Carbon Source Utilization Research Articles

Bacillus pfraonensis sp. nov., a new strain isolated from a probiotic feed additive with low cytotoxicity and antimicrobial activity

Probiotic products containing living microorganisms are gaining popularity, increasing the importance of their taxonomic status. A Bacillus-like isolate, 70 b, cultured from a probiotic feed additive, was ambiguity in taxonomic assignment and could be a novel member of Bacillus cereus group. The results of colony and cellular morphology, physiological and biochemical analysis mainly including growth performance, carbon source utilization, and rMLST and MLST were not conclusive. Fatty acids profile and molecular genetic analysis especially ANI, DDH, and core genome SNPs-based phylogenetic tree confirmed 70 b as one novel species of B. cereus group and proposed as Bacillus pfraonensis sp. nov. Comparative genomic analysis revealed the genetic differences between 70 b and other species of B. cereus group. Pseudomycoicidin was identified in 70 b. 70 b was active against multidrug-resistant pathogenic strains MRSA. The findings support 70 b is a novel species with low cytotoxicity and antimicrobial activity, and provides a better understanding of its unique characteristics and probiotic potential, and exploration of bioactive potential.

Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut

Antibiotic resistance plasmids can be disseminated between different Enterobacteriaceae in the gut. Here, we investigate how closely related Enterobacteriaceae populations with similar nutrient needs can co-bloom in the same gut and thereby facilitate plasmid transfer. Using different strains of Salmonella Typhimurium (S.Tm SL1344 and ATCC14028) and mouse models of Salmonellosis, we show that the bloom of one strain (i.e., recipient) from very low numbers in a gut pre-occupied by the other strain (i.e., donor) depends on strain-specific utilization of a distinct carbon source, galactitol or arabinose. Galactitol-dependent growth of the recipient S.Tm strain promotes plasmid transfer between non-isogenic strains and between E.coli and S.Tm. In mice stably colonized by a defined microbiota (OligoMM12), galactitol supplementation similarly facilitates co-existence of two S.Tm strains and promotes plasmid transfer. Our work reveals a metabolic strategy used by Enterobacteriaceae to expand in a pre-occupied gut and provides promising therapeutic targets for resistance plasmids spread.

Moderate organic fertilizer substitution for partial chemical fertilizer improved soil microbial carbon source utilization and bacterial community composition in rain-fed wheat fields: current year.

Organic fertilizers can partially replace chemical fertilizers to improve agricultural production and reduce negative environmental impacts. To study the effect of organic fertilizer on soil microbial carbon source utilization and bacterial community composition in the field of rain-fed wheat, we conducted a field experiment from 2016 to 2017 in a completely randomized block design with four treatments: the control with 100% NPK compound fertilizer (N: P2O5: K2O = 20:10:10) of 750 kg/ha (CK), a combination of 60% NPK compound fertilizer with organic fertilizer of 150 kg/ha (FO1), 300 kg/ha (FO2), and 450 kg/ha (FO3), respectively. We investigated the yield, soil property, the utilization of 31 carbon sources by soil microbes, soil bacterial community composition, and function prediction at the maturation stage. The results showed that (1) compared with CK, organic fertilizer substitution treatments improved ear number per hectare (13%-26%), grain numbers per spike (8%-14%), 1000-grain weight (7%-9%), and yield (3%-7%). Organic fertilizer substitution treatments increased the total nitrogen, available nitrogen, available phosphorus, and soil organic matter contents by 26%, 102%, 12%, and 26%, respectively, compared with CK treatments. Organic fertilizer substitution treatments significantly advanced the partial productivity of fertilizers. (2) Carbohydrates and amino acids were found to be the most sensitive carbon sources for soil microorganisms in different treatments. Particularly for FO3 treatment, the utilization of β-Methyl D-Glucoside, L-Asparagine acid, and glycogen by soil microorganisms was higher than other treatments and positively correlated with soil nutrients and wheat yield. (3) Compared with CK, organic fertilizer substitution treatments increased the relative abundance of Proteobacteria, Acidobacteria, and Gemmatimonadetes and decreased the relative abundance of Actinobacteria and Firmicutes. Interestingly, FO3 treatment improved the relative abundance of Nitrosovibrio, Kaistobacter, Balneimonas, Skermanella, Pseudomonas, and Burkholderia belonging to Proteobacteria and significantly boosted the relative abundance of function gene K02433 [the aspartyl-tRNA (Asn)/glutamyl-tRNA (Gln)]. Based on the abovementioned findings, we suggest FO3 as the most appropriate organic substitution method in rain-fed wheat fields.

