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AbstractFungicides are commonly applied through root irrigation in tobacco fields to control soil-borne diseases, and they affect soil microorganisms. However, the effects of metalaxyl-M and hymexazol, used to manage tobacco black shank disease, on these soil microecology remain poorly understood. This study employed high-throughput sequencing technology to explore the soil physical and chemical properties, soil enzyme activity, and the diversity, community structure and function of soil fungi in tobacco fields following root irrigation with metalaxyl-M and hymexazol. The results revealed that ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N), soil organic matter (SOM), electrical conductivity (EC) and soil urease (UE) in soil were significantly increased and the pH decreased after root-irrigation with these two fungicides. The abundance of soil fungal community was significantly reduced after the root-irrigation of metalaxyl-M and hymexazol. The relative abundance of Ascomycota increased significantly after the treatment with metalaxyl-M. Following hymexazol treatment, the abundance of Achroiostachys, Nigrospora, Ustilaginoidea, and Trichoderma significantly decreased. Functional prediction analysis indicated an increase in the relative abundance of functional genes of saprophytic fungi after treatment with both fungicides. This study provides a foundational understanding of the environmental behavior and supports the scientific and rational use of metalaxyl-M and hymexazol in soil. [ABSTRACT FROM AUTHOR]

Objective: To investigate ear canal microflora's structure, composition and function in patients with chronic bacterial otitis externa. Methods: A case-control study design method was used to collect the ear canal secretions from 14 patients with chronic bacterial external otitis (CB group) and 14 healthy controls (H group) treated in the Department of Otolaryngology and Head and Neck Surgery in the First Affiliated Hospital of Hainan Medical University. 16S rRNA high-throughput sequencing technology was used to sequence the ear canal microflora's V3 ~ V4 region gene amplification products in the participating population. The α diversity of ear canal microflora in 2 groups was analyzed. Based on the weighted Unifrac distance, principal coordinate analysis was performed to compare the β diversity of ear tract microflora between the two groups. The differences in ear microflora at phylum and genus levels were analyzed. PICRUSt2 function prediction and BugBase phenotype prediction were also performed. Results: α diversity analysis showed that the diversity and richness of auricular microflora in the CB group were significantly lower than those in the H group. β diversity analysis showed that there were some differences between the two groups. At the phylum level, the relative abundance of Bdellovibrionota, Campylobacterota, and WPS-2 in the microbiota of patients in the CB group was significantly lower than that in the H group, and the differences were statistically significant. At the genus level, the relative abundance of Pseudomonas , Acinetobacter , Pelomonas , Sphingomonas , Bradyrhizobium , Brevundimonas , Enhydrobacter , Actinomyces , Paracoccus and Chryseobacterium in the ear canal of Group H is significantly higher than that of Group CB. Functional prediction of PICRUSt2 suggests that amino acid biosynthesis and bacterial microbiota may be related. In BugBase phenotypic prediction, the contribution of aerobic phenotype in group CB was significantly lower than that in group H. Conclusion: The diversity and abundance of the ear canal flora of patients with chronic bacterial otitis externa were significantly lower than those of the healthy population, and their bacterial colony structure was significantly altered. Dysbiosis of the ear canal flora may be an important cause of chronic bacterial otitis externa. [ABSTRACT FROM AUTHOR]

Copyright of Journal of South China Agricultural University is the property of Gai Kan Bian Wei Hui and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Background The plant microbiome is one of the key determinants of healthy plant growth. However, the complexity of microbial diversity in plant microenvironments in different regions, especially the relationship between subsurface and aboveground microorganisms, is not fully understood. The present study investigated the diversity of soil microorganisms in different regions and the diversity of microorganisms within different ecological niches, and compared soil microorganisms and endophytic microorganisms. Methods 16 S and ITS sequencing was used to sequence the soil and endophytes microbiome of honeysuckle. Alpha diversity analysis and principal component analysis (PCoA) were used to study the soil and endophyte microbial communities, and the function of endophyte bacteria and fungi was predicted based on the PICRUST2 process and FUNGuild. Results In total, there were 382 common bacterial genera and 139 common fungal genera in the soil of different producing areas of honeysuckle. There were 398 common bacterial genera and 157 common fungal genera in rhizosphere soil. More beneficial bacteria were enriched in rhizosphere soil. Endophytic bacteria were classified into 34 phyla and 770 genera. Endophytic fungi were classified into 11 phyla and 581 genera, among which there were significant differences in the dominant genera of roots, stems, leaves, and flowers, as well as in community diversity and richness. Endophytic fungal functions were mainly dominated by genes related to saprophytes, functional genes that could fight microorganisms were also found in KEGG secondary functional genes. Conclusion More beneficial bacteria were enriched in rhizosphere soil of honeysuckle, and the microbial network of the rhizosphere is more complex than that of the soil. Among the tissues of honeysuckle, the flowers have the richest diversity of endophytes. The endogenous dominant core bacteria in each part of honeysuckle plant have a high degree of overlap with the dominant bacteria in soil. Functional prediction suggested that some dominant core bacteria have antibacterial effects, providing a reference for further exploring the strains with antibacterial function of honeysuckle. Understanding the interaction between honeysuckle and microorganisms lays a foundation for the study of growth promotion, quality improvement, and disease and pests control of honeysuckle from the perspective of microorganisms.

Based on a polluted site in Tianjin area, the experiment was designed to compare two soil columns in the addition group and the control group by using the screened petroleum hydrocarbon degrading functional bacteria. The effects of the functional bacteria on petroleum hydrocarbon degradation were investigated by measuring the concentrations of petroleum hydrocarbon, HCO3 - and CO3 2-, combining with 16S high-throughput sequencing, comparing the microbial community structure before and after the reaction, and predicting the function of the sequencing results. The results showed that the addition of functional bacteria had a significant effect on the degradation of petroleum hydrocarbons. The species composition of the column showed that the addition of functional bacteria changed the microbial community diversity in the soil column, and the addition of functional bacteria promoted the growth of Desulfobrunum phylum and inhibited the reproduction of Actinobacterium phylum. Desulfoprunum was mainly present at the water outlet of the two groups of experiments, and it was speculated that sulphate redox reactions existed at the water inlet for both groups of experiments. The relative abundance of Thermincola was higher at the outlet of the bacterial addition group, which was accompanied by strong redox reactions such as denitrification and iron reduction. The analyses of alpha diversity showed that the microbial community diversity was higher in the two groups of test outfalls, while the analyses of beta diversity indicated that the microbial community structure may be related to the spatial location of the test columns. In addition, ecological network analysis revealed that Ascomycota was the key phylum in the tests, and the addition of functional bacteria promoted the synergistic and cooperative relationship among species. PICRUSt2 functional prediction analysis showed that the addition of functional bacteria only enhanced the abundance of bamB, bamC in the water intake, and badA, badDEFG in the water outflow. [ABSTRACT FROM AUTHOR]

