Genetic Information Processing Research Articles

Genomic insights into bamboo witches’ broom disease: pathogenicity and phytohormone biosynthesis in Aciculosporium take

Bamboo witches’ broom disease (WBD), caused by Aciculosporium take Miyake, devastates bamboo forests. Understanding the genome and pathogenic factors of pathogen is crucial for disease control. We employed single-molecule real-time sequencing, Illumina paired-end sequencing, and chromatin interaction mapping techniques to assemble the genome of A. take CCTCC-M2023413, analyze pathogenicity- and phytohormone-biosynthesis-related genes, and compare it to 12 other WBD pathogens. The genome of A. take is 59.24 Mb in size, with 54.32% repeats, 7 chromosomes, 7,105 protein-coding genes, 84 ribosomal RNAs, and 115 transfer RNAs. Predictive analysis of pathogenicity genes found 237 carbohydrate-active enzymes, 1,069 membrane transport proteins, 1,040 pathogen-host interaction genes, 315 virulence factors, and 70 effectors. Most of pathogenicity genes overlapped with repeat-rich regions. Additionally, 172 genes were linked to auxin biosynthesis, 53 to brassinosteroid biosynthesis, and 2 to cis-zeatin biosynthesis. Comparative genomic analysis identified 77 core orthogroups shared by 13 WBD pathogens, played roles in metabolites, genetic information processing, pathogenesis, cis-zeatin biosynthesis, lifespan, and quorum sensing. The miaA gene, crucial for cis-zeatin biosynthesis, is structurally conserved and sequence-diverse among 13 WBD pathogens, with upregulated expression during bamboo WBD pathogenesis. This highlights that cis-zeatin is significant contributor to host pathogenesis, and miaA is a new potential target for controlling WBD. This study provides important insights on preventing and controlling bamboo WBD.

Double effects of mitigating cyanobacterial blooms using modified clay technology: regulation and optimization of the microbial community structure

Harmful algal blooms (HABs) are global hazards under global climate change and eutrophication conditions. Modified clay (MC) method is widely used to control HABs in Asian and American coastal waters. However, little research has been conducted on the underlying mechanisms by which MC controls blooms in freshwater environments. Herein, experiments and bioinformatics analyses were conducted for MC-based control of freshwater blooms in a closed water body with an area of approximately 240 m2 in the Fuchun River, China. Results revealed that the dominant bloom species were Microcystis, and an 87.68–97.01% removal efficiency of whole algal biomass was achieved after 3 h of MC treatment. The weaker zeta potentials of Microcystis species and hydrophilic groups such as O-H and P-O-P in the extracellular polymeric substances (EPS) surrounding Microcystis cells made them easier to be flocculated and removed by MC particles, and the relative abundance of Microcystis decreased to 29.12% and that of Cyanobium increased to 40.97%. Therefore, MC changes the cyanobacterial community structure, which is accompanied by the elimination of Microcystis sp. apical dominance and enhanced competition between Cyanobium and Microcystis in the phytoplankton community, increasing cyanobacterial community diversity. Under MC treatment, residual microorganisms, including cyanobacteria, had a high potential for DNA damage repair and were more likely to survive after being subjected to oxidative stress. In the meanwhile, the abundance of genes involved in genetic information processing, signal transduction, and photosynthesis was decreased indicating that the residual microbiome was week in proliferation and light energy harvesting. Therefore, accompanied with the destruction of Microcystis colonies, MC changes the function of cyanobacteria and phycosphere microbiome, further hindering bloom development. These findings illustrate that MC can regulate and optimize the microbial community structure through which MC controls cyanobacterial blooms in ecosystems.

