Carbohydrate Metabolism Genes Research Articles

Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms

Carbohydrates play a pivotal role in nutrient recycling and regulation of algal–bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified—glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)—were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation—observed distinctly in specific genera—highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.

Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna

The cladoceran crustacean Daphnia exhibits phenotypic plasticity, a phenomenon that leads to diverse phenotypes from one genome. Alternative usage of gene isoforms has been considered a key gene regulation mechanism for controlling different phenotypes. However, to understand the phenotypic plasticity of Daphnia, gene isoforms have not been comprehensively analyzed. Here we identified 25,654 transcripts derived from the 9710 genes expressed during environmental sex determination of Daphnia magna using the long-read RNA-Seq with PacBio Iso-Seq. We found that 14,924 transcripts were previously unidentified and 5713 genes produced two or more isoforms. By a combination of Illumina short-read RNA-Seq, we detected 824 genes that implemented switching of the highest expressed isoform between females and males. Among the 824 genes, we found isoform switching of an ortholog of CREB-regulated transcription coactivator, a major regulator of carbohydrate metabolism in animals, and a correlation of this switching event with the sexually dimorphic expression of carbohydrate metabolic genes. These results suggest that a comprehensive catalog of isoforms may lead to understanding the molecular basis for environmental sex determination of Daphnia. We also infer the applicability of the full-length isoform analyses to the elucidation of phenotypic plasticity in Daphnia.

Hsp70 Knockdown in the Brine Shrimp Artemia franciscana: Implication on Reproduction, Immune Response and Embryonic Cuticular Structure.

The potential functional role(s) of heat shock protein 70 (Hsp70) in the brine shrimp, Artemia franciscana, a crucial crustacean species for aquaculture and stress response studies, was investigated in this study. Though we have previously reported that Hsp70 knockdown may have little or no impact on Artemia development, the gestational survival and number of offspring released by adult females were impaired by obscuring Hsp70 synthesis. Transcriptomic analysis revealed that several cuticle and chitin synthetic genes were downregulated, and carbohydrate metabolic genes were differentially expressed in Hsp70-knockdown individuals. A more comprehensive microscopic examination performed in this study revealed exoskeleton structural destruction and abnormal eye lenses featured in Hsp70-deficient adult females 48h after Hsp70 dsRNA injection. Cysts produced by these Hsp70-deficient broods, instead, had a defective shell and were smaller in size, whereas nauplii had shorter first antennae and a rougher body epicuticle surface. Changes in carbohydrate metabolism caused by Hsp70 knockdown affected glycogen levels in adult Artemia females, as well as trehalose in cysts released from these broods, indicating that Hsp70 may play a role in energy storage preservation. Outcomes from this work provided novel insights into the roles of Hsp70 in Artemia reproduction performance, cyst formation, and exoskeleton structure preservation. The findings also support our previous observation that Hsp70 knockdown reduced Artemia nauplius tolerance to bacterial pathogens, which could be explained by the fact that loss of Hsp70 downregulated several Toll receptor genes (NT1 and Spaetzle) and reduced the integrity of the exoskeleton, allowing pathogens to enter and cause infection, ultimately resulting in mortality.

The Genome of Bifidobacterium longum subsp. infantis YLGB-1496 Provides Insights into Its Carbohydrate Utilization and Genetic Stability.