Spartina alterniflora is recognized as one of the most detrimental invasive species along China's coastlines, highlighting the need for effective and environmentally safe management strategies to preserve intertidal zones. This study assessed the effectiveness of combining plant growth regulators (PRGs) with physical cutting to manage S. alterniflora, using 16S rRNA and 18S rRNA gene sequencing to evaluate the impacts on the plant and associated soil micro-organisms. The results showed that compared to the control (CK), the regeneration numbers for treatments with abscisic acid (ABA), gibberellin (GA), paclobutrazol (PP333), garcinol (GC), and glyphosate (GP) decreased by 29.75%, 23.25%, 15.75%, 94.50%, and 40.50%, respectively. Comparative analysis revealed no statistically significant variation in the inhibitory effects of ABA and GP on the germination of S. alterniflora (p > 0.05). Additionally, applying PRGs and herbicides increased the diversity indices of soil bacteria and fungi. Principal Coordinates Analysis (PCoA) showed that the impact of PRGs on the fungal community was less pronounced than that of herbicides. Significant differences were also noted in the abundance of microbial functional genes related to methanotrophy, hydrocarbon degradation, and denitrification compared to the control (p < 0.05). This study aimed to assess the potential of PRGs in controlling the invasion of S. alterniflora and to elucidate their impacts on soil microbial communities and functional gene expression. [ABSTRACT FROM AUTHOR]

This study investigated the response of a bacterial community's structure and function in the rhizosphere soil of C3 and C4 plants under bis(2,4,6-tribromophenoxy) ethane (BTBPE) exposure. The bacterial community composition was determined using 16S rRNA sequencing, while FAPROTAX and PICRUSt 2 were employed for functional predictions. Results showed significant differences between C3 and C4 plants in terms of bacterial community structure. C3 plants exhibited higher abundances of Proteobacteria, Bacteroidetes at the phylum level and Sphingomicrobium at the genus level, compared to C4 plants. Conversely, C4 plants had higher abundances of Actinobacteria and Patescibacteria at the phylum level and Nocardioides at the genus level. LEfSe and function prediction analyses revealed that the rhizosphere soil bacteria in C3 plants exhibited significantly higher enrichment in nitrogen fixation functions (p < 0.05), whereas C4 plants showed a significantly higher relative abundance of bacteria and functions related to organic pollutant degradation (p < 0.05). These findings suggest that the rhizosphere soil bacteria of C3 plants exhibit a stronger response to BTBPE exposure in nitrogen metabolism-related processes, while C4 plants possess superior biodegradation ability compared to C3 plants. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Henan Agricultural Sciences is the property of Editorial Board of Journal of Henan Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

ABSTRACT4-coumaric acid coenzyme A ligase (4CL) plays an important role in plant growth, development and resistance. Based on the Musa acuminata (A genome) genome database, we performed genome-wide identification and evolutionary analysis of the 4CL gene family.The results showed that there were 20 members of 4CL, and the amino acids encoded ranged from 160 to 700, all of which were hydrophobic proteins. All the members of the 4CL gene family had no signal peptide, and phosphorylation sites ranged from 10 to 60. The 4CL genes were uniformly distributed and disordered in the chromosomes. All protein members can interact with each other.Transcriptome expression analysis showed that Ma4CL3-2 expression was down-regulated and Ma4CL11-1 expression was up-regulated. Musa acuminata genomics has 22 and 19 pairs of co-linear members with Musa balbisiana and Musa itinerans genomics, respectively.The above results provide a good foundation for further research on the function of the 4CL genes and resistance breeding.Highlights Twenty 4CL gene family members were found in banana (Musa acuminata) genomes.Banana 4CLs were expressed in response to low temperature stress.The members of the banana 4CL gene family were found to be relatively structurally diverse, and it was further hypothesised that 4CL may be involved in plant lignin synthesis and closely related to the process of plant differentiation into monocotyledons and dicotyledons, based on the hypothesis of Huang et al.

ObjectiveTo investigate ear canal microflora’s structure, composition and function in patients with chronic bacterial otitis externa.MethodsA case-control study design method was used to collect the ear canal secretions from 14 patients with chronic bacterial external otitis (CB group) and 14 healthy controls (H group) treated in the Department of Otolaryngology and Head and Neck Surgery in the First Affiliated Hospital of Hainan Medical University. 16S rRNA high-throughput sequencing technology was used to sequence the ear canal microflora’s V3 ~ V4 region gene amplification products in the participating population. The α diversity of ear canal microflora in 2 groups was analyzed. Based on the weighted Unifrac distance, principal coordinate analysis was performed to compare the β diversity of ear tract microflora between the two groups. The differences in ear microflora at phylum and genus levels were analyzed. PICRUSt2 function prediction and BugBase phenotype prediction were also performed.Resultsα diversity analysis showed that the diversity and richness of auricular microflora in the CB group were significantly lower than those in the H group. β diversity analysis showed that there were some differences between the two groups. At the phylum level, the relative abundance of Bdellovibrionota, Campylobacterota, and WPS-2 in the microbiota of patients in the CB group was significantly lower than that in the H group, and the differences were statistically significant. At the genus level, the relative abundance of Pseudomonas, Acinetobacter, Pelomonas, Sphingomonas, Bradyrhizobium, Brevundimonas, Enhydrobacter, Actinomyces, Paracoccus and Chryseobacterium in the ear canal of Group H is significantly higher than that of Group CB. Functional prediction of PICRUSt2 suggests that amino acid biosynthesis and bacterial microbiota may be related. In BugBase phenotypic prediction, the contribution of aerobic phenotype in group CB was significantly lower than that in group H.ConclusionThe diversity and abundance of the ear canal flora of patients with chronic bacterial otitis externa were significantly lower than those of the healthy population, and their bacterial colony structure was significantly altered. Dysbiosis of the ear canal flora may be an important cause of chronic bacterial otitis externa.

Objective To analyze the composition of microbial community in gut of elderly male Nycticebus bengalensis, aiming to explore the health impact factors associated with artificial captivity. Methods Fecal samples of 4 adult male Nycticebus bengalensis were collected and the V4 region was amplified using bacterial 16S rDNA universal primers. Illumina NovaSeq sequencing platform was used for microbial sequencing analysis. The complexity and similarity of the samples were analyzed using the QIIME software analysis tool. The species structure and abundance of the intestinal flora were analyzed at the phylum and genus levels based on validated data. The PICRUSt software was applied to predict the metabolic function of the flora. Results The results showed that the diversity index (Shannon index) of the flora in the youngest Nycticebus bengalensis was higher than that of the others. PCoA analysis showed that the bacterial community compositions of the four samples had a certain degree of similarity. Bacteria identified in the Nycticebus bengalensis feces included 12 phyla, 18 classes, 28 orders, 49 families, 93 genera, and 59 species. Among them, the dominant phyla were Bacteroidetes and Firmicutes with average relative abundances of 46% and 28%, respectively; The genera Bacteroides, Bifidobacterium, and Fusobacterium had higher abundances, with relative abundances of 33%, 6%, and 6%, respectively; The beneficial genus Bifidobacterium was found in all samples, with the highest relative abundance found in the younger Nycticebus bengalensis. PICRUSt function prediction analysis showed that the abundance of the functional genes related to amino acid transport and metabolism, carbohydrate transport and metabolism,was relatively high. Conclusion The use of Illumina NovaSeq high-throughput sequencing technology can comprehensively detect the fecal microbial community of the Nycticebus bengalensis. The bacterial composition of Nycticebus bengalensis has rich diversity. Many bacteria are not identified and have higher relative abundance, which need further study.