Comparative transcriptome analysis of low- and high-latitude populations of Charybdis japonica under temperature stress

Global climate change has caused rapid temperature changes in marine environments. Understanding how marine organisms respond to temperature changes can help predict their richness of future biodiversity. In this study, we examined the gene expression levels and the difference in the pathways that are responsive to acute temperature stress in low- and high-latitude populations of the shore swimming crab, Charybdis japonica. The two populations of C. japonica were exposed to low- and high-temperature stresses (15°C and 28°C) and used for transcriptome sequencing. Genetic regulatory ability changes were compared to determine the diverse response of the two crab populations to temperature change. The gene expression levels and functional enrichment analysis showed that the low-latitude crab regulated more genes (938) that were mainly enriched in DNA replication and metabolic pathways, whereas the high-latitude crab regulated less genes (309) that were mainly enriched in genetic information processing at low-temperature stress. Furthermore, the low-latitude crab regulated less genes (33) that were mainly enriched in genetic information processing, whereas the high-latitude crab regulated more genes (280) that were mainly enriched in signal transduction and cellular process at high-temperature stress. These results implied that the low-latitude population was more resilient to high-temperature stress, while the high-latitude population was more resilient to low-temperature stress. This study enhances our understanding of how different geographic C. japonica populations respond to varying temperature environments in their living zone, which could be helpful for predicting future biodiversity trends of intertidal crustaceans under global climate change.

Effect of xylo-oligosaccharides on intestinal bacterial diversity in mice with spleen deficiency constipation.

To explore the effect of xylo-oligosaccharides on intestinal bacterial diversity in mice with spleen deficiency constipation. The 16S rDNA sequencing was used to identify microbiota composition in four groups, including the normal group (NG), the model group with spleen-deficiency constipation (SDC), XOS treated groups that include XOS1 groups treated XOS 0.05 g/mL•d, and XOS2 group treated XOS 0.1 g/mL•d. Chao1 and Shannon were used to conduct gut microbes diversity analysis. Linear discriminant analysis coupled with effect size measurements (LEfSe) was used to identify signature gut microbiota, and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to predict the function of altered gut microbiota. Veen map indicated 245 common OTUs were identified from four groups. Especially, 9, 3, 0, and 19 unique OTUs were identified in NG, SDC, XOS1, and XOS2 groups, respectively. The Shannon index was evidently higher in NG group than in the other three groups (p < 0.05). We identified the occurrence of dominant bacterial groups including Bacteroidetes (25.5 ~ 49.9%), Firmicutes (25.4 ~ 39.3%), Proteobacteria (12.5 ~ 24.9%), Deferribacteres (1.6 ~ 19.2%), Cyanobacteria (0.3 ~ 1.8%), Verrucomicrobia (0.02 ~ 1.6%), Actinobacteria (0.01 ~ 0.5%), and Tenericutes (0.03 ~ 0.09%) at the four groups. The XOS2 group was characterized by a higher abundance of Peptostreptococcaceae, Intestinibacter, Aerococcaceae, and Facklamia. XOS1 group enriched in Deferribacteres, Mucispirillum, Deferribacterales, Deferribacteres, Lachnoclostridium, Rhodospirillaceae, and Rhodospirillales. Meanwhile, the SDC mice showed dramatic enrichment in Rikenellaceae, Lachnospiraceae, Rikenellaceae, Roseburia, and Alistipes, which were highly abundant in the NG group. XOS fed-mice evidently increase Deferribcteres abundance compared with NG and SDC groups. However, the abundance of Rikenellaceae was significantly reduced in XOS1 and XOS2 groups compared with NG and SDC groups. We identified that altered gut microbiotas by XOS treatment were associated with various metabolic pathways, including organismal systems, metabolism, human diseases, genetic information processing, and cellular processes. Our research indicated that XOS has the potential to recover intestinal bacteria and contribute to the treatment of spleen deficiency constipation.

Structural and functional differences of gut microbiota in Pomacea canaliculata from different geographical locations and habitats.