Bifidobacterium longum subsp. infantis YLGB-1496 (YLGB-1496) is a probiotic strain isolated from human breast milk. The application of YLGB-1496 is influenced by carbohydrate utilization and genetic stability. This study used genome sequencing and morphology during continuous subculture to determine the carbohydrate utilization characteristics and genetic stability of YLGB-1496. The complete genome sequence of YLGB-1496 consists of 2,758,242 base pairs, 2442 coding sequences, and a GC content of 59.87%. A comparison of carbohydrate transport and metabolism genes of Bifidobacterium longum subsp. infantis (B. infantis) showed that YLGB-1496 was rich in glycosyl hydrolase 13, 20, 25, and 109 gene families. During continuous subculture, the growth characteristics and fermentation activity of the strain were highly stable. The bacterial cell surface and edges of the 1000th-generation strains were progressively smoother and well-defined, with no perforations or breaks in the cell wall. There were 20 SNP loci at the 1000th generation, fulfilling the requirement of belonging to the same strain. The presence of genes associated with cell adhesion and the absence of resistance genes supported the probiotic characteristics of the strain. The data obtained in this study provide insights into broad-spectrum carbohydrate utilization, genomic stability, and probiotic properties of YLGB-1496, which provide theoretical support to promote the use of YLGB-1496.

Metagenome reveals the possible mechanism that microbial strains promote methanogenesis during anaerobic digestion of food waste

For better understanding the mechanism of microbial strains promoting methane production, four strains Hungatella xylanolytica A5, Bacillus licheniformis B1, Paraclostridium benzoelyticum C2 and Advenella faeciporci E1 were inoculated into anaerobic digestion systems. After bioaugmentation, the cumulative methane production of A5, B1, C2 and E1 groups elevated by 11.68%, 8.20%, 18.21% and 15.67% compared to CK group, respectively. The metagenomic analysis revealed that the species diversity and uniformity of the experimental groups was improved, and hydrolytic acidifying bacteria, represented by Clostridiaceae, Anaerolineaceae and Oscillospiraceae, and methanogens, such as Methanotrichaceae and Methanobacteriaceae, were enriched. Meanwhile, the abundance of key genes in carbohydrate, pyruvate and methane metabolism was increased in the inoculated groups, providing reasonable reasons for more methane production. The strengthening mechanism of microbial strains in this study offered a theoretical foundation for selecting a suitable bioaugmentation strategy to solve the problems of slow start-up and low methane production in anaerobic digestion.

Identification and characterization of the TetR family transcriptional regulator NffT in Rhizobium johnstonii.

Symbiotic nitrogen fixation (SNF) by rhizobia is not only the main natural bionitrogen-source for organisms but also a green process leveraged to increase the fertility of soil for agricultural production. However, an insufficient understanding of the regulatory mechanism of SNF hinders its practical application. During SNF, nifA-fixA signaling is essential for the biosynthesis of nitrogenases and electron transfer chain proteins. In the present study, the TetR regulator NffT, whose mutation increased fixA expression, was discovered through a fixA-promoter-β-glucuronidase fusion assay performed with Rhizobium johnstonii. Real-time quantitative PCR analysis showed that nffT deletion increased the expression of symbiotic genes including nifA and fixA in nifA-fixA signaling, and fixL, fixK, fnrN, and fixN9 in fixL-fixN signaling. nffT overexpression resulted in disordered nodules and reduced nitrogen-fixing efficiency. Electrophoretic mobility shift assays revealed that NffT directly regulated the transcription of RL0091-93, which encode an ATP-binding ABC transporter predicted to be involved in carbohydrate transport. Purified His-tagged NffT bound to a 68 bp DNA sequence located -32 to -99 bp upstream of RL0091-93 and NffT deletion significantly increased the expression of RL0091-93. nffT-promoter-β-glucuronidase fusion assay indicated that nffT expression was regulated by the cobNTS genes and cobalamin. Mutations in cobNTS significantly decreased the expression of nffT, and cobalamin restored its expression. These results revealed that NffT affects nodule development and nitrogen-fixing reaction by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes and, thus, plays a pivotal regulatory role during symbiosis of R. johnstonii-Pisum sativum.IMPORTANCESymbiotic nitrogen fixation (SNF) by rhizobia is a green way to maintain soil fertility without causing environmental pollution or consuming chemical energy. A detailed understanding of the regulatory mechanism of this complex process is essential for promoting sustainable agriculture. In this study, we discovered the TetR-type regulator NffT, which suppressed the expression of fixA in Rhizobium johnstonii. Furthermore, NffT was confirmed to play pleiotropic roles in R. johnstonii-Pisum sativum symbiosis; specifically, it inhibited rhizobial growth, nodule differentiation, and nitrogen-fixing reactions. We revealed that NffT indirectly affected R. johnstonii-P. sativum symbiosis by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes. Furthermore, cobalamin, a chemical molecule, was reported for the first time to be involved in TetR-type protein transcription during symbiosis. Thus, NffT identification connects SNF regulation with genetic, metabolic, and chemical signals and provides new insights into the complex regulation of SNF, laying an experimental basis for the targeted construction of rhizobial strains with highly efficient nitrogen-fixing capacity.