Abstract Recent studies have shifted the spotlight from adult disease to gametogenesis and embryo developmental events, and these are greatly affected by various environmental chemicals, such as drugs, metabolites, pollutants, and others. Growing research has highlighted the critical importance of identifying and understanding the roles of chemicals in reproductive biology. However, the functions and mechanisms of chemicals in reproductive processes remain incomplete. We developed a comprehensive database called the Reproductive Chemical Database (RCDB) ( https://yu.life.sjtu.edu.cn/ChenLab/RCDB ) to facilitate research on chemicals in reproductive biology. This resource is founded on rigorous manual literature extraction and precise protein target prediction methodologies. This database focuses on the delineation of chemicals associated with phenotypes, diseases, or endpoints intricately associated with four important reproductive processes: female and male gamete generation, fertilization, and embryo development in human and mouse. The RCDB encompasses 93 sub-GO processes, and it revealed 1447 intricate chemical–biological process interactions. To date, the RCDB has meticulously cataloged and annotated 830 distinct chemicals, while also predicting 614 target proteins from a selection of 3800 potential candidates. Additionally, the RCDB offers an online predictive tool that empowers researchers to ascertain whether specific chemicals play discernible functional roles in these reproductive processes. The RCDB is an exhaustive, cross-platform, manually curated database, which provides a user-friendly interface to search, browse, and use reproductive processes modulators and their comprehensive related information. The RCDB will help researchers to understand the whole reproductive process and related diseases and it has the potential to promote reproduction research in the pharmacological and pathophysiological areas. Graphical Abstract

Recent studies have shifted the spotlight from adult disease to gametogenesis and embryo developmental events, and these are greatly affected by various environmental chemicals, such as drugs, metabolites, pollutants, and others. Growing research has highlighted the critical importance of identifying and understanding the roles of chemicals in reproductive biology. However, the functions and mechanisms of chemicals in reproductive processes remain incomplete. We developed a comprehensive database called the Reproductive Chemical Database (RCDB) (https://yu.life.sjtu.edu.cn/ChenLab/RCDB) to facilitate research on chemicals in reproductive biology. This resource is founded on rigorous manual literature extraction and precise protein target prediction methodologies. This database focuses on the delineation of chemicals associated with phenotypes, diseases, or endpoints intricately associated with four important reproductive processes: female and male gamete generation, fertilization, and embryo development in human and mouse. The RCDB encompasses 93 sub-GO processes, and it revealed 1447 intricate chemical–biological process interactions. To date, the RCDB has meticulously cataloged and annotated 830 distinct chemicals, while also predicting 614 target proteins from a selection of 3800 potential candidates. Additionally, the RCDB offers an online predictive tool that empowers researchers to ascertain whether specific chemicals play discernible functional roles in these reproductive processes. The RCDB is an exhaustive, cross-platform, manually curated database, which provides a user-friendly interface to search, browse, and use reproductive processes modulators and their comprehensive related information. The RCDB will help researchers to understand the whole reproductive process and related diseases and it has the potential to promote reproduction research in the pharmacological and pathophysiological areas. [ABSTRACT FROM AUTHOR]

Objective To analyze the composition of microbial community in gut of elderly male Nycticebus bengalensis, aiming to explore the health impact factors associated with artificial captivity. Methods Fecal samples of 4 adult male Nycticebus bengalensis were collected and the V4 region was amplified using bacterial 16S rDNA universal primers. Illumina NovaSeq sequencing platform was used for microbial sequencing analysis. The complexity and similarity of the samples were analyzed using the QIIME software analysis tool. The species structure and abundance of the intestinal flora were analyzed at the phylum and genus levels based on validated data. The PICRUSt software was applied to predict the metabolic function of the flora. Results The results showed that the diversity index (Shannon index) of the flora in the youngest Nycticebus bengalensis was higher than that of the others. PCoA analysis showed that the bacterial community compositions of the four samples had a certain degree of similarity. Bacteria identified in the Nycticebus bengalensis feces included 12 phyla, 18 classes, 28 orders, 49 families, 93 genera, and 59 species. Among them, the dominant phyla were Bacteroidetes and Firmicutes with average relative abundances of 46% and 28%, respectively; The genera Bacteroides, Bifidobacterium, and Fusobacterium had higher abundances, with relative abundances of 33%, 6%, and 6%, respectively; The beneficial genus Bifidobacterium was found in all samples, with the highest relative abundance found in the younger Nycticebus bengalensis. PICRUSt function prediction analysis showed that the abundance of the functional genes related to amino acid transport and metabolism, carbohydrate transport and metabolism, was relatively high. Conclusion The use of Illumina NovaSeq high-throughput sequencing technology can comprehensively detect the fecal microbial community of the Nycticebus bengalensis. The bacterial composition of Nycticebus bengalensis has rich diversity. Many bacteria are not identified and have higher relative abundance, which need further study. [ABSTRACT FROM AUTHOR]

In order to explore the bacterial community composition of mung bean sour pulp, the core element of Luoyang traditional and special pulp noodles, the bacteria 16S rDNA of mung bean sour pulp from six pulp workshops in Lu-oyang was sequenced using Illumina MiSeq high-throughput sequencing technology. The results showed that 8 bacterial phyla were identified from 6 samples of mung bean sour pulp, involving 75 genera and 106 species; and Firmicutes is the dominant phylum (78.57%-97.17%), Lactobacillus (20.95%-90.36%) and Lactococcus (3.26%-62.68%) are the dominant genus, Lactobacillus oligofermentans, unclassified_Lactococcus are the corresponding dominant species, while Lactobacillus plantarum, Lactobacillus curvatus and Lactobacillus manihotivorans are common sub dominant bacteria. These dominant bacteria are all lactic acid bacteria, which have extensive prebiotic effects. The functional prediction of the bacterial community in mung bean sour pulp showed that the carbohydrate metabolism and amino acid metabolism abundance of the bacterial community are high, especially the abundance of flavor amino acid metabolic pathway and L-lactate dehydrogenase are relatively high. It was inferred that the unique acid and flavor of mung bean sour pulp was related to the bacterial amino acid metabolism and lactic acid synthesis. The results of this study provided a theoretical basis for further study on the fermentation mechanism of mung bean sour pulp and development of corresponding starter. [ABSTRACT FROM AUTHOR]

Soil salinization adversely affects soil quality and ecosystem. Many researches have tried to ameliorate saline soils by soil conditioners. However, little is known about the differences in the responses of soil bacterial communities to natural and artificial conditioners applied to saline soils. Therefore, in this study, the effects of natural humic acid (IK), synthetic polymer (IP), and composite material (IF) (mixture of IK and IP (1:1)) on bacterial community structure and functional genes in saline soil were evaluated to clarify their differences. The results showed that the application of the three soil conditioners significantly reduced soil pH and Na+ content but increased soil alkaline phosphatase, urease, invertase and catalase activities, bacterial diversity, and nutrients, compared to the control (no conditioner). IK application increased bacterial relative abundance (e.g., Subgroup_6, RB41, MND1, and KD4‐96) and metabolic functions (e.g., Two‐component system and Biosynthesis of amino acids) by increasing soil nitrogen and maintaining K+ and Na+ balance. IP application increased soil alkaline phosphatase and urease activities as well as bacterial relative abundance (e.g., Subgroup_6, RB41, MND1, Gemmatimonadaceae, and KD4‐96) and metabolic functions (e.g., Quorum sensing and carbon metabolism) by increasing soil organic carbon/nitrogen content. IF application increased the bacterial relative abundance of Subgroup_6, RB41, and MND1 by increasing soil available nitrogen and regulated their metabolic pathways (e.g., ABC transporters and microbial metabolism). On the whole, IK, IP, and IF could regulate the structure and function of soil bacterial community in saline soils. This study clarifies difference in the effects of different soil conditioners on the amelioration of saline soils from the perspective of soil microbiology, and provides a reference for the amelioration of saline soils in arid areas. [ABSTRACT FROM AUTHOR]