Differential Responses of Bacterial and Fungal Communities to Siderophore Supplementation in Soil Affected by Tobacco Bacterial Wilt (Ralstonia solanacearum).

Siderophores secreted by microorganisms can promote ecological efficiency and could be used to regulate the unbalanced microbial community structure. The influence of the siderophore activity of Trichoderma yunnanense strain 2-14F2 and Beauveria pseudobassiana strain (2-8F2) on the physiological/biochemical functions and community structure of soil microbes affected by tobacco bacterial wilt (TBW) was studied. DNS Colorimetry and Biolog-eco plates were used to quantify the impacts of strain siderophores on soil enzyme activities and microbial metabolism. Based on Illumina MiSeq high-throughput sequencing, the soil 16S rDNA and ITS sequences were amplified to dissect the response characteristics of alpha/beta diversity and the structure/composition of a soil microbial community toward siderophores. The KEGG database was used to perform the PICRUSt functional prediction of the microbial community. We found that siderophores of 2-14F2 and 2-8F2, at certain concentrations, significantly increased the activities of sucrase (S-SC) and urease (S-UE) in the TBW soil and enhanced the average well color development (AWCD, carbon source utilization capacity) of the microbial community. The metabolic capacity of the diseased soil to amino acids, carbohydrates, polymers, aromatics, and carboxylic acids also increased significantly. The response of the bacterial community to siderophore active metabolites was more significant in alpha diversity, while the beta diversity of the fungal community responded more positively to siderophores. The relative abundance of Actinobacteria, Chloroflexi, and Acidobacteria increased and was accompanied by reductions in Proteobacteria and Firmicutes. LEfSe analysis showed that Pseudonocardiaceae, Gemmatimonas, Castellaniella, Chloridiumand and Acrophialophora altered the most under different concentrations of siderophore active metabolites. The PICRUSt functional prediction results showed that siderophore increased the abundance of the redox-related enzymes of the microbial community in TBW soil. The BugBase phenotypic prediction results showed that the siderophore activity could decrease the abundance of pathogenic bacteria. The study concludes that siderophore activity could decrease the abundance of pathogenic bacteria and regulate the composition of the microbial community in TBW soil. The activities of sucrase (S-SC) and urease (S-UE) in TBW soil were significantly increased. Overall, the siderophore regulation of community structures is a sustainable management strategy for soil ecosystems.

Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability.

Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, in coupling codon non-optimality to enhanced degradation, and as a translational repressor, but its functions in cells are incompletely understood. RNA-Seq analyses coupled with CAGE sequencing of all capped mRNAs revealed increased abundance of hundreds of mRNAs in dcp2Δ cells that appears to result directly from impaired decapping rather than elevated transcription. Interestingly, only a subset of mRNAs requires Dhh1 for targeting by Dcp2, and also generally requires the other decapping activators Pat1, Edc3 or Scd6; whereas most of the remaining transcripts utilize NMD factors for Dcp2-mediated turnover. Neither inefficient translation initiation nor stalled elongation appears to be a major driver of Dhh1-enhanced mRNA degradation. Surprisingly, ribosome profiling revealed that dcp2Δ confers widespread changes in relative translational efficiencies (TEs) that generally favor well-translated mRNAs. Because ribosome biogenesis is reduced while capped mRNA abundance is increased by dcp2&Delta, we propose that an increased ratio of mRNA to ribosomes increases competition among mRNAs for limiting ribosomes to favor efficiently translated mRNAs in dcp2Δ cells. Interestingly, genes involved in respiration or utilization of alternative carbon or nitrogen sources are up-regulated, and both mitochondrial function and cell filamentation are elevated in dcp2Δ cells, suggesting that decapping sculpts gene expression post-transcriptionally to fine-tune metabolic pathways and morphological transitions according to nutrient availability.