Gut microbiota is related to host fitness, and influenced by geographical locations and habitats. Pomacea canaliculata is a malignant invasive alien snail that threatens agricultural production and ecosystem functions worldwide. Clarifying the general rules of the gut microbial community structure and function of the snails in different geographical locations and habitats is of great significance for understanding their invasion at different spatial scales. This study used high-throughput sequencing technology to compare and analyze the differences in community structure and function of gut microbiota in P. canaliculata from five geographical locations (Liuzhou, Yulin, Nanning, Wuzhou, and Hezhou) and three different habitats (pond, paddy field, and ditch) in Guangxi Province. The results showed that intestinal microbial alpha diversity of P. canaliculata was higher in Liuzhou, Yulin, lower in Nanning, Wuzhou, Hezhou, and higher in ponds compared with paddy fields and ditches. The dominant phyla of gut microbiota in snails were Firmicutes, Cyanobacteria, Proteobacteria, Fusobacteriota, Bacteroidota, and the dominant genus was Lactococcus. The community structure of gut microbiota in snails varied significantly across different geographical locations and habitats, and the phyla Firmicutes, Cyanobacteria had significantly higher relative abundance in snails collected from Nanning and Yulin, respectively. Moreover, the relative abundance of gut functional microbiota associated with human disease in P. canaliculata was significantly affected by geographical locations and habitats, and with the highest abundance in ponds. However, the relative abundance of functional microbiota related to metabolism, genetic information processing, organizational system, environmental information processing, and cellular processes were only significantly affected by geographical locations. Collectively, geographical locations and habitats had significantly different effects on the community structure and function of gut microbiota in P. canaliculata, and the greater differences were caused by geographical locations rather than by habitats.

Exploring the effect of lipid loading on acidogenic fermentation of food waste: Insights from microbiome, quorum sensing and carbon metabolic pathway

The high lipid loading in food waste (FW) is widely regarded as one of the main bottlenecks in the traditional anaerobic digestion, but the effect of lipid on FW acidogenic fermentation has been historically ignored. This study attempted to reveal the influence of lipid loading on volatile fatty acids (VFAs) production and the corresponding synthesis mechanisms during FW acidogenic fermentation. The VFAs production reached 27.10 ± 1.00 g COD/L when the lipid loading comprised 25 % of the FW dry weight, increasing by 36.88 % compared to the CK group. Lactobacillus, with a relative abundance of 59.43 %, was the predominant genus under lipid loading. In quorum sensing (QS) system, the relative abundance of luxS that is involved in the biosynthetic pathway of the Autoinducer-2 (AI-2) signal molecule increased from 0.066 % to 0.10 % in the presence of lipid. The relative abundance of Genetic Information Processing increased from 16.36 % to 24.25 % under lipid loading, with up-regulation of Translation and Replication and repair. Lipid loading not only promoted the conversion of acetyl-CoA to acetic acid, as evidenced by a 1.36-fold increase in pta gene abundance, but also concurrently suppressed the consumption of acetic acid, reflected in the 96.83 % and 77.16 % decreases in ALDH and aldB abundance, thus accumulating acetic acid. Carbon emission was also constrained under lipid loading, in which the conversion from formate to CO2 and passing Tricarboxylic acid (TCA) cycle were restricted over 60 %. Together, lipid loading in FW represents a potential strategy for enhancing VFAs production in FW acidogenic fermentation.

Essential genes for Haemophilus parainfluenzae survival and biofilm growth.

Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.

Dysbiosis of the gut microbiota in glioblastoma patients and potential biomarkers for risk assessment

BackgroundThe significant death rate of glioblastoma is well-known around the world. The link between gut microbiota and glioma is becoming more studied. The goal of this study was to look at the relationships between intestinal flora and glioblastoma, and to provide a new perspective for the diagnosis as well as treatment of glioblastoma. MethodsFecal samples from 80 participants with glioblastoma (n = 40) and healthy individuals (n = 40) in this study were collected as well as analyzed utilizing 16S rRNA gene amplicon sequencing in order to characterize the gut microbial community. ResultsEach group has its own microbial community, and the microbial environment of glioblastoma patients had lower richness and evenness. The structure of gut microbiota community in glioblastoma patients showed profound changes, which includes the increase of pathogens in Fusobacteria and Bacteroidetes, and the reduction of probiotic bacteria in Firmicutes, Actinobacteria and Verrucomicrobia. Meanwhile, the significant correlations and clustering of OTUS (operational taxonomic units) in glioblastoma patients were discovered, and a biomarker panel (Fusobacterium, Escherichia/Shigella, Ruminococcus gnavus group, Lachnospira, Akkermansia, Parasutterella) had been used to discriminate the patients with glioblastoma from the healthy subjects (AUC: 0.80). Furthermore, the glioblastoma group exhibited multiple disturbed pathways through KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, particularly in genetic information processing. Moreover, the prediction of phenotypic characteristics of microbiome proposed that the glioblastoma patients might have more Gram-negative bacteria and opportunistic pathogens than the healthy controls. ConclusionsWhen compared to healthy people, glioblastoma sufferers have a different host-microbe interaction. Furthermore, certain types of intestinal flora could be regarded as biomarkers and drug targets for the diagnosis as well as treatment of glioblastomas.

Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.

Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2cm) and bottom depth (250cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.

Multiomics-Based Biocargo Components Analysis in Enterococcus faecium Membrane Vesicles.

Enterococcus spp. have been shown to have gastrointestinal tract protective functions; our recent results suggest that membrane vesicles (MVs) play an important role in the gastric protection of Enterococcus faecium (E. faecium). The specific function is determined by molecular compositions of MVs. To resolve biocargo components in E. faecium MVs (EfmMVs), MVs were isolated from E. faecium culture. Transcriptomics, label-free quantitative proteomics, and untargeted metabolomics were performed to obtain information about the complexity of ribonucleic acids (RNAs), proteins, and metabolites biocargo they carry, respectively. RNA-sequencing identified a total of 2122 transcripts. The top 20 transcripts accounted for 27.63% of total counts, which, including enzymes, participate in glycolysis, ribosomal proteins, DNA-directed RNA polymerases, protein-synthesizing relative enzymes, molecules associated with protein post-translational processing and transport, and peptidoglycan lyases. Label-free quantitative proteomics analysis identified a total of 711 proteins. The top 20 proteins accounted for 48.02% of all identified proteins, which including ribosomal proteins, enzymes participate in glycolysis, DNA-directed RNA polymerases, protein-synthesizing relative enzymes, peptidoglycan lyases, and autolysin. Untargeted metabolomics analysis identified a total of 519 metabolites. The top 20 metabolites accounted for 79.55% of all identified metabolites, which included amino acids, substrates, or products in the metabolism of amino acids, natural organic acids, products in the metabolism of organic acids, ketone compounds, and two other compounds. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that the identified biocargo components enriched in metabolism, genetic, and environmental information processing. Overall, we hope that the current exploration of multiple "-omics" analyses of this EfmMVs will provide useful information and further groundwork for future studies on E. faecium application.

Ultrasonic treatment can improve maize seed germination and abiotic stress resistance

Constant-frequency ultrasonic treatment helped to improve seed germination. However, variable-frequency ultrasonic treatment on maize seed germination were rarely reported. In this study, maize seeds were exposed to 20–40 kHz ultrasonic for 40 s. The germination percentage and radicle length of maize seeds increased by 10.4% and 230.5%. Ultrasonic treatment also significantly increased the acid protease, α-amylase, and β-amylase contents by 96.4%, 73.8%, and 49.1%, respectively. Transcriptome analysis showed that 11,475 differentially expressed genes (DEGs) were found in the ultrasonic treatment and control groups, including 5,695 upregulated and 5,780 downregulated. Metabolic pathways and transcription factors (TFs) were significantly enriched among DEGs after ultrasonic treatment. This included metabolism and genetic information processing, that is, ribosome, proteasome, and pyruvate metabolism, sesquiterpenoid, triterpenoid, and phenylpropanoid biosynthesis, and oxidative phosphorylation, as well as transcription factors in the NAC, MYB, bHLH, WRKY, AP2, bZIP, and ARF families. Variable-frequency ultrasonic treatment increased auxin, gibberellin, and salicylic acid by 5.5%, 37.3%, and 28.9%, respectively. Abscisic acid significantly decreased by 33.2%. The related DEGs were upregulated and downregulated to varying degrees. Seed germination under the abiotic stress conditions of salt stress (NaCl solution), drought (PEG solution), and waterlogging (water-saturated sand bed) under ultrasonic treatment were promoted, radicle length was significantly increased by 30.2%, 30.5%, and 27.3%, respectively; and germination percentage by 14.8%, 20.1%, and 21.6%, respectively. These findings provide new insight into the mechanisms through ultrasonic to promote maize seed germination.

Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae.

Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N = 14) and high-quality draft H. influenzae genomes (N = 2297). The draft genome dataset was divided into a development dataset (N = 921) and a validation dataset (N = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R 2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen.