While spent mushroom substrate (SMS) has shown promise in increasing soil organic carbon (SOC) and improving soil quality, research on the interplay between SOC components and microbial community following the application of diverse SMS types remains scant. A laboratory soil incubation experiment was conducted with application of two types of SMSs from cultivation of Pleurotus eryngii (PE) and Agaricus bisporus (AB), each at three application rates (3, 5.5, and 8%). Advanced techniques, including solid-state 13C nuclear magnetic resonance (NMR) and high-throughput sequencing, were employed to investigate on SOC fractions and chemical structure, microbial community composition and functionality. Compared to SMS-AB, SMS-PE application increased the relative abundances of carbohydrate carbon and O-alkyl C in SOC. In addition, SMS-PE application increased the relative abundance of the bacterial phylum Proteobacteria and those of the fungal phyla Basidiomycota and Ascomycota. The relative abundances of cellulose-degrading bacterial (e.g., Flavisolibacter and Agromyces) and fungal genera (e.g., Myceliophthora, Thermomyces, and Conocybe) were increased as well. The application of SMS-AB increased the aromaticity index of SOC, the relative abundance of aromatic C, and the contents of humic acid and heavy fraction organic carbon. In addition, SMSAB application significantly increased the relative abundances of the bacterial phyla Firmicutes and Actinobacteria. Notably, the genera Actinomadura, Ilumatobacter, and Bacillus, which were positively correlated with humic acid, experienced an increase in relative abundance. Functional prediction revealed that SMS-PE application elevated carbohydrate metabolism and reduced the prevalence of fungal pathogens, particularly Fusarium. The application of highrate SMS-AB (8%) enhanced bacterial amino acid metabolism and the relative abundances of plant pathogenic fungi. Our research provides strategies for utilizing SMS to enrich soil organic carbon and fortify soil health, facilitating the achievement of sustainable soil management. [ABSTRACT FROM AUTHOR]

Copyright of Modern Food Science & Technology is the property of Editorial Office of Modern Food Science & Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Journal of Hydrobiology is the property of Editorial Department of Journal of Hydrobiology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.

The fungal community structure, the relationship between fungal flora and physicochemical factors, and the prediction of fungal function in pit muds from different spatial positions of 10- and 50-year-old cellars at Jinhui liquor Co. Ltd. were studied by using Illumina NovaSeq high-throughput sequencing, redundancy analysis and Fungi Functional Guild (FUNGuild). The results showed that the fungal diversity and richness of the 10-year-old pit mud decreased with increasing depth; the fungal diversity of the 50-year-old pit mud showed an overall increasing trend, while the fungal richness initially decrease and then increased. Moreover, for the 10-year-old pit, the fungal diversity and richness of the upper layer of the pit wall were significantly higher than those of the other positions (P < 0.05), while for the 50-year-old cellar, the fungal diversity and richness of the bottom layer were significantly higher than those of the other locations (P < 0.05). The fungal diversity and richness were significantly higher in the wall of the 10-year-old cellar than the 50-year-old cellar (P < 0.05), but were significantly higher in the bottom of the 50-year-old cellar than the 10-year-old cellar (P < 0.05). A total of 21 fungal phyla and 520 genera were detected in all pit mud samples, the relative abundance of four dominant phyla (Ascomycota, Basidiomycota, Mortierellomycota and Rozellomycota) and most dominant genera such as Aspergillus and Kazachstania showed significant changes among pit ages and spatial locations (P < 0.05). Fusarium, Aspergillus, Saccharomyces and Monascus were positively correlated with the contents of water, humus, K+ and Ca2+, while Cladosporium and Vishniacozyma were positively correlated with pH. Seven nutritional modes of fungi were observed, mainly including saprophytic and pathological-saprophytic-symbiotic nutritional modes, and four single and seven mixed functional groups were determined. This study provides a theoretical basis for clarifying the structure and spatial distribution of fungal community in Jinhui Baijiu pit mud.

[Objective] To study the changes of physico-chemical characteristics and microbial community structure during natural aerobic composting under low temperature in the field, realize the resource utilization of breeding waste in low temperature season. [Method] Using pig manure and rice husk as raw materials for aerobic composting in the field, the temperature, pH, water content, NH+4-N, NO-3-N and germination index (GI) of seeds during composting process were analyzed, the bacterial 16S rDNA V3-V4 region and fungal ITS region were further selected for high-throughput sequencing. The diversity and composition of microbial communities in different stages of aerobic composting process were compared. [Result] When the environmental temperature was -6.7-6.4 ℃, the high-temperature stage of the entire composting process lasted for 11 days. After 38 days of aerobic composting treatment, the moisture content, pH, NH+4-N, NO-3-N and other indicators of the pile tended to be stable. At the end of composting, the GI reached 122.12%, indicating that the compost product was completely decomposed. The analysis of microbial communities in samples from different stages of composting under low temperature conditions showed that Acinetobacter was the dominant bacterial genus in the early and heating stages of composting, Pseudofulvimonas and Ensifer had the highest abundance in the high temperature stage of composting, and Parapedactor was the dominant bacterial genus in the late stage of composting. Ascobolus was the dominant fungal genus in the early stages of composting, while Mycothermus was the dominant microbial community in the heating, high temperature and maturation stages of aerobic composting. The predicted results of bacterial community function showed that amino acid transport and metabolism, carbohydrate transport and metabolism et al were the main metabolic functions of bacteria in composting process. The correlation analysis between physicochemical indexes and microbial diversity showed that the pH and genus abundance were highly correlated, followed by water content, temperature, NH+4-N and GI. [Conclusion] Natural aerobic compost can be carried out smoothly and completely decomposed in the field under low temperature conditions, it provide a basi for natural aerobic composting in the field under low temperature environment. [ABSTRACT FROM AUTHOR]

In this study, we sought to determine the effects of different vegetation types on soil microorganisms in karst areas of China, and to examine the impacts of vegetation restoration on soil ecosystem function in these areas. For the purposes of the study, we used soil collected from typical vegetation types (coniferous forest, broad-leaved forest, and natural grassland) in mountainous karst areas of northern Guangdong, among which, we analyzed differences in soil physicochemical properties, bacterial community diversity, and functional composition. Results showed that in terms of bacterial community diversity, there were no significant differences among the different vegetation types' soil with the exception being those of coniferous forests, which were characterized by lower levels of evenness and phylogenetic diversity. The community composition of soil bacteria was differed significantly among the different vegetation types, and soil physicochemical parameters (pH value and the contents of water, ammonia salts, nitrate, total nitrogen, total phosphorus, and organic matter) had a significant influence on the composition of the soil bacterial community. The pH value of grassland soil was close to neutral, and was significantly higher than that of the soils of coniferous forest and broad-leaved forest land. Similarly, grassland soil was characterized by higher contents of nitrogen, phosphorus, and organic matter. Results obtained based on functional annotation of prokaryotic taxa functional prediction revealed that chemoheterotrophic expression was highest in soils of different vegetation types. Nitrogen fixation was higher in nitrogen cycle-related functions, and there were significant differences in different types of soils, with total nitrogen, total phosphorus, pH value, and soil moisture being identified as the main environmental factors contributing to these differences. In conclusion, differences in vegetation restoration and ecological succession among forests and grasslands in karst areas may influence soil bacterial community structure and potential functions, and thus have differing effects on soil ecosystem functions. [ABSTRACT FROM AUTHOR]