The Regulation of the Growth and Pathogenicity of Valsa mali by the Carbon Metabolism Repressor CreA.

Carbon catabolite repression (CCR) is a very important mechanism for efficient use of carbon sources in the environment and is necessary for the regulation of fungal growth, development, and pathogenesis. Although there have been extensive studies conducted regarding this mechanism in fungi, little is yet known about the effects of CreA genes on Valsa mali. However, based on the results obtained in this study for the identification of the VmCreA gene in V. mali, it was determined that the gene was expressed at all stages of fungal growth, with self-repression observed at the transcriptional level. Furthermore, the functional analysis results of the gene deletion mutants (ΔVmCreA) and complements (CTΔVmCreA) showed that the VmCreA gene played an important role in the growth, development, pathogenicity, and carbon source utilization of V. mali.

Deciphering the Impact of Induced Drought in Agriculture Soils: Changes in Microbial Community Structure, Enzymatic and Metabolic Diversity

Prolonged drought stress may have a significant impact on the structure and activity of the soil microbial community. Our study aims to investigate the impact of short-term drought (2 months) on the microbial community structure, enzymes, and metabolic diversity in four agricultural soils (Gniewkowo (G), Lulkowo (L), Wielka Nieszawka (N) and Suchatówka (S) sites) in Poland. These four types of soil were selected based on differences in their texture (gleyic luvisol Phaeozem in G (rich in clay and humus), stagnic luvisol in L, fluvisol in N and haplic luvisol in S (sandy)). We investigated the (1) number of bacteria, actinomycetes (formally phylum Actinomycetota) and fungi; (2) microbial community (16S rRNA and ITS amplicon regions); (3) biological activity by community-level physiological profiling (CLPP); (4) soil enzyme activities (dehydrogenases (DH), phosphatases (acid ACP and alkaline ALP) and urease (UR)); and (5) soil chemical properties. At the end of our experiment, we observed a significant decrease in soil moisture content with the highest in the soil from the S site. Overall, there was no change in total bacteria, but actinomycetes and fungal numbers increased after the 1st week with a decrease in moisture content. ACP activity decreased in three out of four analyzed soil samples. The exception was in sample G, where activity increased for 1–2 weeks and then decreased. ALP activity significantly increased with a decrease in moisture in the 1st week and was lowest at the end of the experiment. DH activity increased up to the 4th week in the G and N samples and up to the 2nd week in the L and S samples. UR activity showed variations in the analyzed samples. A reduction in the utilization of carbon sources (except D-mannitol and L-asparagine) was noted with the highest reduction in the G sample followed by the L, N and S samples. Thus, the pattern of changes was different depending on the analyzed soil type. The 16S rRNA and ITS amplicon sequencing revealed a decrease in the relative abundance of Pseudomonadota, Basidiomycota, Apicomplexa, and increased abundance of Actinomycetota, Bacillota and Ascomycota under prolonged drought conditions. With this, we concluded that drought conditions resulted in a significant alteration of soil microbial communities, enzyme activities, and metabolic diversity in the investigated soils.

Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum.