Humic acid biosynthesis and bacterial community evolution during aerobic composting of rice straw

In this study, the effects of inoculum ratio, substrate particle size and aeration rate on humic acid (HA) biosynthesis during aerobic composting of rice straw were investigated, respectively. The contents of total organic carbon, total nitrogen and HA, as well as lignocellulose degradation in the composting were evaluated, respectively. It is found that the maximal HA yield of 356.9 g kg−1 was obtained at an inoculum ratio of 20%, a substrate particle size of 0.83 mm and an aeration rate of 0.3 L·kg−1 DM min−1 in the process of composting. The changes of microbial communities and metabolic functions at different stages of the composting were also analyzed through high-throughput sequencing. The result demonstrates that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the dominant phyla and their relative abundance significantly varied over time (p < 0.05), and Rhizobium, Phenylobacterium, Pseudoxanthomonas and Paenibacillus were positively related to HA content in the compost. Furthermore, the metabolic function profiles of bacterial community indicate that these functional genes in carbohydrate metabolism and amino acid metabolism were involved in lignocellulose biodegradation and HA biosynthesis. This work may be conducive to explore new regulation strategy to improve bioconversion efficiency of agricultural residues to applicable biofertilizers.Key points• Temperature, pH, TOC, TN and C/N caused a great influence on humic acids synthesis• The succession of the microbial community during the composting were evaluated• The metabolisms of carbohydrate and amino acids were involved in HA synthesisGraphical abstract

Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov

IntroductionPectobacterium cacticida was identified as the causative agent of soft rot disease in cacti. Due to a high potential of spread in the face of global warming, the species poses a significant threat to horticultural and crop industry. The aim of this study was to revise the genomic, physiology and virulence characteristics of P. cacticida and update its phylogenetic position within the Pectobacterium genus.MethodsWhole genome sequences of five P. cacticida strains were obtained and subjected to comprehensive genomic and phylogenomic data analyses. We assessed the presence of virulence determinants and genes associated with host and environmental adaptation. Lipidomic analysis, as well as biochemical and phenotypic assays were performed to correlate genomic findings.ResultsPhylogenomic analysis revealed that P. cacticida forms a distinct lineage within the Pectobacterium genus. Genomic evaluation uncovered 516 unique proteins, most of which were involved in cellular metabolism. They included genes of carbohydrate metabolism and transport and ABC transporters. The main differing characteristics from other Pectobacterium species were the lack of a myo-inositol degradation pathway and the presence of the malonate decarboxylase gene. All tested strains were pathogenic towards Opuntia spp., chicory, Chinese cabbage, and potato, but exhibited only mild pathogenicity towards carrot.DiscussionThis study sheds light into the genomic characteristics of P. cacticida and highlights the pathogenic potential of the species. Unique genes found in P. cacticida genomes possibly enhance the species’ survival and virulence. Based on phylogenomic analyses, we propose the reclassification of P. cacticida to a new genus, Alcorniella comb. nov.

Ecological relevance of flagellar motility in soil bacterial communities.

Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.