The MYB transcription factor (TF) are among the largest gene families of plants being responsible for several biological processes. The R2R3-MYB gene family are integral player regulating plant primary and secondary metabolism, growth and development, and responses to hormones and stresses. The phylogenetic analysis combined with gene structure analysis and motif determination resulted in division of R2R3-MYB gene family into 27 subgroups. Evidence generated from synteny analyses indicated that CqR2R3-MYBs gene family is featured by tandem and segmental duplication events. On the basis of RNA-Seq data, the expression patterns of different tissues under salt treatment were investigated resulting CqR2R3-MYB genes high expression both in roots and stem of quinoa (Chenopodium quinoa) plants. More than half of CqR2R3-MYB genes showed expression under salt stress. Based on this result, CqR2R3-MYB s may regulate quinoa plant growth development and resistance to abiotic stresses. These findings provided comprehensive insights on role of CqR2R3-MYBs gene family members in quinoa and candidate MYB gene family members can be further studies on their role for abiotic stress tolerance in crop plants. Quinoa (Chenopodium quinoa) produces nutritious and gluten-free grains with a fine balance between carbohydrates, essential amino acids, oils, minerals, vitamins, and dietary fibres. The transcription factors (TFs) are the proteins regulating rate of transcription of genetic information from DNA to messenger RNA. The R2R3-MYB transcription factors are the largest subfamily of the MYB family in plants, whereas the numbers of 4R-MYB and 3R-MYB genes are relatively small. In this study, we identified 103 poplar R2R3-MYB transcription factor genes. This article belongs to the Collection Functional Genomics for Developing Climate Resilient Crops. [ABSTRACT FROM AUTHOR]

Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant development and stresses, controlling various essential traits of plants. However, the systematic investigation of the Aux/IAA gene family in A. argyi remains limited. In this study, a total of 61 Aux/IAA genes were comprehensively identified and characterized. Gene structural analysis indicated that 46 Aux/IAA proteins contain the four typical domains, and 15 Aux/IAA proteins belong to non-canonical IAA proteins. Collinear prediction and phylogenetic relationship analyses suggested that Aux/IAA proteins were grouped into 13 distinct categories, and most Aux/IAA genes might experience gene loss during the tandem duplication process. Promoter cis-element investigation indicated that Aux/IAA promoters contain a variety of plant hormone response and stress response cis-elements. Protein interaction prediction analysis demonstrated that AaIAA26/29/7/34 proteins are possibly core members of the Aux/IAA family interaction. Expression analysis in roots and leaves via RNA-seq data indicated that the expression of some AaIAAs exhibited tissue-specific expression patterns, and some AaIAAs were involved in the regulation of salt and saline-alkali stresses. In addition, RT-qPCR results indicated that AaIAA genes have differential responses to auxin, with complex response patterns in response to other hormones, indicating that Aux/IAA may play a role in connecting auxin and other hormone signaling pathways. Overall, these findings shed more light on AaIAA genes and offer critical foundational knowledge toward the elucidation of their function during plant growth, stress response, and hormone networking of Aux/IAA family genes in A. argyi. [ABSTRACT FROM AUTHOR]

Background: Freshwater snails are not only intermediate hosts for parasites but also an important part of the food chain as they convert plant biomass and humus into animal biomass. However, being widely distributed in freshwater environments, snails are highly affected by human activities, which makes their adaptation to altering environments challenging. The gut microbiome helps animals in their digestion, immune system, growth and adapting to changing environments. The effect of host species on intestinal microbial community has been poorly studied in snails. Methods: In this study, single-molecule real-time sequencing technology (SMRT) was used to obtain full-length 16S rRNA genes to determine the intestinal microbiomes of three species of freshwater snails (SQ: Sinotaia quadrata, BU: Boreoelona ussuriensis, RP: Radix plicatula) with similar feeding habits in a same water environment. Results: Unifrac PCoA (P<0.05), hierarchical cluster and Ternary analyses showed distinct and significant segregation of the intestinal microbiomes of the three hosts. The phyla Cyanobacteria, Proteobacteria, Firmicutes and Planctomycetota dominated snail guts, comprising 93.47%, 86.22%, and 94.34% of the total reads in SQ, BU and RP, respectively. Of these, only 25.26% of OTUs were identified up to species level, while 72.07% of OTUs were identified at the genus level. Although 72.94% of the total bacterial species (566) were common to three snails, significant differences were observed in terms of their abundance (P < 0.05). Several genera can help to determine the phenotype of the intestinal microbiota. In this case, Lelliottia contributed mainly to stress tolerance, biofilm formation, potential pathogenicity, mobile elements and facultatively anaerobic phenotypes in RP. Furthermore, Romboutsia and Clostridium_sensu_stricto_1 contributed to the anaerobic phenotype of SQ and RP, while Pirellula contributed to the aerobic phenotype in SQ. Moreover, PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) predicted 68 GH (glycoside hydrolase) genes, with these including monosaccharide-, disaccharide-, polysaccharide-, and starch-digesting enzyme genes as well as enzymes specific to aquatic plants. Many of the identified pathways were related to Infectious diseases and Xenobiotics biodegradation and metabolism, which expanded the resistance of freshwater snails. Concludes: Lelliottia, Romboutsia, Clostridium_sensu_stricto_l, and Pirellula play an important role in the intestinal microbiota phenotype of the host snails. In general, the host species affects the structure of the gut microbial community, which in turn helps gastropods improve their environmental adaptability, but further study is still needed. [ABSTRACT FROM AUTHOR]

Sewer systems play vital roles in wastewater treatment facilities, and the microbial communities contribute significantly to the transformation of domestic wastewater. Therefore, this study conducted a 180-day experiment on a sewer system and utilized the high-throughput sequencing technology to characterize the microbial communities. Additionally, community assembly analysis was performed to understand the early-stage dynamics within the sewer system. The results demonstrated that the overall diversity of microbial communities exhibited fluctuations as the system progressed. The dominant phyla observed were Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, accounting for over 85.4% of the total relative abundances. At the genus level, bacteria associated with fermentation displayed a high relative abundance, particularly during days 75 to 180. A random-forest machine-learning model identified a group of microbes that confirmed the substantial contribution of fermentation. During the process of fermentation, microorganisms predominantly utilized propionate formation as the main pathway for acidogenesis, followed by acetate and butyrate formation. In terms of nitrogen and sulfur cycles, dissimilatory nitrate reduction and assimilatory sulfate reduction played significant roles. Furthermore, stochastic ecological processes had a dominant effect during the experiment. Dispersal limitation primarily governed the assembly process almost the entire experimental period, indicating the strong adaptability and metabolic plasticity of microorganisms in response to environmental variations. This experiment provides valuable insights into the metabolic mechanisms and microbial assembly associated with sewer systems. [ABSTRACT FROM AUTHOR]

