Genetic Information Processing Research Articles

Soil Bacterial Community Structure and Function under the Substitution of Chemical Fertilizer with Maize Straw

The long-term extensive application of chemical fertilizers wreaks havoc on soil bacterial structure and function. To reduce the damage caused by chemical fertilizers, a six-year experiment was performed to study the effects of replacing 0% (CK), 25% (S25), 50% (S50), 75% (S75), and 100% (S100) of 225 kg ha−1 mineral nitrogen fertilizer with an equivalent amount of nitrogen from maize straw on the soil bacterial community structure, diversity, and function. The results showed that Proteobacteria, Acidobacteria, and Gemmatimonadetes were the dominant soil bacterial phyla after the replacement treatments. Replacing mineral nitrogen fertilizer with an equivalent amount of nitrogen from maize straw significantly reduced the number of Photobacterium and bacterial populations involved in genetic information processing in soil, but significantly increased the number of bacterial populations involved in organismal systems, human diseases, and environmental information processing. Compared with other treatments, the relative abundance of TK10 significantly increased by 33.52–76.36% in S25. The number of subgroup 6, Gram-negative, biofilm-forming, potentially pathogenic, and anaerobic bacteria significantly increased, whereas that of Chloroflexi and Blastocatellia subgroup 4 significantly decreased in S50 and S75 compared with CK. The number of TK10 and Blastocatellia subgroup 4 in S50 and S100, respectively, was significantly lower than that in CK. Bacterial species were significantly more present in S25 than in S75. The diversity of bacterial species in S75 was significantly lower than that in CK. S25 and S100 were more favorable to increasing the number of Gram-positive, aerobic, mobile-element containing, and stress-tolerant bacteria. Rhodobacteraceae, Pyrinomonadaceae, Xanthobacteraceae, Nocardioidaceae, and Vulgatibacteraceae with statistical differences in CK, S25, S50, S75, and S100, respectively, could be used as biomarkers. Chloroflexi, Acidobacteria, and Nitrospirae could be used as the main basis for the bacterial classification of soil samples in the equivalent substitution of nitrogen chemical fertilizer with maize straw. S25 is ideal for increasing soil bacterial species richness and abundance.

Proteomics of the haemolymph of the terrestrial crustacean Porcellio scaber reveals components of its innate immunity under baseline conditions

The terrestrial crustacean Porcellio scaber is an established test organism in environmental research. We analysed the haemolymph proteome of P. scaber using a classical proteomic approach based on one-dimensional gel electrophoresis and tandem mass spectrometry. Using a publicly available protein database and our P. scaber transcriptome data, we have identified 76 proteins involved in cytoskeleton formation, protein degradation, vesicular transport, genetic information processing, detoxification, carbohydrate and lipid metabolism reflecting haemocyte metabolic activity, active intracellular transport, and intercellular communication. Compared with the data reported for other crustaceans, 28 of these P. scaber proteins have been linked to its immunity, among them hemocyanin, α-2-macroglobulin, phenoloxidase 3, superoxide dismutase, glutathione S-transferase, haemolymph clottable protein, and histones H4 and H2B. Our results thus provide a firm base for studying the innate immune response of P. scaber at the level of the haemolymph proteome. This knowledge is of particular importance in ecotoxicity studies with various environmental stressors where understanding physiological changes is important to reveal possible modes of action.

Transcriptome-wide identification and expression analysis of the NAC gene family in lowland bamboo (Oxytenanthera abyssinica (A.Rich) Munro)under abiotic stresses

NAC (NAM, no apical meristem, ATAF and CUC) is one of the largest gene families of the plant-specific transcription factors (TF). NAC TFs have immense involvement in plant growth and developmental processes and have particular importance in enhancing plant resistance to multiple abiotic stresses. NAC members have unique structural makeup and a range of biological activities. Despite their enormous roles in plants, comprehensive study on identification, characterization and expression profiling of NACs under abiotic stress is lacking in Lowland bamboo [Oxytenanthera abyssinica (A.Rich) Munro]. Thus, this study aimed to identify NAC members, characterize their protein properties, construct their phylogenetic relationships and more importantly, establish their expression profiling under abiotic stress. From this abiotic stress-induced transcriptome, 220 lowland bamboo TFs with intact and complete NAC DNA binding domains (PF01849) were identified. Following their identification, analysis of functional annotation, protein characterization, phylogenetic relationships and expression profiling were conducted. The analysis presented up-regulation of 142 unigenes in response to abiotic stress, the association of 26 unigenes directly to stress response and the involvement of 92 unigenes in genetic information processing and 29 in environmental information processing according to KEGG analysis. These results suggest the most likely involvement of NACs in lowland bamboo stress response and adaptation. As a species best survived in a moisture-stressed environment, this study has provided valuable information that could shed light on further functional analysis research efforts aiming to exploit NACs in developing stress-resilient bamboo and related plants.