The mechanisms of energy generation and carbon-source utilization in the syphilis spirochete Treponema pallidum have remained enigmatic despite complete genomic sequence information. Whereas the bacterium harbors enzymes for glycolysis, the apparatus for more efficient use of glucose catabolites, namely the citric-acid cycle, is apparently not present. Yet, the organism's energy needs likely exceed the modest output from glycolysis alone. Recently, building on our structure-function studies of T. pallidum lipoproteins, we proposed a "flavin-centric" metabolic lifestyle for the organism that partially resolves this conundrum. As a part of the hypothesis, we have proposed that T. pallidum contains an acetogenic energy-conservation pathway that catabolizes D-lactate, yielding acetate, reducing equivalents for the generation and maintenance of chemiosmotic potential, and ATP. We already have confirmed the D-lactate dehydrogenase activity in T. pallidum necessary for this pathway to operate. In the current study, we focused on another enzyme ostensibly involved in treponemal acetogenesis, phosphotransacetylase (Pta). This enzyme is putatively identified as TP0094 and, in this study, we determined a high-resolution (1.95 Å) X-ray crystal structure of the protein, finding that its fold comports with other known Pta enzymes. Further studies on its solution behavior and enzyme activity confirmed that it has the properties of a Pta. These results are consistent with the proposed acetogenesis pathway in T. pallidum, and we propose that the protein be referred to henceforth as TpPta.

Biological control of Fusarium-wilt and quality improvement of Sesamum indicum cv. ST-1 using fluorescent Pseudomonas

Seven plant growth-promoting bacterial strains (LES1-LES7) were isolated from rhizosphere of Lycoperscion esculentum Mill. (Tomato) and further screened based on colony morphology, carbon source utilization and biochemically characterized as fluorescent Pseudomonads. Among the isolates prominent strain identified as Pseudomonas aeruginosa LES4 produced maximum siderophores in vitro besides indole acetic acid, hydrocyanic acid, solubilized insoluble inorganic phosphate and secreted β-1, 3-glucanase urease and chitin solubilizing enzymes chitinase. It also exhibited a strong antagonism against Fusarium oxysporum f.sp. sesami when co-cultured on nutrient agar medium and inhibiting the growth of the pathogen by 69% after 5 days incubation at 28 ± 1°C. Sesame (Sesamum indicum L. cv. ST-1). When surface sterilized seeds bacterized with P. aeruginosa LES4 showed enhancement in seedling sprouting early vegetative growth, and increased seed yield components viz. biomass accumulation, and all other yield and quality improving components. Strain LES4 significantly reduced the wilt disease of sesame in F. oxysporum f.sp. sesami-infested soil. Moreover, Tn5 induced streptomycin resistant trans-conjugants of spontaneous tetracycline-resistant LES4 (designated LES4tetra+strep+) used to exhibit efficient rhizosphere colonization of sesame. Such properties of fluorescent P. aeruginosa LES4 prove it as a beneficial and potential microbial agent against wilt causing sesame.

Effects of the Transformation from Natural Alpine Grassland to Mixed Artificial Grassland on the Characteristics of Soil Microbial Community

This study aimed to analyze the effects of the transformation from natural alpine grassland (NAG) to mixed artificial grassland (MAG) on the characteristics of soil microbial community. We used Illumina Miseq high-throughput sequencing technology to investigate the soil microbial community of natural grassland and mixed artificial grassland. The results showed that plant diversity and the content of soil organic matter decreased significantly from NAG to MAG. In total, 29 and 11 phyla bacteria and fungi were detected, respectively. Compared with that in NAG, the Shannon indexes of the bacterial community increased significantly in MAG (from 9.51 to 9.89), whereas these differences were not significant between the NAG and MAG fungal community. The structure and composition of the soil microbial community showed significant differences between NAG and MAG. In addition, Mantel test results suggested that soil total organic matter, total nitrogen, and soil moisture were significantly correlated with variations in the bacterial community, and soil total organic matter and soil moisture were significantly correlated with variations in fungal community. The results of linear discriminant analysis (LEfSe) indicated that Atribacteria and Ascomycota microorganisms could be considered as the indicator groups for NAG, whereas Gemmata and Trichocomaceae microorganisms could be considered as the indicator groups for MAG. Tax4Fun2 results showed that the transition from NAG to MAG affected the utilization of different carbon sources by bacteria.