【Objective】The present paper aimed to explore the effects of different mulching measures on fungal community structure, ecological function and species interaction in rhizosphere soil of Allium chinense, in order to provide theoretical basis and data support for the use and selection of mulching film for production.【Method】At the harvest period of A. chinense, rhizosphere soil covered with ordinary transparent film, blue film and no film treatment was collected, and the fungal community in the rhizosphere soil under each treatment was studied using high-throughput sequencing technology, FUNGuild database, molecular ecological network and other analytical methods.【Result】The mulching treatment reduced the diversity of fungal communities, but under the blue mulching treatment, beneficial fungal communities such as Humicola, Talaromyces and Aspergillus with higher relative abundance were enriched; From the molecular ecological network of fungi, it could be seen that although plastic film coverage simplified the network, the resistance of fungal communities to the external environment had been improved, with blue plastic film exhibiting more stability than ordinary plastic film; In addition, after functional prediction of the fungal communities in each treatment, it was found that the relative abundance of saprophytic functional microbial communities was higher under blue plastic film, promoting the decomposition of organic matter and nutrient cycling.【Conclusion】The fungal community structure, ecological functions, and species relationships in the rhizosphere soil of A. chinense show significant differences under different film covering treatments. Among them, the fungal community under blue film covering treatment is more conducive to the growth and development of A. chinense, but at the same time, the potential risks caused by the increase of pathogenic functional bacterial communities caused by film covering measures should also be considered. [ABSTRACT FROM AUTHOR]

Background: Urbanization has an ecological and evolutionary effect on urban microorganisms. Microorganisms are fundamental to ecosystem functions, such as global biogeochemical cycles, biodegradation and biotransformation of pollutants, and restoration and maintenance of ecosystems. Changes in microbial communities can disrupt these essential processes, leading to imbalances within ecosystems. Studying the impact of human activities on urban microbes is critical to protecting the environment, human health, and overall urban sustainability. Methods: In this study, bacterial communities in the sediments of an urban artificial river were profiled by sequencing the 16S rRNA V3-V4 region. The samples collected from the eastern side of the Jiusha River were designated as the JHE group and were marked by persistent urban sewage discharges. The samples collected on the western side of the Jiusha River were categorized as the JHW group for comparative analysis. Results: The calculated alpha diversity indices indicated that the bacterial community in the JHW group exhibited greater species diversity and evenness than that of the JHE group. Proteobacteria was the most dominant phylum between the two groups, followed by Bacteroidota. The relative abundance of Proteobacteria and Bacteroidota accumulated in the JHE group was higher than in the JHW group. Therefore, the estimated biomarkers in the JHE group were divided evenly between Proteobacteria and Bacteroidota, whereas the biomarkers in the JHW group mainly belonged to Proteobacteria. The Sulfuricurvum, MND1, and Thiobacillus genus were the major contributors to differences between the two groups. In contrast to JHW, JHE exhibited higher enzyme abundances related to hydrolases, oxidoreductases, and transferases, along with a prevalence of pathways associated with carbohydrate, energy, and amino acid metabolisms. Our study highlights the impact of human-induced water pollution on microorganisms in urban environments. [ABSTRACT FROM AUTHOR]

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Endophytic fungi in flowers influence plant health and reproduction. However, whether floral volatile organic compounds (VOCs) affect the composition and function of the endophytic fungal community remains unclear. Here, gas chromatography–mass spectrometry (GC–MS) and high-throughput sequencing were used to explore the relationship between floral VOCs and the endophytic fungal community during different flower development stages in Osmanthus fragrans 'Rixiang Gui'. The results showed that the composition of the endophytic fungal community and floral VOCs shifted along with flowering development. The highest and lowest α diversity of the endophytic fungal community occurred in the flower fading stage and full blooming stage, respectively. The dominant fungi, including Dothideomycetes (class), Pleosporales (order), and Neocladophialophora, Alternaria, and Setophoma (genera), were enriched in the flower fading stage and decreased in the full blooming stage, demonstrating the enrichment of the Pathotroph, Saprotroph, and Pathotroph–Saprotroph functions in the flower fading stage and their depletion in the full blooming stage. However, the total VOC and terpene contents were highest in the full blooming stage and lowest in the flower fading stage, which was opposite to the α diversity of the endophytic fungal community and the dominant fungi during flowering development. Linalool, dihydro-β-ionone, and trans-linalool oxide(furan) were key factors affecting the endophytic fungal community composition. Furthermore, dihydro-β-ionone played an extremely important role in inhibiting endophytic fungi in the full blooming stage. Based on the above results, it is believed that VOCs, especially terpenes, changed the endophytic fungal community composition in the flowers of O. fragrans 'Rixiang Gui'. These findings improve the understanding of the interaction between endophytic fungi and VOCs in flowers and provide new insight into the mechanism of flower development. [ABSTRACT FROM AUTHOR]

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This study aimed to clarify the impact of land use conversion on the composition and diversity of soil bacterial communities, and to provide a reference for the selection of scientific restoration methods for degraded wetlands in the Sanjiang Plain, Northeastern of China. In 2018, Illumina MiSeq highthroughput sequencing was used to sequence amplicons of the 16S rDNA of soil bacteria in three types of land use: natural wetlands, rice fields, and restored wetlands in the Sanjiang Plain. The diversity and function of soil bacterial communities was analyzed. The results showed that wetland converted into paddy fields caused a significant decrease (P<0.05) in the Ace, Chao1 and Shannon indices of soil bacteria, and restoration of agricultural lands into wetlands significantly increased (P<0.05) these indices. The soil bacterial community structure of natural wetland, rice field and restored wetland differed significantly (P<0.05). The detected soil bacteria represented 38 phyla, 101 classes, 251 orders, 418 families, 786 genera and 1563 species. The phyla of Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Bacteroidetes, Nitrospirae, Latescibacteria and Verrucomicrobia were dominant in all plots, reaching a relative abundance >1%. Wetland soil bacteria have 6 types of primary functions by PICRUST2 analysis: metabolism, environmental information processing, genetic information processing, cellular processes, human diseases, and organic systems. The soil pH, content of organic carbon and total nitrogen, and the carbon to nitrogen ratio are all factors affecting the diversity of soil bacterial communities in the investigated soils. Changes in wetland land use reduce the stability of the soil ecosystem and increases the potential ecological risk of wetland degradation. [ABSTRACT FROM AUTHOR]

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This study investigated the response of a bacterial community’s structure and function in the rhizosphere soil of C3 and C4 plants under bis(2,4,6-tribromophenoxy) ethane (BTBPE) exposure. The bacterial community composition was determined using 16S rRNA sequencing, while FAPROTAX and PICRUSt 2 were employed for functional predictions. Results showed significant differences between C3 and C4 plants in terms of bacterial community structure. C3 plants exhibited higher abundances of Proteobacteria, Bacteroidetes at the phylum level and Sphingomicrobium at the genus level, compared to C4 plants. Conversely, C4 plants had higher abundances of Actinobacteria and Patescibacteria at the phylum level and Nocardioides at the genus level. LEfSe and function prediction analyses revealed that the rhizosphere soil bacteria in C3 plants exhibited significantly higher enrichment in nitrogen fixation functions (p < 0.05), whereas C4 plants showed a significantly higher relative abundance of bacteria and functions related to organic pollutant degradation (p < 0.05). These findings suggest that the rhizosphere soil bacteria of C3 plants exhibit a stronger response to BTBPE exposure in nitrogen metabolism-related processes, while C4 plants possess superior biodegradation ability compared to C3 plants.