Comparative Serum Proteome Analysis Indicates a Negative Correlation between a Higher Immune Level and Feed Efficiency in Pigs.

Identifying and verifying appropriate biomarkers is instrumental in improving the prediction of early-stage pig production performance while reducing the cost of breeding and production. The main factor that affects the production cost and environmental protection cost of the pig industry is the feed efficiency of pigs. This study aimed to detect the differentially expressed proteins in the early blood index determination serum between high-feed efficiency and low-feed efficiency pigs and to provide a basis for further identification of biomarkers using the isobaric tandem mass tag and parallel reaction monitoring approach. In total, 350 (age, 90 ± 2 d; body weight, 41.20 ± 4.60 kg) purebred Yorkshire pigs were included in the study, and their serum samples were obtained during the early blood index determination. The pigs were then arranged based on their feed efficiency; 24 pigs with extreme phenotypes were grouped as high-feed efficiency and low-feed efficiency, with 12 pigs in each group. A total of 1364 proteins were found in the serum, and 137 of them showed differential expression between the groups with high- and low-feed efficiency, with 44 of them being upregulated and 93 being downregulated. PRM (parallel reaction monitoring) was used to verify 10 randomly chosen differentially expressed proteins. The proteins that were differentially expressed were shown to be involved in nine pathways, including the immune system, digestive system, human diseases, metabolism, cellular processing, and genetic information processing, according to the KEGG and GO analyses. Moreover, all of the proteins enriched in the immune system were downregulated in the high-feed efficiency pigs, suggesting that a higher immune level may not be conducive to improving feed efficiency in pigs. This study provides insights into the important feed efficiency proteins and pathways in pigs, promoting the further development of protein biomarkers for predicting and improving porcine feed efficiency.

Whole-Genome Sequence Insight into the Plant-Growth-Promoting Bacterium Priestia filamentosa Strain AZC66 Obtained from Zygophyllum coccineum Rhizosphere.

This study aimed to isolate, screen the plant-growth-enhancing features, and explore the whole-genome sequence of AZC66 isolated from the rhizosphere of Zygophyllum coccineum and determine its biostimulating effects on the growth of cowpea under greenhouse conditions. Salkowski reagent was used to measure AZC66's indole acetic acid production. AZC66's inorganic phosphate solubility on Pikovskaya agar was evaluated using tricalcium phosphate. The results indicated the ability of AZC66 to fix nitrogen, produce IAA (66.33 ± 0.44 μg mL-1), solubilize inorganic phosphate, and exhibit the activity of ACC deaminase (278.40 ± 21 mol -ketobutyrate mg-1 h-1). Cowpea's root and shoot dry weights were also significantly increased after in vitro inoculation with AZC66. The identity of AZC66 was confirmed as Priestia filamentosa, and 4840 genes were predicted in its genome. The gene sequences were compared against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the results showed that the top three pathways wherein the maximum number of genes are involved are signaling and cellular processes, genetic information processing, and carbohydrate metabolism. The genome sequencing of the strain AZC66 revealed a number of genes implicated in plant biostimulation activities such as nitrogen fixation (nifU), phytohormone synthesis (trpAB genes), phosphate solubilization (PhbCEF, pstABCS, and phoU), and siderophore formation (FbpA, feoAB, and fetB). The AZC66 genome contained numerous genes involved in nitrogen metabolism, nitrogen regulation, and the nitrate reduction pathway. The phenazine biosynthetic gene in AZC66 demonstrated biocontrol and soil survival properties. The trehalose synthesis genes in AZC66 may help plants resist osmotic and salt stress. The discovery of glycine betaine, cold shock, and heat shock protein genes demonstrated that AZC66 could withstand harsh conditions. AZC66 might be used to create robust, sustainable biological fertilizers for future agricultural use in Saudi Arabia. Furthermore, the predicted adaptable metabolic pathways might serve as the basis for potential biotechnological applications in agriculture and industry.