Polyphasic characterization of rhizobial isolates obtained from different common bean-producing regions

In Brazil, the common bean is a crop with significant social and economic importance. The prospecting of N2 fixing bacteria is crucial since biological nitrogen fixation (BNF) is an eco-friendly technique. This work aimed to obtain and characterize rhizobium isolates based on morpho-physiological, molecular, and symbiotic efficiency parameters, using the strains SEMIA 4077, SEMIA 4080, and SEMIA 4088 as references. The characteristics of the isolates and colonies, their tolerance to salinity and temperature, as well as their utilization of carbon sources, served as the basis for the morpho-physiological characterization. BOX-PCR, REP-PCR, and ERIC-PCR markers were used for genotypic characterization. Assessment of the symbiotic efficiency was carried out in a greenhouse, determining the number of nodules (NN), nodule dry weight (NDW), shoot dry weight (SDW), and total-N (Total-N) accumulation in the shoot. Among the isolates, those exhibiting: neutral culture medium pH, fast growth, colony diameter <2 mm, opaque transparency, homogeneous appearance, and cream color were predominant. Compared to temperature, salinity was the most restrictive factor to the growth of the isolates. Most of the isolates grew on sucrose (88.43%) and mannitol (87.28%). Genotypic analysis revealed that 90% of the isolates clustered in the same group as the reference strain SEMIA 4080. The TaMsG2R1 and BaDeG4R2 isolates showed higher Total-N in the shoot than the reference strains and should be evaluated in future studies under field conditions.

Long-term hypoxia exposure impairs metabolic pathways of de novo lipogenesis in young mouse adipocytes

Introduction: Obstructive sleep apnea syndrome, manifested by tissue hypoxia, is causally linked with the development of metabolic diseases such as Type 2 diabetes. Although there is convincing epidemiological evidence, molecular mechanisms mediating the adverse metabolic effects remain unclear. Hypoxia may play an important role and modulate metabolic pathways in young adipocytes including the utilization of glucose and acetate or the activation of the reverse tricarboxylic acid cycle (rTCA) leading to increase de novo lipogenesis and excessive fat accumulation. The aim of this study was to investigate the impact of long-term hypoxia on important pathways of de novo lipogenesis in mouse early and late adipocytes. Hypothesis: Hypoxia affects the utilization of carbon sources for de novo lipogenesis differently in early and late adipocytes. Methods: Mouse 3T3-L1 cells were differentiated into adipocytes for 7 days - early adipocytes (EA) or 14 days - late adipocytes (LA). The cells were cultured in gas-permeable cultureware allowing exposure to sustained oxygen levels of 21% O 2 or 4% O 2 . [ 13 C-5]-glutamine (2.5mM) was added to culture media for 7 and 14 days to assess 13 C incorporation to newly synthesized lipids via rTCA and [ 13 C-1]-glutamine (2.5mM) was added to media for 24h to assess 13 C incorporation to rTCA metabolites. The 13 C incorporation studies were analyzed via gas chromatography-mass spectrometry. The contribution of glucose and acetate to de novo lipogenesis was assessed using [ 14 C]-glucose and [ 14 C]-acetate (both 0.2 μCi) provided in culture media for 2h at the end of experiments. Subsequently, radioactivity in extracted lipids was measured via scintillation counter. Statistical significance was assessed by 2-way ANOVA followed by Tukey's test. Data are presented as means ± SD, N=9. Data Hypoxia had no effect on lipid accumulation in EA, lipid accumulation in LA was increased by 134,41% vs control. The 13 C incorporation to lipids was increased in EA by 42,2% vs control and by 13,33% vs LA. The 13 C incorporation in citrate was increased by 8,71%, in malate by 9,58% in EA vs control, in LA the incorporation remained unchanged. The [ 14 C]-glucose incorporation to lipids was elevated in EA vs control by 209,98% and EA vs LA by 60,02%. The [ 14 C]-acetate incorporation to lipids was increased in EA by 198,43% vs control and decreased by 45,13% vs LA. Differences are statistically significant (p <0.05). Summary: The effect of hypoxia on lipid accumulation was observed at the late stages of adipocyte maturation. However, in EA hypoxia initially stimulated the activation of rTCA to partially contribute to de novo lipogenesis and significantly increased 14 C-glucose incorporation. In LA the rTCA and 14 C-glucose incorporation were reduced to the control level and the contribution of acetate was increased. Conclusion: Hypoxia modified metabolic pathways in maturating adipocytes leading to increased de novo lipogenesis and thus hypertrophic mature adipocytes. Project was supported by Grant Agency of the Charles University project GAUK 294822 and by grant AZV project NU21-01-00259 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Contrasting response strategies of microbial functional traits to polycyclic aromatic hydrocarbons contamination under aerobic and anaerobic conditions