Coastal upwelling systems as dynamic mosaics of bacterioplankton functional specialization

Coastal upwelling areas are extraordinarily productive environments where prokaryotic communities, the principal remineralizers of dissolved organic matter (DOM), rapidly respond to phytoplankton bloom and decay dynamics. Nevertheless, the extent of variability of key microbial functions in such dynamic waters remains largely unconstrained. Our metatranscriptomics analyses of 162 marker genes encoding ecologically relevant prokaryotic functions showed distinct spatial-temporal patterns in the NW Iberian Peninsula upwelling area. Short-term (daily) changes in specific bacterial functions associated with changes in biotic and abiotic factors were superimposed on seasonal variability. Taxonomic and functional specialization of prokaryotic communities, based mostly on different resource acquisition strategies, was observed. Our results uncovered the potential influence of prokaryotic functioning on phytoplankton bloom composition and development (e.g., Cellvibrionales and Flavobacteriales increased relative gene expression related to vitamin B12 and siderophore metabolisms during Chaetoceros and Dinophyceae summer blooms). Notably, bacterial adjustments to C- or N-limitation and DMSP availability during summer phytoplankton blooms and different spatial-temporal patterns of variability in the expression of genes with different phosphate affinity indicated a complex role of resource availability in structuring bacterial communities in this upwelling system. Also, a crucial role of Cellvibrionales in the degradation of DOM (carbohydrate metabolism, TCA cycle, proteorhodopsin, ammonium, and phosphate uptake genes) during the summer phytoplankton bloom was found. Overall, this dataset revealed an intertwined mosaic of microbial interactions and nutrient utilization patterns along a spatial-temporal gradient that needs to be considered if we aim to understand the biogeochemical processes in some of the most productive ecosystems in the world´s oceans.

Disorders of carbohydrate metabolism and candidate genes for the pathophysiology of polycystic ovary syndrome. A literature review

Polycystic ovary syndrome is a common heterogeneous disease with metabolic disorders. In the last decade, the study of polycystic ovary syndrome pathogenesis has been associated with the modern development of molecular genetics, transcriptomics, and sequencing methods. Numerous studies have shown that the study of genetic markers and epigenetic changes in metabolic disorders, oxidative stress, chronic inflammation, and mitochondrial dysfunction in polycystic ovary syndrome is an important direction in the pathogenesis and etiology of the disease. The aim of this literature review was to describe candidate genes involved in the pathophysiology of polycystic ovary syndrome and associated with disorders of carbohydrate metabolism according to modern domestic and foreign literature over the past five years. The candidate gene data presented were assessed based on the main aspects of polycystic ovary syndrome pathophysiology, namely, metabolic dysfunction, androgen and gonadotropin imbalance, and inflammation. The insulin genes (variable number of tandem repeats), such as INS-VNTR, IRS-1, IRS-2, and INSR, adiponectin and calpain-10 genes, as well as CY1A1, CYP11A1, PON1, DENND1A and TCF7L2 genes are associated with metabolic disorders in polycystic ovary syndrome. Genetic variants of genes involved in regulating the expression and mechanism of action of insulin, as well as its receptors and substrates (IRS-1, IRS-2, INSR), have been suggested as possible factors involved in the development and severity of the clinical and metabolic manifestations of polycystic ovary syndrome. The presented data on PPARγ gene (and its coactivator PGC-1α) expression levels in women with polycystic ovary syndrome revealed the presence of PPARγ gene polymorphisms associated with insulin resistance. Thus, the data presented in this review from genome-wide association studies (GWAS) and the study of candidate genes showed that numerous pleiotropic effects cause carbohydrate metabolism disorders in polycystic ovary syndrome. The study of genetic markers and epigenetic changes in the development of metabolic disorders, oxidative stress, chronic inflammation, and mitochondrial dysfunction in polycystic ovary syndrome is an important direction in the pathogenesis of the disease.

Transcriptional plasticity of schizotrophic Sclerotinia sclerotiorum responds to symptomatic rapeseed and endophytic wheat hosts.

Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, is also a reciprocal endophytic fungus in monocot plants. However, it is unclear how it responds to two distinct plants. Comparative transcriptomic analyses uncovered a network rewiring, with 14.1% up-differentially expressed genes overlapping upon colonizing the endophytic host wheat and a symptomatic host rapeseed. The divergent transcript of genes originating from host-specific induction is central to infection and colonization, including genes related to appressorium, oxalic acid, carbohydrate-active enzymes, and effector-like proteins. We confirmed that appressorium is required for S. sclerotiorum during colonization in symptomatic hosts but not in endophytic wheat via the observation of the infection process of ΔSs-caf1, a compound appressorium formation-defective mutant with hypovirulence to symptomatic hosts. SS1G_10617 and SS1G_13809 are components of the starch degradation pathways. ΔSS1G_10617 displayed lower virulence on symptomatic host plants and abnormal endophytic growth on wheat, and ΔSS1G_13809 only showed an abnormal symbiotic relationship with wheat, implying that starch may be the major carbon source for S. sclerotiorum in the symbiosis with wheat. Our results herein suggest that S. sclerotiorum modulates biphasic colonization via a divergent transcriptional landscape. This study contributes to a better understanding of schizotrophic fungi and provides new clues for cultivating disease-resistant varieties and adjusting reasonable farming strategies. IMPORTANCE The broad host range of fungi with differential fungal responses leads to either a pathogenic or an endophytic lifestyle in various host plants. Yet, the molecular basis of schizotrophic fungal responses to different plant hosts remains unexplored. Here, we observed a general increase in the gene expression of S. sclerotiorum associated with pathogenicity in symptomatic rapeseed, including small protein secretion, appressorial formation, and oxalic acid toxin production. Conversely, in wheat, many carbohydrate metabolism and transport-associated genes were induced, indicating a general increase in processes associated with carbohydrate acquisition. Appressorium is required for S. sclerotiorum during colonization in symptomatic hosts but not in endophytic wheat. These findings provide new clues for understanding schizotrophic fungi, fungal evolution, and the emergence pathways of new plant diseases.

Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract.

Extra-intestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multidrug resistance (MDR) is not uniform across the phylogenetic spectrum of E. coli. Instead, AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model, we demonstrate that an MDR E. coli ST131 is capable of out-competing and displacing non-MDR E. coli from the gut in vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E. coli strains, challenge with MDR E. coli either by oral gavage or co-housing with MDR E. coli colonised mice results in displacement and dominant intestinal colonisation by MDR E. coli ST131. To investigate the genetic basis of this superior gut colonisation ability by MDR E. coli, we assayed the metabolic capabilities of our strains using a Biolog phenotypic microarray revealing altered carbon metabolism. Functional pangenomic analysis of 19,571 E. coli genomes revealed that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E. coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E. coli via carriage and spread.

The Effects of Rhizophagus irregularis Inoculation on Transcriptome of Medicago lupulina Leaves at Early Vegetative and Flowering Stages of Plant Development.

The study is aimed at revealing the effects of Rhizophagus irregularis inoculation on the transcriptome of Medicago lupulina leaves at the early (second leaf formation) and later (flowering) stages of plant development. A pot experiment was conducted under conditions of low phosphorus (P) level in the substrate. M. lupulina plants were characterized by high mycorrhizal growth response and mycorrhization parameters. Library sequencing was performed on the Illumina HiseqXTen platform. Significant changes in the expression of 4863 (padj < 0.01) genes from 34049 functionally annotated genes were shown by Massive Analysis of cDNA Ends (MACE-Seq). GO enrichment analysis using the Kolmogorov-Smirnov test was performed, and 244 functional GO groups were identified, including genes contributing to the development of effective AM symbiosis. The Mercator online tool was used to assign functional classes of differentially expressed genes (DEGs). The early stage was characterized by the presence of six functional classes that included only upregulated GO groups, such as genes of carbohydrate metabolism, cellular respiration, nutrient uptake, photosynthesis, protein biosynthesis, and solute transport. At the later stage (flowering), the number of stimulated GO groups was reduced to photosynthesis and protein biosynthesis. All DEGs of the GO:0016036 group were downregulated because AM plants had higher resistance to phosphate starvation. For the first time, the upregulation of genes encoding thioredoxin in AM plant leaves was shown. It was supposed to reduce ROS level and thus, consequently, enhance the mechanisms of antioxidant protection in M. lupulina plants under conditions of low phosphorus level. Taken together, the obtained results indicate genes that are the most important for the effective symbiosis with M. lupulina and might be engaged in other plant species.