Effects of dietary N-carbamylglutamate on rumen fermentation parameters, and bacterial community diversity of Holstein dairy cows in Tibet.

The Tibetan Plateau is characterized by low temperature and hypoxia. N-carbamylglutamic acid (NCG) can increase blood oxygen saturation, and have the potential to be used to prevent the high-altitude hypoxia stress state of cows. However, its beneficial effect on the rumen microbiota of Holstein dairy cows remains unclear. Hence, the experiments 12 multiparous (parity ranged from 2 to 7) Holstein dairy cows (413.0 ± 42 kg) were randomly assigned to 2 treatments with 6 replicates in each treatment: basal diet (CON, control group) and basal diet plus 20 g/d/cow of NCG (NCG, experiment group), respectively. To study the effects of dietary NCG supplementation on rumen microbiota of Holstein dairy cows in Tibet. The experiment lasted for 45 days, with 15 days of pre-feeding and 30 days of formal trail period. The results showed that ruminal NH3-N concentration in NCG group was lower (p < 0.05) than that in the CON group, while molar proportion of acetic acid and total volatile fatty acid (VFA) concentration were increased (p < 0.05) with the addition of NCG. Microbial diversity increased (p < 0.05) in NCG group, with Bacteroidetes, Firmicutes, and Patescibacteria as the most abundant phyla. The KEGG pathway analysis showed that the potential function of ruminal bacteria was mainly enriched in metabolism (carbohydrates, amino acids, lipids, energy, and nucleotides) and genetic information processing (replication, repair, and translation). In conclusion, NCG can improve rumen nitrogen utilization, total VFA and acetic acid production, and increase rumen microbial diversity, all of which could make the introduced Holstein dairy cows to better adapt to the harsh environment in Tibet and improve their production performance.

Analysis of gut microbiota in rats with bile duct obstruction after biliary drainage

The abundance of specific gut microorganisms is strongly associated with the concentrations of microbially modified bile acids. This study aimed to investigate the composition of intestinal microbiota in rats subjected to bile duct ligation or biliary drainage. Extrahepatic bile duct ligation was conducted to induce bile duct obstruction in rats. The bile was drained via a percutaneous biliary drainage catheter to cause bile deficiency. The total DNA extracted from fecal samples was sequenced with 16S DNA sequencing. Taxonomic classifications were conducted using the Mothur algorithm and SILVA138 database and were presented along with the abundance presented using a heatmap. The inter- and intra-group differences in the intestinal microbiome composition were analyzed by ANOSIM test. The biomarker microorganisms were screened using the Linear discriminant analysis Effect size method. The possible functional pathways were predicted using the Tax4Fun package. A total of 3277 operational taxonomic units (OTUs) were examined, with 2410 in the Kongbai group, 2236 in the Gengzu group, and 1763 in the Yinliu group. The composition of microorganisms at the levels of phylum, class, order, family, and genus was altered in rats with bile duct obstruction. This composition was then restored by biliary drainage. The top 10 predominant microorganisms were identified that led to the inter-group differences. Functional annotation revealed that the potential functions of the microorganisms with significant differences were enriched in metabolism, cellular processes, and genetic and environmental information processing. The intestinal microbial community was significantly changed in rats with bile duct obstruction. The changes in the abundance of intestinal microbiota Prevotellaceae and Enterobacteriaceae were statistically significant after biliary drainage treatment.

Effects of biochar amendment on bacterial communities and their function predictions in a microplastic-contaminated Capsicum annuum L. soil