PAHs (Polycyclic aromatic hydrocarbons) are widely distributed in soil ecosystems, but our knowledge regarding the impacts of PAHs effects on soil microbial functional traits is limited. In this study, we evaluated the response and regulating strategies of microbial functional traits that are associated with the typical C, N, P, S cycling processes in a pristine soil under aerobic and anaerobic conditions after the addition of PAHs. Results revealed that indigenous microorganisms had strong degradation potential and adaptability to PAHs especially under aerobic conditions, while anaerobic conditions favored the degradation of high molecular weight PAHs. PAHs exhibited contrasting effects on soil microbial functional traits under different aeration conditions. It would probably change microbial carbon source utilization preference, stimulate inorganic P solubilization and strengthen the functional interactions between soil microorganisms under aerobic conditions, while might cause the increase of H2S and CH4 emissions under anaerobic conditions. This research provides an effective theoretical support for the ecological risk assessment of soil PAHs pollution.

Effects of Pruning on Tea Tree Growth, Soil Enzyme Activity and Microbial Diversity

In order to investigate the effect of pruning on the soil environment in which tea trees grow and the growth of tea trees, this study used Wuyi Meizhan (Camellia sinensis) as a research object and measured its growth indexes, soil physicochemical indexes, soil enzyme activity and microbial functional diversity to analyze the effects of pruning treatments on the growth of tea trees, soil enzyme activity and soil microbial functional diversity and the correlation between them. The results of the analysis of tea tree growth indexes showed that the hundred-bud weight, leaf area and yield in the pruning treatment were significantly higher than those in the unpruned treatment. The results of soil physicochemical index analysis showed that pH, available phosphorus, available potassium and organic matter were significantly higher in the pruning treatment than in the unpruned treatment (p < 0.05), while available nitrogen and total phosphorus were significantly lower than in unpruned treatment (p < 0.05). The results of soil enzyme activities showed that only polyphenol oxidase and catalase activities were significantly higher in the pruning than in the unpruned treatment, while urease, protease, acid phosphatase, asparaginase and glutaminase activities were significantly lower than in the unpruned treatment (p < 0.05). Biolog analysis showed that the utilization of microbial carbon sources, especially amino acid and amine, increased in the rhizosphere soil of the pruned tea tree, while there was a significant decrease (p < 0.05) in microbial diversity. It is evident that pruning promoted tea tree growth and some enzyme activity, while inhibiting the activity of enzymes associated with the nitrogen cycle, and the utilization of microbial carbon sources increased, but their diversity decreased. This study provides a theoretical basis for the daily management of tea plantation after pruning.

Lipid Accumulation by Snf-β Engineered Mucor circinelloides Strains on Glucose and Xylose.