A mutated algal species of Isochrysis sp. obtained via atmospheric room temperature plasma mutagenesis promoted lipid accumulation through the abscisic acid pathway

Isochrysis sp. is an economically important algae rich in unsaturated fatty acids, but its susceptibility to strain degeneration poses challenges for practical applications. To address this, we used atmospheric room temperature plasma (ARTP) for mutagenesis, creating a stable mutant strain, Yield 8 (Y8), with rapid growth and high lipid content. Transcriptome analysis showed upregulation of genes in genetic information processes and metabolic pathways, with notable upregulation of long-chain fatty acid CoA ligase and acyl-CoA acyltransferase (ACAT), consistent with the trend of fatty acid accumulation. Interestingly, the expression levels of ζ-carotene desaturase (ZDS), zeaxanthin epoxidase (ZEP), and phosphatase 2C (PP2C) were upregulated in the Y8 mutant, indicating activation of the ABA pathway. Further, the increased endogenous ABA levels in Y8, along with a 1.17-fold increase in DHA and a 1.26-fold increase in ω3 fatty acids after exogenous ABA application, suggest that Y8's improved traits are mediated by the ABA pathway. These findings highlight Y8's potential for practical applications and further research.

Interspecific and Intraspecific Transcriptomic Variations Unveil the Potential High-Altitude Adaptation Mechanisms of the Parnassius Butterfly Species.

Parnassius butterflies have significantly advanced our understanding of biogeography, insect-plant interactions, and other fields of ecology and evolutionary biology. However, to date, little is known about the gene expression patterns related to the high-altitude adaptation of Parnassius species. In this study, we obtained high-throughput RNA-seq data of 48 adult Parnassius individuals covering 10 species from 12 localities in China, and deciphered their interspecific and intraspecific expression patterns based on comparative transcriptomic analyses. Though divergent transcriptional patterns among species and populations at different altitudes were found, a series of pathways related to genetic information processing (i.e., recombination, repair, transcription, RNA processing, and ribosome biogenesis), energy metabolism (i.e., oxidative phosphorylation, thermogenesis, and the citrate cycle), and cellular homeostasis were commonly enriched, reflecting similar strategies to cope with the high-altitude environments by activating energy metabolism, enhancing immune defense, and concurrently inhibiting cell growth and development. These findings deepen our understanding about the molecular mechanisms of adaptative evolution to extreme environments, and provide us with some theoretical criteria for the biodiversity conservation of alpine insects.

Fe(III)-mediated changes in microalgae-associated bacterial communities and dissolved organic matter characteristics: A case study for Chlorococcum sp. GD

Trivalent iron ions (Fe(III)) have important effects on aquatic ecosystems, especially on the functional diversity and stability of microorganisms and ecosystems. Here, a cultivable microalgae (Chlorococcum sp. GD) from the natural environment (Shanxi, China) were isolated and identified. A combined high-throughput 16S rRNA gene amplicon sequencing/excitation-emission matrix coupled with parallel factor (EEM-PARAFAC) analysis was used to integrated the results of Fe(III) influence on Chlorococcum sp. GD bacterial community and dissolved organic matter (DOM) characteristics through laboratory experiments. Due to the addition of Fe(III) in the form of ferric nitrate (Fe(NO3)3·9H2O), complexed with EDTA to maintain solubility and bioavailability, the bacterial community was altered. This led to a decrease in the relative abundance of Proteobacteria and Actinobacteria and an increase in the relative abundance of Cyanobacteria, especially under excessive Fe(III) treatment. In addition, the relative contribution of bacterial community dispersal limitation and homogenizing dispersal was 100 %, which may lead to differences in their local adaptation and ecological processes with homogenization of bacterial diversity and loss of function. Excessive Fe(III) caused a significant increase in the abundance of genes involved in the carbon cycle (p < 0.01) and a significant decrease in genes involved in the nitrogen cycle (p < 0.01), further affecting the overall regulatory network of gene expression. This led to an increase in the abundance of genes involved in metabolism, cellular processes, environmental information processing, genetic information processing, and human diseases. The moderate amount of Fe(III) promoted the production of microbial components and accelerated the degree of DOM humification. It is also worth mentioning that excessive Fe(III) inhibited DOM degradation. Overall, this work explored the characteristics of bacterial community and DOM changes in Fe(III)-stressed Chlorococcum sp. GD as an example, which contributes to an in-depth understanding of microbial community diversity and element cycling in aquatic ecosystems.