Microplastics (MPs) have been confirmed as a novel type of environmental pollutant. They have long-term existence in the soil environment and threaten the soil ecological environment system. Biochar soil amendment is capable of enhancing the water and nutrient holding capacity and improving the soil structure and quality of terrestrial ecosystems. However, the effect of biochar amendment on bacterial community in MPs-contaminated soil–plant system remain unclear, in particular the prediction of bacterial function of these systems. In this study, the effects of biochar amendment on the bacterial community structure of MPs-contaminated soil were investigated through different treatments at three pepper growth stages, and the bacterial function of MPs-contaminated soil was predicted. As indicated by the results of this study, biochar amendment led to the increased species evenness and richness of bacterial community in MPs-contaminated soil, the enhanced relative abundance of MPs-contaminated tolerant bacteria (e.g., Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes), as well as the improved relative abundance of Massilia, Lysobacter, and Terrimonas. Furthermore, soil total phosphorus (TP), soil organic carbon (SOC), NH4+-N, NO3−-N, and pH served as the main factors for the composition of soil bacterial community, as revealed by the result of Pearson correlation analysis and redundancy analysis. Bacterial genera Massilia, Lysobacter, and Terrimonas significantly affected the growth indicator of pepper. PICRUSt functional prediction suggested that the bacterial community of MPs-contaminated soil primarily comprised four level-1 functional layers and 16 level-2 functional layers, and the active soil bacterial community was identified in Metabolism, Genetic information processing, as well as Cellular processes. Biochar amendment enhanced the abundance of genes correlated with Amino acid metabolism and Carbohydrate metabolism of bacteria in MPs-contaminated soil, thus facilitating the nitrogen and phosphorus metabolism cycle of MPs-contaminated soil plants. Our results confirmed that biochar amendment increase the beneficial bacteria in MPs-contaminated soil, more significantly facilitate the nitrogen and phosphorus metabolism cycle within MPs-contaminated soil plants, while effectively expediting the growth of plants in MPs-contaminated soil. This study provides more insights into the correlation of plant and bacterial communities in response to biochar amendment in MPs-contaminated soil system.

Complete genome analysis of pathogenic Metschnikowia bicuspidata strain MQ2101 isolated from diseased ridgetail white prawn, Exopalaemon carinicauda

BackgroundMetschnikowia bicuspidata is a pathogenic yesst that can cause disease in many different economic aquatic animal species. In recent years, there was a new disease outbreak in ridgetail white prawn (Exopalaemon carinicauda) in coastal areas of Jiangsu Province China that was referred to as zombie disease by local farmers. The pathogen was first isolated and identified as M. bicuspidata. Although the pathogenicity and pathogenesis of this pathogen in other animals have been reported in some previous studies, research on its molecular mechanisms is still very limited. Therefore, a genome-wide study is necessary to better understand the physiological and pathogenic mechanisms of M. bicuspidata.ResultIn this study, we obtained a pathogenic strain, MQ2101, of M. bicuspidata from diseased E. carinicauda and sequenced its whole genome. The size of the whole genome was 15.98 Mb, and it was assembled into 5 scaffolds. The genome contained 3934 coding genes, among which 3899 genes with biological functions were annotated in multiple underlying databases. In KOG database, 2627 genes were annotated, which were categorized into 25 classes including general function prediction only, posttranslational modification, protein turnover, chaperones, and signal transduction mechanisms. In KEGG database, 2493 genes were annotated, which were categorized into five classes, including cellular processes, environmental information processing, genetic information processing, metabolism and organismal systems. In GO database, 2893 genes were annotated, which were mainly classified in cell, cell part, cellular processes and metabolic processes. There were 1055 genes annotated in the PHI database, accounting for 26.81% of the total genome, among which 5 genes were directly related to pathogenicity (identity ≥ 50%), including hsp90, PacC, and PHO84. There were also some genes related to the activity of the yeast itself that could be targeted by antiyeast drugs. Analysis based on the DFVF database showed that strain MQ2101 contained 235 potential virulence genes. BLAST searches in the CAZy database showed that strain MQ2101 may have a more complex carbohydrate metabolism system than other yeasts of the same family. In addition, two gene clusters and 168 putative secretory proteins were predicted in strain MQ2101, and functional analysis showed that some of the secretory proteins may be directly involved in the pathogenesis of the strain. Gene family analysis with five other yeasts revealed that strain MQ2101 has 245 unique gene families, including 274 genes involved in pathogenicity that could serve as potential targets.ConclusionGenome-wide analysis elucidated the pathogenicity-associated genes of M. bicuspidate while also revealing a complex metabolic mechanism and providing putative targets of action for the development of antiyeast drugs for this pathogen. The obtained whole-genome sequencing data provide an important theoretical basis for transcriptomic, proteomic and metabolic studies of M. bicuspidata and lay a foundation for defining its specific mechanism of host infestation.