Sucrose non-fermenting 1 (SNF1) protein kinase plays the regulatory roles in the utilization of selective carbon sources and lipid metabolism. Previously, the role of β subunit of SNF1 in lipid accumulation was evaluated by overexpression and knockout of Snf-β in oleaginous fungus M. circinelloides. In the present study, the growth and lipid accumulation of Snf-β overexpression and knockout strains were further analyzed and compared with glucose or xylose as a single or mixed carbon sources. The results showed that the lipid contents in Snf-β knockout strain improved by 23.2% (for glucose), 28.4% (for xylose), and 30.5% (for mixed glucose and xylose) compared with that of the control strain, respectively. The deletion of Snf-β subunit also altered the transcriptional level of acetyl-CoA carboxylase (ACC). The highest transcriptional levels of ACC1 in Snf-β knockout strain at 24h were increased by 2.4-fold (for glucose), 2.8-fold (for xylose), and 3.1-fold (for mixed glucose and xylose) compared with that of the control strain, respectively. Our results indicated that Snf-β subunit enhanced lipid accumulation through the regulation of ACC1 in response to xylose or mixed sugars of glucose and xylose more significantly than that of response to glucose. This is the first study to explore the effect of Snf-β subunit of M. circinelloides in regulating lipid accumulation responding to different carbon nutrient signals of glucose and xylose. This study provides a foundation for the future application of the Snf-β engineered strains in lipid production from lignocellulose.

Taxonomic, metabolic traits and species description of aromatic compound degrading Indian soil bacterium Pseudomonas bharatica CSV86T

A soil bacterium, strain CSV86T isolated from a petrol station in Bangalore, India displays a unique carbon source utilization hierarchy with preferential utilization of various genotoxic aromatic compounds over glucose. Cells were Gram-negative, motile rods, oxidase- and catalase-positive. Strain CSV86T possess a 6.79 Mb genome with 62.72 G + C mol%. 16S rRNA gene phylogeny relates strain CSV86T to the genus Pseudomonas, with highest similarity to Pseudomonas japonica WLT (99.38%). Multi-locus sequence analyses of gyrB-rpoB-rpoD-recA and 33 ribosomal proteins (rps) displayed overall low similarities to its phylogenetic relatives with poor similarity score (6%). Average nucleotide identity (ANI) and in-silico DNA-DNA hybridization (DDH) showed poor (87.11% and 33.2%, respectively) genomic relatedness of strain CSV86T to its closest relatives, indicating genomic distinctiveness. The major cellular fatty acids were 16:0, 17:0cyclo, summed-feature-3 (16:1ω7c/16:1ω6c) and −8 (18:1ω7c). Further, differential abundance of 12:0, 10:0 3-OH and 12:0 3-OH and phenotypic differences distinguished strain CSV86T from closest relatives, hence designated as Pseudomonas bharatica. The unique aromatic degradation ability, resistance to heavy metals, efficient nitrogen-sulfur assimilation, beneficial eco-physiological traits (production of indole acetic acid, siderophore and fusaric acid efflux) and plasmid-free genome suggest strain CSV86T to be a model organism for bioremediation and ideal host for metabolic engineering.

Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria.

Methylotrophic bacteria are widely distributed in nature and can be applied in bioconversion because of their ability to use one-carbon source. The aim of this study was to investigate the mechanism underlying utilization of high methanol content and other carbon sources by Methylorubrum rhodesianum strain MB200 via comparative genomics and analysis of carbon metabolism pathway. The genomic analysis revealed that the strain MB200 had a genome size of 5.7 Mb and two plasmids. Its genome was presented and compared with that of the 25 fully sequenced strains of Methylobacterium genus. Comparative genomics revealed that the Methylorubrum strains had closer collinearity, more shared orthogroups, and more conservative MDH cluster. The transcriptome analysis of the strain MB200 in the presence of various carbon sources revealed that a battery of genes was involved in the methanol metabolism. These genes are involved in the following functions: carbon fixation, electron transfer chain, ATP energy release, and resistance to oxidation. Particularly, the central carbon metabolism pathway of the strain MB200 was reconstructed to reflect the possible reality of the carbon metabolism, including ethanol metabolism. Partial propionate metabolism involved in ethyl malonyl-CoA (EMC) pathway might help to relieve the restriction of the serine cycle. In addition, the glycine cleavage system (GCS) was observed to participate in the central carbon metabolism pathway. The study revealed the coordination of several metabolic pathways, where various carbon sources could induce associated metabolic pathways. To the best of our knowledge, this is the first study providing a more comprehensive understanding of the central carbon metabolism in Methylorubrum. This study provided a reference for potential synthetic and industrial applications of this genus and its use as chassis cells.