Short-term warming-induced increase in non-microbial carbon emissions from semiarid abandoned farmland soils

Soil warming is expected to accelerate microbial carbon (C) degradation, increasing carbon dioxide (CO2) emissions. This process greatly contributes to global warming. To validate this positive feedback loop in semiarid restored ecosystems, we examined the effects of 2 years of open-top chamber warming on soil CO2 efflux (soil respiration) and microbial metabolic characteristics in abandoned farmland on the Chinese Loess Plateau. Soil warming of 1.3 °C above ambient at 10 cm depth significantly stimulated CO2 emissions by 40.5 %. Despite short-term warming alleviating the C (energy) limitation on microbial activity, no substantial differences in microbial C use efficiency or biomass turnover rate were noted compared to those in the control. Importantly, we found little evidence that warming altered the expression levels of carbohydrate metabolism genes annotated using the eggNOG, KEGG, and CAZy databases. All expressed genes targeting the degradation of diverse carbonaceous components were assigned to bacterial taxa unaffected by warming. Therefore, short-term warming stimulated soil CO2 emissions from non-microbial sources but did not drive the abandoned farmland in the reverse direction to a C source. Our findings highlight the importance of conducting long-term comparisons of microbial metabolic profiles and soil respiration components to elucidate the mechanisms underlying changes in C-cycling in ecosystems that have undergone restoration and experienced warming.

Full-length transcriptome analysis revealed that 2,4-dichlorophenoxyacetic acid promoted in vitro bulblet initiation in lily by affecting carbohydrate metabolism and auxin signaling.

Bulblet initiation, including adventitious bud initiation and bulblet formation, is a crucial process for lily and other bulbous flowers that are commercially propagated by vegetative means. Here, by a hybrid strategy combining Pacific Biosciences (PacBio) full-length sequencing and Illumina RNA sequencing (RNA-seq), high-quality transcripts of L. brownii (Lb) and its variety, L. brownii var. giganteum (Lbg), during in vitro bulblet initiation were obtained. A total of 53,576 and 65,050 high-quality non-redundant full-length transcripts of Lbg and Lb were generated, respectively. Morphological observation showed that Lbg possessed a stronger capacity to generate bulblets in vitro than Lb, and 1 mg L-1 2,4-dichlorophenoxyacetic acid (2,4-D) significantly increased bulblet regeneration rate in two lilies. Screening of differentially expressed transcripts (DETs) between different stages and Mfuzz analysis showed 0 DAT to 1 DAT was the crucial stage with the most complex transcriptional change, with carbohydrate metabolism pathway was significantly enriched. In addition, 6,218 and 8,965 DETs were screened between the 2,4-D-treated group and the control group in Lbg and Lb, respectively. 2,4-D application had evident effects on the expression of genes involved in auxin signaling pathway, such as TIRs, ARFs, Aux/IAAs, GH3s and SAURs. Then, we compared the expression profiles of crucial genes of carbohydrate metabolism between different stages and different treatments. SUSs, SUTs, TPSs, AGPLs, GBSSs and SSs showed significant responses during bulblet initiation. The expression of CWINs, SUTs and SWEETs were significantly upregulated by 2,4-D in two lilies. In addition, 2,4-D increased the expression of starch degradation genes (AMYs and BAMs) and inhibited starch synthesis genes (AGPLs, GBSSs and SSs). SBEs were significantly upregulated in Lbg but not in Lb. Significant co-expression was showed between genes involved in carbohydrate metabolism and auxin signaling, together with transcription factors such as bHLHs, MYBs, ERFs and C3Hs. This study indicates the coordinate regulation of bulblet initiation by carbohydrate metabolism and auxin signaling, serving as a basis for further studies on the molecular mechanism of bulblet initiation in lily and other bulbous flowers.