Brevetoxin induces a shift in the redox state of the proteome and unfolded protein response in human lymphoblast cells that can be alleviated with the acrolein scavenger MESNA

Human lymphoblast cells were treated with the marine algal toxin, brevetoxin-2 (PbTx-2), and its effects on the proteome were assessed by redox proteomics using cysteine reactive tandem mass tags (TMT). Additionally, cells were simultaneously treated with PbTx-2 and the antioxidant and acrolein scavenger sodium 2-mercaptoethylsulfonate (MESNA) to determine if MESNA could prevent the proteomic effects of brevetoxin-2. A massive shift in the redox state of the proteome of brevetoxin-2 treated cells was observed. The main pathway affected was genetic information processing. Significantly oxidized proteins included Trx-1, peroxyredoxins (Prxs), ribosomal proteins, and the eukaryotic initiation factor 2 β subunit (eIF2β). Proteins that were overexpressed in brevetoxin-treated cells included four folding chaperones. These effects were diminished in the presence of MESNA indicating that MESNA may act through its antioxidant properties or as a brevetoxin scavenger. These studies provide novel insights into new prophylactics for brevetoxicosis in humans and wildlife.

Prenatal Exposure to Metabolism-Disrupting Chemicals, Cord Blood Transcriptome Perturbations, and Birth Weight in a Belgian Birth Cohort.

Prenatal exposure to metabolism-disrupting chemicals (MDCs) has been linked to birth weight, but the molecular mechanisms remain largely unknown. In this study, we investigated gene expressions and biological pathways underlying the associations between MDCs and birth weight, using microarray transcriptomics, in a Belgian birth cohort. Whole cord blood measurements of dichlorodiphenyldichloroethylene (p,p'-DDE), polychlorinated biphenyls 153 (PCB-153), perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), and transcriptome profiling were conducted in 192 mother-child pairs. A workflow including a transcriptome-wide association study, pathway enrichment analysis with a meet-in-the-middle approach, and mediation analysis was performed to characterize the biological pathways and intermediate gene expressions of the MDC-birth weight relationship. Among 26,170 transcriptomic features, we successfully annotated five overlapping metabolism-related gene expressions associated with both an MDC and birth weight, comprising BCAT2, IVD, SLC25a16, HAS3, and MBOAT2. We found 11 overlapping pathways, and they are mostly related to genetic information processing. We found no evidence of any significant mediating effect. In conclusion, this exploratory study provides insights into transcriptome perturbations that may be involved in MDC-induced altered birth weight.

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus).

Previous studies regarding the gastrointestinal biogeography of microbiomes generally focused on longitudinal comparisons, whereas few studies have compared luminal and mucosal microbiomes. Investigations of the snake gut microbiome have attracted interest because of the unique digestive physiology and hibernation behavior, but adequate sampling methods must be developed. Here, we used an omics approach combining 16S rRNA gene sequencing with untargeted metabolomics to profile the luminal and mucosal gut microbiomes and metabolomes in oriental rat snakes, with the goal of revealing the heterogeneity and co-occurrence at these sites. The α-diversity of the gut microbiome was significantly higher at mucosal sites than at luminal sites. Microbial composition also differed according to sampling site, with significant differences in the abundances of dominant phyla and genera, as well as β-diversity clustering and distribution. Metabolome profiling revealed differences that were mainly related to cholinergic substances and nucleic acids. Analysis of variations in Kyoto Encyclopedia of Genes and Genomes functions of microbes and metabolites showed that the mucosal microbiome was more frequently involved in genetic information processing and cellular processes, whereas the luminal microbiome generally participated in metabolic regulation. Notably, we found a greater abundance of the opportunistic pathogen genus Escherichia-Shigella at luminal sites and higher levels of the lipid-regulator metabolite fenfluramine at mucosal sites. Despite the extensive differences between the two sampling sites, the results revealed similarities in terms of amplicon sequence variant composition and dominant core microbes. This pilot exploration of luminal and mucosal microbiomes and metabolites provides key insights to guide future research. KEY POINTS: • Snake luminal and mucosal microbiota was distinct in composition and function. • Metabolome profiling revealed differences related to different metabolites. • The pathogenic microbes are more likely to colonize the gut lumina.

Yield and Rhizosphere Soil Environment of Greenhouse Zucchini in Response to Different Planting and Breeding Waste Composts.