New insight into Na+-promoted microbial electrolysis cell towards hydrogen energy recovery: Feasibility and dual mechanism in salt-containing wastewater treatment

The salt-containing wastewater treatment has become serious challenge, while conductivity and micro-ecosystem disorder severely limited microbial electrolysis cell (MEC) efficiency. In order to synchronously overcome the above bottlenecks, this study proposed an innovative Na+-promoted MEC system for efficient salt-containing wastewater treatment. The Na+ presence greatly improved conductivity to impair electric resistance, resulting in rapid electron transfer pattern towards organic degradation in anode and hydrogen synthesis in cathode. Furthermore, the selective Na+ stress triggered microbial community evolution and improved electroactive bacteria activity after salinity cultivation in MEC (0.09–0.17 mol Na+/L), which played “bacteria screening” role for salt-tolerant “electrochemical hydrogen-producing” bacteria community formation. The organic-degrading and hydrogen-producing bacteria with their assistors were tolerant to Na+ stress, which were considerably enriched into dominant microorganisms, while the unfavorable bacteria responsible for hydrogen consumption and competition were inhibited due to salinity-sensitivity. Correspondingly, the metabolic pathways for metabolism, genetic information processing and environmental information processing were improved, positively associating with organic degradation and hydrogen production. Such dual driving contributions of Na+-improved electron transfer-utilization pattern and Na+-modified microbial metabolisms boosted the organic pollutant degradation at anode to 91.34 % while improving the performance and speeds of hydrogen production by 1.57–1.70 times. The hydrogen abundance was also increased to 71.57 % in biogas. The energy efficiencies relative to external electricity and substrates were elevated by 8.80–28.44 %, the coulombic efficiency raised by 14.05 % and reached 109.72 %, suggesting the positive net energy benefits. The findings provided inspirations to the feasible application of MEC in salt-containing wastewater treatment with efficiency benefits.

Gestational exposure to environmental chemicals and epigenetic alterations in the placenta and cord blood mononuclear cells

BackgroundExposure to environmental chemicals such as phthalates, phenols, and polycyclic aromatic hydrocarbons (PAHs) during pregnancy can increase the risk of adverse newborn outcomes. We explored the associations between maternal exposure to select environmental chemicals and DNA methylation in cord blood mononuclear cells (CBMC) and placental tissue (maternal and fetal sides) to identify potential mechanisms underlying these associations.MethodThis study included 75 pregnant individuals who planned to give birth at the University of Cincinnati Hospital between 2014 and 2017. Maternal urine samples during the delivery visit were collected and analyzed for 37 biomarkers of phenols (12), phthalates (13), phthalate replacements (4), and PAHs (8). Cord blood and placenta tissue (maternal and fetal sides) were also collected to measure the DNA methylation intensities using the Infinium HumanMethylation450K BeadChip. We used linear regression, adjusting for potential confounders, to assess CpG-specific methylation changes in CBMC (n = 54) and placenta [fetal (n = 67) and maternal (n = 68) sides] associated with gestational chemical exposures (29 of 37 biomarkers measured in this study). To account for multiple testing, we used a false discovery rate q-values < 0.05 and presented results by limiting results with a genomic inflation factor of 1±0.5. Additionally, gene set enrichment analysis was conducted using the Kyoto Encyclopedia of Genes and Genomics pathways.ResultsAmong the 29 chemical biomarkers assessed for differential methylation, maternal concentrations of PAH metabolites (1-hydroxynaphthalene, 2-hydroxyfluorene, 4-hydroxyphenanthrene, 1-hydroxypyrene), monocarboxyisononyl phthalate, mono-3-carboxypropyl phthalate, and bisphenol A were associated with altered methylation in placenta (maternal or fetal side). Among exposure biomarkers associated with epigenetic changes, 1-hydroxynaphthalene, and mono-3-carboxypropyl phthalate were consistently associated with differential CpG methylation in the placenta. Gene enrichment analysis indicated that maternal 1-hydroxynaphthalene was associated with lipid metabolism and cellular processes of the placenta. Additionally, mono-3-carboxypropyl phthalate was associated with organismal systems and genetic information processing of the placenta.ConclusionAmong the 29 chemical biomarkers assessed during delivery, 1-hydroxynaphthalene and mono-3-carboxypropyl phthalate were associated with DNA methylation in the placenta.

DeTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets.

Errors in the processing of genetic information during protein synthesis can lead to phenotypic mutations, such as amino acid substitutions, e.g. by transcription or translation errors. While genetic mutations can be readily identified using DNA sequencing, and mutations due to transcription errors by RNA sequencing, translation errors can only be identified proteome-wide using mass spectrometry. Here, we provide a Python package implementation of a high-throughput pipeline to detect amino acid substitutions in mass spectrometry datasets. Our tools enable users to process hundreds of mass spectrometry datasets in batch mode to detect amino acid substitutions and calculate codon-specific and site-specific translation error rates. deTELpy will facilitate the systematic understanding of amino acid misincorporation rates (translation error rates), and the inference of error models across organisms and under stress conditions, such as drug treatment or disease conditions. deTELpy is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://git.mpi-cbg.de/tothpetroczylab/detelpy and https://pypi.org/project/deTELpy/ and can be easily installed via pip install deTELpy.

Mutation in the Bombyx mori BmGMC2 gene impacts silk production and silk protein synthesis

Silk is a natural protein fiber that is predominantly comprised of fibroin and sericin. In addition, it contains seroins, protease inhibitors, enzymes, and other proteins. We found an ecdysone oxidase BmGMC2, notably, which is specifically and highly expressed only in the silk glands of silkworms (Bombyx mori L.). It is also one of the main components of non-cocoon silk, however, its precise function remains unclear. In this study, we examined the spatiotemporal expression pattern of this protein and obtained a homozygous mutant strain (K-GMC2) using the CRISPR-Cas9 system. Compared to the wild-type strain (WT), the silk production and main silk proteins significantly decreased in the larval stage, and the adhesive strength of native silk proteins decreased in the final instar. Proteomic data indicated the abundance of ribosomal proteins decreased significantly in K-GMC2, differentially expressed proteins (DEPs) were enriched in pathways related to neurodegenerative diseases and genetic information processing, indicating that knockout may lead to a certain degree of cell stress, affecting the synthesis of silk proteins. This study investigated the expression pattern and gene function of ecdysone oxidase BmGMC2 in silk and silk glands, laying the groundwork for understanding the role of enzymes in the production of silk fibers.

Integrated Analysis of Microbiome and Metabolome Reveals Disease-Specific Profiles in Inflammatory Bowel Diseases and Intestinal Behçet's Disease.

The gut microbial and metabolic characteristics of intestinal Behçet's disease (BD), a condition sharing many clinical similarities with ulcerative colitis (UC) and Crohn's disease (CD), are largely unexplored. This study investigated the gut microbial and metabolic characteristics of intestinal BD as well as potential biomarkers, comparing them with those in UC, CD, and healthy controls. Colon tissue and stool samples from 100 patients (35 UC, 30 CD, and 35 intestinal BD) and 41 healthy volunteers were analyzed using 16S ribosomal RNA sequencing to assess microbial diversity, taxonomic composition, and functional profiling. Plasma metabolomic analyses were performed using gas chromatography and ultra-performance liquid chromatography-mass spectrometry. Results indicated reduced microbial diversity in CD but not in intestinal BD, with intestinal BD showing fewer changes compared to controls yet distinct taxonomic features from UC, CD, and controls. Common alterations across all diseases included a reduction in beneficial bacteria producing short-chain fatty acids. Intestinal BD-specific changes featured a decreased abundance of Bacteroides fragilis. Metabolomic profiles in intestinal BD were similar to those in CD but distinct from those in UC, displaying significant changes in energy metabolism and genetic information processing. This integrative analysis revealed both shared and unique profiles in intestinal BD compared with UC, CD, and controls, advancing our understanding of the distinctive features of these diseases.