Comprehensive analyses of the citrus WRKY gene family involved in the metabolism of fruit sugars and organic acids.

Sugars and organic acids are the main factors determining the flavor of citrus fruit. The WRKY transcription factor family plays a vital role in plant growth and development. However, there are still few studies about the regulation of citrus WRKY transcription factors (CsWRKYs) on sugars and organic acids in citrus fruit. In this work, a genome-wide analysis of CsWRKYs was carried out in the citrus genome, and a total of 81 CsWRKYs were identified, which contained conserved WRKY motifs. Cis-regulatory element analysis revealed that most of the CsWRKY promoters contained several kinds of hormone-responsive and abiotic-responsive cis-elements. Furthermore, gene expression analysis and fruit quality determination showed that multiple CsWRKYs were closely linked to fruit sugars and organic acids with the development of citrus fruit. Notably, transcriptome co-expression network analysis further indicated that three CsWRKYs, namely, CsWRKY3, CsWRKY47, and CsWRKY46, co-expressed with multiple genes involved in various pathways, such as Pyruvate metabolism and Citrate cycle. These CsWRKYs may participate in the metabolism of fruit sugars and organic acids by regulating carbohydrate metabolism genes in citrus fruit. These findings provide comprehensive knowledge of the CsWRKY family on the regulation of fruit quality.

Differences in Bacterial Communities of Retail Raw Pork in Different Market Types in Hangzhou, China.

Pork is widely consumed globally, and pigs' microbiota can potentially harbor foodborne pathogens. Contaminated pork in retail markets poses significant implications for food quality and safety. However, limited studies have compared pork microbiomes in various marketing environments. In this study, we utilized traditional microbial culture methods and high-throughput 16S rRNA sequencing to assess pathogen contamination and bacterial diversity in raw pork samples purchased from farmers' markets and two types of supermarkets (upscale and ordinary) in Hangzhou, China. Traditional microbial plate cultures identified E. coli and Salmonella spp. in 32.1% (27/84) and 15.5% (13/84) of the collected pork samples, respectively. Moreover, 12 out of 13 Salmonella strains were found in farmers' markets. The MIC results indicated a high prevalence of MDR strains, accounting for 51.9% in E. coli and 53.8% in Salmonella. The prevalence of NaClO tolerant strains was 33.3% and 92.3% for E. coli and Salmonella, respectively. Sequencing results indicated significantly higher microbial diversity in farmers' market samples compared to supermarket samples. Farmers' market pork samples exhibited a greater abundance of Acinetobacter, while Pseudomonas and Brochothrix were predominant in supermarket samples. The total abundance of pathogenic and spoilage bacteria was also higher for the farmers' market samples. Cross-contamination during market trading was evident through a high correlation between bacterial abundance in pork from different stalls within the same farmers' market. PICRUSt2 analysis identified significant differences in the average proportions of genes for carbohydrate, energy, and lipid metabolism from the farmers' markets, suggesting an exacerbation of microbial metabolic activity and increased perishability of pork in this environment. In conclusion, this study revealed variations in the characteristics of raw pork bacterial contamination across different types of retail stores, as well as differences in the composition and diversity of their respective bacterial communities.