Composting, planting, and breeding waste for return to the field is the most crucial soil improvement method under the resource utilization of agricultural waste. However, how the vegetable yield and rhizosphere soil environment respond to different composts is still unknown. Therefore, eight formulations were designed for compost fermentation using agricultural waste [sheep manure (SM), tail vegetable (TV), cow manure (CM), mushroom residue (MR), and corn straw (CS)] without fertilizer (CK1) and local commercial organic fertilizer (CK2) as controls to study the yield and rhizosphere soil environment of greenhouse zucchini in response to different planting and breeding waste compost. Applying planting and breeding waste compost significantly increased the soil's organic matter and nutrient content. It inhibited soil acidification, which T4 (SM:TV:CS = 6:3:1) and T7 (SM:TV:MR:CS = 6:2:1:1) treatments affected significantly. Compared to CK2 treatment, T4 and T7 treatments showed a greater increase, with a significant increase of 14.69% and 11.01%, respectively. Therefore, T4, T7, and two control treatments were selected for high-throughput sequencing based on yield performance. Compared with the CK1 treatment, although multiple applications of chemical fertilizers led to a decrease in bacterial and fungal richness, planting and breeding waste compost maintained bacterial diversity and enhanced fungal diversity. Compared to CK2, the relative abundance increased in T7-treated Proteobacteria (Sphingomonas, Pseudomonas, and Lysobacter) and T4-treated Bacteroidetes (Flavobacterium) among bacteria. An increase in T4-treated Ascomycota (Zopfiella and Fusarium) and Basidiomycota among fungi and a decrease in T7-treated Mortierellomycota have been observed. Functional predictions of the bacterial Tax4Fun and fungal FUNGuild revealed that applying planting and breeding waste compost from the T4 treatment significantly increased the abundance of soil bacterial Metabolism of Cities, Genetic Information Processing, and Cellular Processes decreased the abundance of Pathotroph and Saprotroph-Symbiotroph fungi and increased the abundance of Saprotroph fungi. Overall, planting and breeding waste compost increased zucchini yield by improving soil fertility and microbial community structure. Among them, T4 treatment has the most significant effect, so T4 treatment can be selected as the optimized formulation of local commercial organic fertilizer. These findings have valuable implications for sustainable agricultural development.

Composition and Functional Capacity of Gut Microbes are Associated with Arterial Stiffness: A Prospective Study

Objective: Arterial stiffness is an important predictor of cardiovascular disease. Microbial diversity in the gut has been shown to be associated inversely with arterial stiffness in Caucasian populations. However, due to the different profiles of the gut microbiota among ethnicities, the relationship between gut-microbiota dysbiosis and the progression of arterial stiffness merits further investigation. This study aimed to investigate the association between the composition and functional capacity of the gut microbiota and the progression of arterial stiffness. Methods: “Shotgun” metagenomics sequencing were undertaken in 96 individuals from a hypertension-associated gut-microbiota study in the Kailuan cohort, who measured brachial-ankle pulse wave velocity (baPWV) and provided fecal samples between September 2014 and February 2015 at Kailuan General Hospital and 11 affiliated hospitals. The different composition and functional capacity of the gut microbiota were compared between individuals without arterial stiffness (normal arterial stiffness group, baPWV &lt;1,400 cm/s, n = 27) and participants with arterial stiffness (increased arterial stiffness group, baPWV ≥1,400 cm/s, n = 69) at baseline. These participants were followed up prospectively for a mean duration of 2.6 years, and 50 underwent a repeat baPWV measurement. Associations between the gut microbiota and severity and progression of arterial stiffness were assessed using MaAsLin2 software after adjustment for age, sex, and mean arterial blood pressure and correction for multiple testing. Gene “catalogs” were aligned to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to obtain information for potential functional capacities of the gut microbiota. Results: In this study, 14 genera and 50 species of bacteria were identified to be abundant in participants with normal arterial stiffness compared with those with increased arterial stiffness. Of 14 genera, the prevalence of beneficial bacteria of the genera Leadbetterella and Cytophaga was correlated inversely with baPWV (P &lt; 0.05). Analyses of functional capacity revealed gut-microbial dysfunctions in the synthetic processes of “threonine dehydratase” “hypothetical protein” “mannosyl transferase” and “type-IV secretion-system proteins” in individuals suffering from arterial stiffness. During follow-up, bacteria of the proinflammatory genera Escherichia, Shigella, and Ruegeria were enriched in individuals with increased baPWV. Functional analyses showed that 26 KEGG orthologs of gut microbes were associated with an increase in baPWV and involved in “carbohydrate metabolism” “amino acid metabolism” and “protein families related to genetic information processing.” Conclusions: The composition and functional capacity of the microbial community in the gut of people suffering from arterial stiffness differed from those in individuals not suffering from arterial stiffness. Our data provide a new direction for the causality of the host-gut microbiota in arterial stiffness.

