</i> gene fragment.

<p>Lane M, 100; lane 1, PCR products with the template of total RNA extraction; lane 2, PCR products with the template of total RNA extracting digested by RNase.</p

Classification of total <i>nif</i> genes obtained from metagenomic sequencing reads.

<p>742 <i>nif</i> sequences were classified into different phyla based on the similarities to the known sequences. The community is massively dominated by γ<i>-proteobacteria</i>, followed in smaller amounts by <i>α-, β-proteobacteria</i> and <i>Verrucomicrobia</i>.</p

Additional file 1 of The succession pattern of soil microbial communities and its relationship with tobacco bacterial wilt

Figure S1. Rarefaction curves of 16r RNA gene sequencing data. Figure S2. Composition and structure of soil microbial communities in each group. Figure S3. Phylogenetic molecular ecological networks (pMEN) of microbial communities in each group, and number of nodes and links of each pMEN. Table S1. Soil properties. Table S2(a). Correlation of microbial populations in abundance between two periods at the phylum level. (b). Correlation of microbial populations in abundance between two periods at the genus level. Table S3. Topological properties of the empirical pMENs of microbial communities in eight groups. Table S4(a). Correlation between abundance of microbial populations and tobacco morbidity at the phylum level. (b). Correlation between abundance of microbial populations and tobacco morbidity at the genus level. Table S5(a). Mantel test of sequencing data with environmental attributes at the phylum level. (b). Mantel test of sequencing data with environmental attributes at the genus level. (DOCX 1100 kb