Pseudomonas isolates from raw milk with high level proteolytic activity display reduced carbon substrate utilization and higher levels of antibiotic resistance

Milk is an ideal food but can be easily contaminated during milking, transportation and storage by Pseudomonas spp. That secrete proteases resulting in milk spoilage. However, genomic features and functional metabolic diversity of Pseudomonas with different protease activity have not been extensively studied. With this aim, the genomic features and functional metabolic diversity of Pseudomonas with differing proteolytic activity were evaluated using whole genome sequencing and metabolomic approaches, respectively as well as, the presence of genes encoding the aprX protease and antibiotic resistance were screened. Pseudomonas strains with higher protease activity possessed more carbohydrate transport and metabolism, signal transduction, secondary metabolite synthesis, polysaccharide lyase and carbohydrate esterase genes. These isolates were more efficient at carbon source utilization and this phenotype was positively related to incubation temperature. The high protease activity group also displayed a multidrug resistance index that was significantly higher than that for the low protease activity group. This is the first report comparing the gene function and metabolic diversity of Pseudomonas with differing levels of proteolytic activity in raw milk.

New Insights on Metabolic Features of Bacillus subtilis Based on Multistrain Genome-Scale Metabolic Modeling.

Bacillus subtilis is an effective workhorse for the production of many industrial products. The high interest aroused by B. subtilis has guided a large metabolic modeling effort of this species. Genome-scale metabolic models (GEMs) are powerful tools for predicting the metabolic capabilities of a given organism. However, high-quality GEMs are required in order to provide accurate predictions. In this work, we construct a high-quality, mostly manually curated genome-scale model for B. subtilis (iBB1018). The model was validated by means of growth performance and carbon flux distribution and provided significantly more accurate predictions than previous models. iBB1018 was able to predict carbon source utilization with great accuracy while identifying up to 28 metabolites as potential novel carbon sources. The constructed model was further used as a tool for the construction of the panphenome of B. subtilis as a species, by means of multistrain genome-scale reconstruction. The panphenome space was defined in the context of 183 GEMs representative of 183 B. subtilis strains and the array of carbon sources sustaining growth. Our analysis highlights the large metabolic versatility of the species and the important role of the accessory metabolism as a driver of the panphenome, at a species level.

Effects of Plant-Growth-Promoting Rhizobacteria on Soil Bacterial Community, Soil Physicochemical Properties, and Soil Enzyme Activities in the Rhizosphere of Alfalfa under Field Conditions

Background: Inoculation with plant-growth-promoting rhizobacteria (PGPR) effectively increases plant growth in agriculture. However, the role of the rhizobiome in plant growth remains unclear. Methods: Biolog Ecoplate and 16S rRNA gene high-throughput sequencing techniques were used to analyze the changes in microbial community diversity, composition, and function after PGPR inoculation. Soil physicochemical and enzyme activities were also measured. Results: PGPR inoculation significantly promoted the growth of alfalfa. Using a Biolog Ecoplate, inoculation improved the metabolic activity and carbon source utilization of soil microorganisms. PGPR inoculation significantly increased the diversity and richness of the soil bacterial community in the rhizosphere of alfalfa and increased the relative abundance of key bacterial taxa such as Arthrobacter, Sphingomonas, and Bacillus, which are conducive to plant growth. Conclusions: Inoculation with PGPR enriched bacterial taxa and improved the utilization of carbon sources beneficial for plant growth. PGPR inoculation induced changes in microbial community diversity, and relevant functions in the rhizosphere contributed to alfalfa growth under field conditions.