Bacterial diversity and function shift of strawberry root in different cultivation substrates

With the increasing use of soilless cultivation, artificial substrates are becoming more common, which inevitably leads to changes in the crop root environment. However, the impact of artificial substrate application on crop root microflora remains incompletely investigated. This study collected strawberry root samples from two artificial substrates and one greenhouse soil and used. 16S rRNA amplicon sequencing method to analyze the changes in the bacterial communities surrounding strawberry roots in different cultivation substrates. The corresponding root microbiota was predicted by PICRUSt. The results demonstrated that the α and β diversity of bacterial microbiota in samples from artificial substrates and greenhouse soil were significantly different. Almost all bacteria detected in root samples from greenhouse soils were also found in root samples from artificial substrates. The abundance of the genera Cellvibrio and Streptomyces in root samples from greenhouse soil were significantly higher than those of artificial substrate 1 and substrate 2. Bacteria found in substrate 1 including Acidocella, Vibrio and other 8 genera were significantly enriched compared to greenhouse soil; Bacteria identified in substrate 2 including Asticcacaulis, Bordetella, and other 13 genera were significantly higher than those in greenhouse soil. According to PICRUSt prediction, there were 34 pathways in substrate 1 and 47 pathways in substrate 2, including pathways related to cellular processes, environmental information processing, genetic information processing, human diseases, metabolism, and organismal systems in root microbiota from different substrates might significantly shifted. Among these pathways, those related to plant growth promotion, such as flavonoids and flavanols synthesis, were significantly up-regulated and pathways regarding antimicrobial compound synthesis including clavulanic acid, stilbenoid, and macrolides were significantly down-regulated in root microbiota from artificial substrates. This work provides basic information on root bacterial diversity of strawberries grown in different substrates and help to explore beneficial root microorganisms for sustainable strawberry production.

Integrating omics reveals insights into tomato abaxial/adaxial leafy supplemental lighting.

Research revealed that the abaxial leafy supplemental lighting (AB) can significantly improve the net photosynthetic rate and stomatal conductance in the leaves of tomato plants compare to the adaxial leafy supplemental lighting (AD) method. However, the underlying regulatory mechanisms are still poorly understood. Here, we conducted AB and AD on tomato and assessed transcriptomic, and proteomic changes in leaves. The result showed that under the two supplemental lighting methods, a total of 7352 genes and 152 proteins were differentially expressed. Significant differences were observed in genes expression levels and proteins abundances across multiple pathways, mainly including cell process, metabolism process, biological regulation, environment information processing, genetic information processing, metabolism, and organismal systems. Additionally, we also found that some key genes that plant hormone signaling, light perception, photosynthesis, plant fitness, and promoting fruit ripening, have increased significantly, which can explain the effect of AB on plant growth and development. Finally, through the qPCR, we determined that AB mainly up-regulate a series of auxin-responsive genes or factors, auxin polarity transport genes, gibberellin synthesis genes, cell cycle regulator genes, sugar transporters, and fleshy fruit ripening genes. These results help us to understand plant light response mechanism and discover genes which contribute to efficient light energy utilization.

Identification of candidate genes responsible for chasmogamy in wheat

BackgroundThe flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pollination within closed flowers (cleistogamy), while the second one possesses the ability to open flowers during processes mentioned above (chasmogamy). The swelling of lodicules is involved in the flowering of cereals and among others their morphology, calcium and potassium content differentiate between cleistogamic and non-cleistogamous flowers. A better understanding of the chasmogamy mechanism can lead to the development of tools for selection of plants with the desired outcrossing rate. To learn more, the sequencing of transcriptomes (RNA-Seq) and Representational Difference Analysis products (RDA-Seq) were performed to investigate the global transcriptomes of wheat lodicules in two highly chasmogamous (HCH, Piko and Poezja) and two low chasmogamous (LCH, Euforia and KWS Dacanto) varieties at two developmental stages—pre-flowering and early flowering.ResultsThe differentially expressed genes were enriched in five, main pathways: “metabolism”, “organismal systems”, “genetic information processing”, “cellular processes” and “environmental information processing”, respectively. Important genes with opposite patterns of regulation between the HCH and LCH lines have been associated with the lodicule development i.e. expression levels of MADS16 and MADS58 genes may be responsible for quantitative differences in chasmogamy level in wheat.ConclusionsWe conclude that the results provide a new insight into lodicules involvement in the wheat flowering process. This study generated important genomic information to support the exploitation of the chasmogamy in wheat hybrid breeding programs.