We report here an assessment of the model refinement category of the 14th round of Critical Assessment of Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range of starting quality. The ability of groups to accurately rank their submissions and to predict coordinate error varied widely. Overall, only four groups out-performed a "naïve predictor" corresponding to the resubmission of the starting model. Among the top groups, there are interesting differences of approach and in the spread of improvements seen: some methods are more conservative, others more adventurous. Some targets were "double-barreled" for which predictors were offered a high-quality AlphaFold 2 (AF2)-derived prediction alongside another of lower quality. The AF2-derived models were largely unimprovable, many of their apparent errors being found to reside at domain and, especially, crystal lattice contacts. Refinement is shown to have a mixed impact overall on structure-based function annotation methods to predict nucleic acid binding, spot catalytic sites, and dock protein structures.

In order to understand the diversity of endophytic bacteria community in different tissues of Pyracantha fortuneana, the 16S rRNA V5-V7 variable region of endophytic bacteria in P. fortuneana was sequenced by high-throughput sequencing technology, and the diversity of endophytic bacteria community in different tissue parts of P. fortuneana was analyzed. The results were as follows: (1) A total of 1 818 endophytic bacteria OTU were obtained, in which 754 endophytic bacteria were from root, 308 from stem and 756 from leaf, and with a total of 152 OTU. (2) Species classification showed that endophytic bacteria in different P. fortuneana tissues had abundant community diversities, and the endophytic bacteria in root belonged to 557 species, 373 genera, 216 families, 137 orders, 53 classes, 23 phyla, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Streptomyces were the dominant genera, and their relative abundance was 10.57% and 8.00%, respectively. The endophytic bacteria in stem belonged to 270 species, 204 genera, 126 families, 76 orders, 32 classes, 21 phyla, Massilia and unclassified_f_Comamonadaceae were the dominant genera, and their relative abundance was 31.10% and 12.82%, respectively. The endophytic bacteria in leaf belonged to 581 species, 380 genera, 210 families, 130 orders, 52 classes, 21 phyla, Geobacillus and Pseudomonas were the dominant genera, and their relative abundance was 12.31% and 9.84%, respectively. (3) PICRUSt function prediction analysis showed that the species richness of root endophytic bacteria involved in te regulation of various metabolic pathways was the highest. These results provide a reference for endophytic bacteria functions and exploiting new beneficial microbial resources.

After comparing the bacterial load of black-yolked salted duck eggs (BSE) and that of duck eggs with different cleanliness degrees, it was found that the total bacterial count on the shell of severely stained eggs (DE) was distinctly higher than that on the shell of non-visually stained eggs (CE), and the total bacterial count in the shell membrane and contents of BSE increased greatly. Furthermore, 16S rDNA gene sequencing was used to analyze the differences in the composition and abundance of bacterial communities in CE, DE and BSE. It turned out that Proteobacteria, Firmicutes and Actinobacteria were the dominant phyla, accounting for 34.35%, 27.25% and 17.28% of the total abundance, respectively, while Bacteroidetes accounted for 8.29% of the total abundance. Proteobacteria was the dominant bacteria in DE and accounted for 89.01% of the total abundance, while the relative abundance of Firmicutes and Actinobacteria were 6.16% and 3.98%. The dominant phyla in BSE were Proteobacteria (76.50%), Bacteroidetes (8.00%), Actinobacteria (6.76%) and Firmicutes (5.43%). The abundance of Proteobacteria in DE and BSE was significantly increased. The dominant bacterial genera in CE were Nesterdella (9.08%), Campylobacter (7.91%), Streptococcus (3.41%) and Oligomonas (2.92%). In DE, Psychrobacter was the dominant genus, accounting for 86.01% of the total abundance, and the relative abundance of Acinetobacter was 2.20%. The dominant bacteria in BSE were Rolstonia (22.91%), Serratia (5.05%) and Actinomycetes (3.32%). The cluster analysis of bacterial diversity showed that the dominant microorganisms of BSE were close to those of DE. The microbial phenotype analysis showed that the dominant microorganisms of BSE were Gram-negative bacteria, had high oxidative stress tolerance and pathogenicity, and could tolerate oxidizing detergents. The results of microbial gene function prediction and species composition of metabolic pathways demonstrated that bacterial carbohydrate decomposition, lipid transport and metabolic oxidation in DE were stronger than those in CE. More coenzyme transport and metabolic pathways could make the biochemical reactions of bacteria from DE faster to produce more secondary metabolites, thus resulting in changes in the quality of duck eggs. This is consistent with the highest bacterial abundance in the secondary metabolite biosynthesis, transport and catabolism pathways in BSE. The results of this study provide theoretical support for the cleaner production of duck eggs.

To investigated the effect of restoration years on soil bacterial community structure and functional characteristics in seabuckthorn plantation. Seabuckthorn plantation (3, 4, 5, 6, 7 a) was used as the study object, while felled grassland was used as a control. Soil samples were collected from the study area and soil bacterial communities were sequenced using Illumina Miseq highthroughput sequencing technology and PICRUSt. The results indicate that 29 families, 91 classes, 193 orders, 305 families, and 438 genera of bacteria are detected in the study area, with Actinobacteria and Proteobacteria being the dominant groups at the phylum level. Acinetobacter and Nocardioides are the common groups at the genus level. The planting of seabuckthorn plantation increases soil organic matter, alkaline hydrolysis nitrogen, available potassium, and water content compared to grassland, while the soil pH and total phosphorus do not change significantly. The relative abundance of Acinetobacter and Nocardioides in the soil of seabuckthorn forest is higher than that of grassland. Moreover, the relative abundance of Thermus and Deinococcus decreases gradually with the increase of recovery years, while CL500-29 marine group and Streptomyces increases gradually. Soil pH and available potassium are identified as the main influencing factors of soil bacterial community structure in seabuckthorn plantation in the study area. Bacteria in seabuckthorn forests and grassland soils in the study area are found to consist mainly of five first-order functions and 35 sub-functions, with bacterial metabolism being the most important function. The activity of bacterial metabolism in seabuckthorn forest is higher than in grassland. The establishment of seabuckthorn forest is found to be beneficial to the improvement of bacterial metabolism and soil nutrients. [ABSTRACT FROM AUTHOR]

With the development of high-throughput sequencing, circular RNA has come into people's vision and attracted more and more attention. Many studies have found that circular RNA plays an important role in a variety of biological processes and the occurrence and development of diseases. According to the previous sequencing results, circRNA_3238 was differentially expressed in ALV-J infected group and the non-infected group was selected for subsequent verification and analysis. We found that circRNA_3238 is a stable, circular transcript, which mainly exists in the cytoplasm. And it is widely expressed in various tissues of chickens, and highly expressed in lung, lymph, and bursa of fabricius. Bioinformatics results show that circRNA_3238 and the predicted target genes enriched MAPK signaling pathway, Notch signaling pathway, and other pathways related to disease or immune, revealing circRNA_3238 may indirectly regulate the process of ALV-J infection by regulating target genes. [ABSTRACT FROM AUTHOR]