Whole genome sequencing and the lignocellulose degradation potential of Bacillus subtilis RLI2019 isolated from the intestine of termites

BackgroundLignocellulosic biomass is the most abundant and renewable terrestrial raw material for conversion into bioproducts and biofuels. However, the low utilization efficiency of lignocellulose causes environmental pollution and resource waste, which limits the large-scale application of bioconversion. The degradation of lignocellulose by microorganisms is an efficient and cost-effective way to overcome the challenge of utilizing plant biomass resources. This work aimed to screen valuable cellulolytic bacteria, explore its molecular mechanism from genomic insights, and investigate the ability of the strain to biodegrade wheat straw.ResultsBacillus subtilis (B. subtilis) RLI2019 was isolated from the intestine of Reticulitermes labralis. The strain showed comprehensive enzyme activities related to lignocellulose degradation, which were estimated as 4.06, 1.97, 4.12, 0.74, and 17.61 U/mL for endoglucanase, β-glucosidase, PASC enzyme, filter paper enzyme, and xylanase, respectively. Whole genome sequencing was performed to better understand the genetic mechanism of cellulose degradation. The genome size of B. subtilis RLI2019 was 4,195,306 bp with an average GC content of 43.54%, and the sequence characteristics illustrated an extremely high probability (99.41%) as a probiotic. The genome contained 4,381 protein coding genes with an average GC content of 44.20%, of which 145 genes were classified into six carbohydrate-active enzyme (CAZyme) families and 57 subfamilies. Eight cellulose metabolism enzyme-related genes and nine hemicellulose metabolism enzyme-related genes were annotated by the CAZyme database. The starch and sucrose metabolic pathway (ko00500) was the most enriched with 46 genes in carbohydrate metabolism. B. subtilis RLI2019 was co-cultured with wheat straw for 7 days of fermentation, the contents of neutral detergent fiber, acid detergent fiber, hemicellulose, and lignin were significantly reduced by 5.8%, 10.3%, 1.0%, and 4.7%, respectively. Moreover, the wheat straw substrate exhibited 664.9 μg/mL of reducing sugars, 1.22 U/mL and 6.68 U/mL of endoglucanase and xylanase activities, respectively. Furthermore, the fiber structures were effectively disrupted, and the cellulose crystallinity was significantly reduced from 40.2% to 36.9%.ConclusionsThe complex diversity of CAZyme composition mainly contributed to the strong cellulolytic attribute of B. subtilis RLI2019. These findings suggest that B. subtilis RLI2019 has favorable potential for biodegradation applications, thus it can be regarded as a promising candidate bacterium for lignocellulosic biomass degradation.

Transformation of water states and succession of functional microorganisms during synergistic bioevaporation process

A synergistic bioevaporation process was applied to treat the food waste (FW) by using the biofilm-developed corncob as the bulking agent and microbial carrier. During the process, interstitial water was the main water states, accounting for 55.6–76.8% of the total water amount. After the bioevaporation, 3079.27 g (61.05%) of the interstitial water and 48.46 g (3.45%) of the vicinal water was removed from the matrix, while 93.82 g (79.36%) of the bound water was formed. The removal of interstitial water mainly occurred in the cooling stage and the warming stage only lowered the binding energy of bound water, vicinal water and interstitial water. At the end of 1st cycle, the remained interstitial water trapped more tightly and the boundary between vicinal water and interstitial water nearly disappeared. The biofilm thickness in corncob particles was 350–440 µm and mainly dominated by bacteria and fungi with an abundance above 98.0%, in which the fungal Aspergillus reached as high as 22.7%. It seemed the fungi tended to survive in vicinal water abundant environment, but the bacteria preferred to habitat in interstitial water rich condition. Microorganisms had abundant metabolism genes of 29.3–38.5%, and the lipid transport and metabolic genes reached the maximum at Peak 54 ℃, while the carbohydrate transport and metabolic genes was the highest at Warming 46 ℃.