Microbial diversity and community composition of fecal microbiota in dual-purpose and egg type ducks.

Ducks are important agricultural animals, which can be divided into egg and dual-purpose type ducks according to economic use. The gut microbiota of ducks plays an important role in their metabolism, immune regulation, and health maintenance. Here, we use 16S rDNA V4 hypervariable amplicon sequencing to investigate the compositions and community structures of fecal microbiota between egg (five breeds, 96 individuals) and dual-purpose type ducks (four breeds, 73 individuals) that were reared under the same conditions. The alpha diversity of fecal microflora in egg type ducks was significantly higher than that in dual-type ducks. In contrast, there is no significant difference in the fecal microbial community richness between the two groups. MetaStat analysis showed that the abundance of Peptostreptococcaceae, Streptococcaceae, Lactobacillus, Romboutsia, and Campylobacter were significantly different between the two groups. The biomarkers associated with the egg and dual-purpose type ducks were identified using LEfSe analysis and IndVal index. Function prediction of the gut microbiota indicated significant differences between the two groups. The functions of environmental information processing, carbohydrate metabolism, lipid metabolism, xenobiotic biodegradation and metabolism, and metabolism of terpenoids and polyketides were more abundant in egg type ducks. Conversely, the genetic information processing, nucleotide metabolism, biosynthesis of amino acids and secondary metabolites, glycan biosynthesis and metabolism, fatty acid elongation, and insulin resistance were significantly enriched in dual-purpose type ducks. This study explored the structure and diversity of the gut microbiota of ducks from different economic-use groups, and provides a reference for improving duck performance by using related probiotics in production.

Diosgenin reduces bone loss through the regulation of gut microbiota in ovariectomized rats

Diosgenin (DIO) is an aglycone of steroid saponins acquired from plants, including Dioscorea alata, Smilax China, and Trigonella foenum graecum, acting as an anti-osteoporosis, anti-diabetic, anti-hyperlipidemic, anti-inflammatory. Recent studies have demonstrated that DIO reduces bone loss. This study aimed to investigate the effects of DIO on the gut microbiota (GM) of ovariectomized (OVX) osteoporotic rats. Female Sprague-Dawley rats were randomly divided into sham operation (sham + vehicle group) or ovariectomy. For 12 weeks, OVX rats were treated using a vehicle (OVX + vehicle group) and DIO (OVX + DIO group). Subsequently, ELISA was conducted to determine serum estradiol levels, micro-CT scanning was performed to evaluate bone quality, and feces were collected for metagenomics sequencing to examine the structure and function of GM. Raw reads were filtered to remove chimera sequences. Operational taxonomic units (OTUs) were clustered in the filtered reads. A Venn diagram analysis was conducted to study the common and unique OTUs in the sham + vehicle, OVX + vehicle, and OVX + DIO groups. LEfSe analysis was conducted to evaluate the specific GM of the three groups. The GM functions were analyzed using the KEGG and CAZy databases. After a 12-week treatment, DIO administration prevented OVX-induced weight gain and increased the estradiol levels. DIO treatment improved the bone microstructure and structural parameters of rat tibias. Metagenomics sequencing results identified 1139, 1207, and 1235 operational taxonomic units (OTUs) in the sham + vehicle, OVX + vehicle, and OVX + DIO groups, respectively. The percentage of common OTUs was 41.2%. Treatment with DIO restored the composition of GM in OVX rats by increasing the abundance of Coriobacteriia Adlercreutzia, Romboutsia, and Romboutsia_idealis and reducing the abundance of Betaproteobacteria, Gammaproteobacteria, Methanobacteria, Bacteroides, Phocaeicola, Alistipes, Bacteroids_uniformis, Bacteroids_xylanisolvens. The anti-osteoporosis effect of DIO can be regulated through environmental information processing, organismal Systems, Cellular Processes, human diseases, metabolism, and genetic information processing. Meanwhile, treatment with DIO improved GM homeostasis by increasing the metabolism of carbohydrates, other amino acids, and glycans and reducing translation, energy metabolism, and nucleotide metabolism. DIO can reduce bone loss by regulating the structural composition and function of GM, a novel strategy for preventing osteoporosis.

Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa.

Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further.