The high salt content in saline–alkaline land leads to insufficient nutrients, thereby reducing agricultural productivity. This has sparked widespread interest in improving saline–alkaline soil. In this investigation, 16S rRNA gene high-throughput sequencing was employed to examine the impacts of three cropping systems (monoculture, rotation, and mixture) on soil bacterial communities. It was found that cropping rotations and mixtures significantly increased soil bacterial α-diversity. Random forest analysis showed a significant linear relationship between AK and EC and bacterial α-diversity. In addition, principal coordinates analysis (PCoA) further confirmed the significant differences in β-diversity between different soil layers. Through co-occurrence network analysis, it was found that cropping rotations and mixtures increased the stability and complexity of co-occurrence networks. By calculating NST to analyze the assembly process of soil bacterial communities in different cropping systems, it was found that the assembly process of soil bacterial communities was dominated by a stochastic process. Functional prediction results showed that a large number of C, N, and S cycling microbes appeared in soil bacterial communities. Our study aims to establish a fresh perspective on the improvement and recovery of saline–alkaline soil. [ABSTRACT FROM AUTHOR]

[Objective] This study's objective was to investigate the diversity of intestinal microorganisms in adult Vespa velutina (Asian hornet) killed by natural causes. This study investigates the composition of intestinal fungi and bacteria and predicts the pathogenic pathogen in adult Vespa velutina (Asian hornet). [Methods] We determined the ITS1 sequence of fungi and the V3–V4 variant region of 16S rRNA of bacteria using Illumina MiSeq technology. Operational taxonomic units (OTU) of gut symbiotic microorganisms were quantified, and the resulting data were subjected to analysis of species abundance, composition, and alpha diversity. OTU function was predicted using PICRUSt2/FUNGuild. In addition, cultured microorganisms from the gut microbiota of adult Vespa velutina were isolated and identified. A number of 3610 (fungi) and 8373 (bacteria) were identified via cluster analysis. A total of 13 strains, 51 classes, 126 orders, 285 families, and 586 genera were identified for fungi and 44 strains, 113 classes, 319 orders, 662 families, and 1394 genera were identified for bacteria. E. shigella, Herbaspirillum, and Aaaia were the most abundant classes of bacteria, and Fusarium, Mortierella, and Starmerella were the most abundant classes of fungi. In addition, 16 community genera of fungi and 11 of bacteria were outlined as core taxa. Species diversity and richness for the gut fungal and bacterial communities with VN were found to be higher than those with VA. Furthermore, bacterial species diversity and richness were found to be higher than those of fungi in VA and VN. Functional analysis revealed that Vespa velutina gut bacteria exhibited 20 functions, while fungi were classified into three types of nutrient modes. Cultivable bacteria were obtained from two phyla and two classes, but no fungi could be cultivated. [Conclusion] Variations in the species diversity and abundance of both fungi and bacteria in the gut were observed between the VA and the VN. The involvement of bacteria in the death of adult Vespa velutina was found to be significant. In addition, VA1 (the self-named strain) may be a pathogenic bacterium derived from the gut of the VA that exhibits virulence. [ABSTRACT FROM AUTHOR]

[Objective] The study aimed to reveal the microbial community structure and soil physicochemical properties of apple rhizosphere under the intercropping system of persimmon and apple trees. [Method] In the study, rhizosphere soil of intercropping (I) and non-intercropping (NI) apples were used as materials to analyze the rhizosphere microbial community structure by high-throughput sequencing technology. [Result] lnter-cropping of persimmon significautly increased the contents of organic matter (OM), available nitrogen (AN), total phosphorus (TP), decreased the contents of available potassium (AK) in apple rhizosphere soil. The Alpha diversity analysis showed that intercropping had no significant effect on the bacterial richness index and diversity index of apple rhizosphere soil, whereas significantly reduced the Ace index of rhizosphere soil fungi (P = 0. 03). β diversity analysis showed that there were significant differences in bacterial and fungal community structure between intercropped and non-intercropped soils. Further LEfSe analysis showed that intercropping significantly increased the abundance of 17 bacterial genera in apple rhizosphere soil, of which, 9 were known genera, and 8 were unknown genera. These nine known genera included Sporacetigenium, Tepidisphaera, Agromyces, Alkanindiges, Phycisphaera, Pseudoxanthomonas, Terrimonas, Pseudohaliea, Paenisporosarcina; The abundances of four bacterial genera, namely Sporichthya, Methylocystis, Devosia and Alter-erythrobacter were significantly decreased. Intercropping significantly increased the abundance of 1 fungal genus Arthrographis and decreased the abundance of 3 fungal genera, namely Cylindrocarpon, Metacordyceps and Exophiala. Spearman's correlation analysis showed that Pseudomonas was positively correlated with available phosphorus (AP) and TP, while Naganishia was positively correlated with AP. The fungal genera Polyscytalum and Minimedusa showed a significant negative correlation with AP. PICRUSt2 functional prediction analysis showed that intercropping significantly decreased the abundance of carbohydrate transport and metabolism, and extracellular structure in rhizosphere bacteria. FUNGuild analysis showed that intercropping significantly reduced the abundance of pathogen-saprophytic transitional fungi in apple rhizosphere soil. [Conclusion] Intercropping of apple and persimmon trees can increase the contents of OM, AN, TP in apple rhizosphere soil, significantly increase the relative abundance of beneficial rhizosphere microorganisms, and reduce the relative abundance of pathogenic fungi microorganisms, which will provide data reference for exploring the mechanism of intercropping disease resistance. [ABSTRACT FROM AUTHOR]

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Instruction: Citrus is a globally important fruit tree whose microbiome plays a vital role in its growth, adaptability, and resistance to stress. Methods: With the high throughput sequencing of 16S rRNA genes, this study focused on analyzing the bacterial community, especially in the leaf midribs, of healthy and Huanglongbing (HLB)-infected plants. Results: We firstly identified the shared bacterial taxa in the midribs of both healthy and HLB-infected plants, and then analyzed their functions. Results showed that the shared bacterial taxa in midribs belonged to 62 genera, with approximately 1/3 of which modified in the infected samples. Furthermore, 366 metabolic pathways, 5851 proteins, and 1833 enzymes in the shared taxa were predicted. Among these, three metabolic pathways and one protein showed significant importance in HLB infection. With the random forest method, six genera were identified to be significantly important for HLB infection. Notably, four of these genera were also among the significantly different shared taxa. Further functional characterization of these four genera revealed that Pseudomonas and Erwinia likely contributed to plant defense against HLB, while Streptomyces might have implications for plant defense against HLB or the pathogenicity of Candidatus Liberibacter asiaticus (CLas). Disccusion: Overall, our study highlights that the functions of the shared taxa in leaf midribs are distinguished between healthy and HLB-infected plants, and these microbiome-based findings can contribute to the management and protection of citrus crops against CLas. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Food Safety & Quality is the property of Journal of Food Safety & Quality Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)