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Simple Summary: This study investigated the gut microbiota of captive Chinese monals across different seasons and age groups. The results revealed significant seasonal fluctuations and age-related factors that shape its composition. Specific biomarkers, including PaeniGlutamicibacter, Pseudarthrobacter, Micrococcaceae, and Micrococcales, were linked to seasonal changes, while mid-aged adults exhibited a higher abundance of Kaistella, Escherichia, Enterobacteriaceae, and Enterobacterales. Furthermore, captive Chinese monals may be more susceptible to bacterial-induced intestinal diseases in spring and summer. This research highlights the dynamic impact of seasonal cycles and age on gut microbiota, offering important findings that support improved conservation strategies and management of captive Chinese monal populations. The Chinese monal (Lophophorus lhuysii) is a large-sized and vulnerable (VU in IUCN) bird from southwestern China. This study applied 16S rRNA high-throughput sequencing to comprehensively examine the gut microbiota of captive Chinese monals (located in Baoxing, Sichuan, China) across varying seasons and life stages. Dominant bacterial phyla identified included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Significant seasonal and age-associated shifts were observed within specific bacterial groups, particularly marked by seasonal fluctuations in beta diversity. Moreover, linear discriminant analysis effect size (LEfSe) and functional predictions highlighted distinct winter signatures, indicating possible functional shifts in energy metabolism and disease resistance. In mid-aged adults, an expansion of Gamma-Proteobacteria suggested an elevated susceptibility of the gut microbiota of Chinese monals to chronic disorders and microbial imbalance. Putative pathogenic bacteria exhibited increased abundance in spring and summer, likely driven by temperature, host physiological cycles, interspecies interactions, and competition. These findings imply that the diversity, and structure of the gut microbiota in captive Chinese monals are strongly influenced by seasonal and age-related factors. The insights provided here are essential for improving breeding strategies and preventing gastrointestinal diseases in captivity. [ABSTRACT FROM AUTHOR]

Importance: Obstructive sleep apnea (OSA) in children is linked with alterations in the gut microbiome. The influence of adenotonsillectomy (AT), a primary intervention for OSA, on gut microbiota dynamics relative to disease severity remains to be elucidated. Objective: This study aimed to investigate the impact of OSA severity and AT on the gut microbiome in pediatric patients. Design: A prospective observational study. Setting: Tertiary referral center. Participants: A cohort of 55 pediatric patients treated with AT for OSA. Intervention: Total tonsillectomy and adenoidectomy procedures. Main Outcome Measures: Comprehensive evaluations included in-laboratory polysomnography and 16S rRNA gut microbiome profiling at baseline, and again at 3rd and 12thmonth following surgery. Results: Initial findings showed uniform α-diversity across different severities of OSA, while β-diversity was significantly elevated in the severe OSA subgroup. Certain gut microbiota taxa (Lachnospiraceae NK4A136 group, Ruminococcaceae UCG-002, Ruminococcaceae UCG-014, Alloprevotella, Christensenellaceae R-7 group, Ruminococcaceae UCG-005, Lactobacillus murinus, and Prevotella nigrescens) were found to inversely correlate with the apnea-hypopnea index (AHI). Significant post-AT improvements in AHI and other polysomnographic metrics were observed. Notably, AHI changes post-AT were positively associated with microbial α-diversity (species richness), β-diversity, and specific bacterial taxa (Enterobacter, Parasutterella, Akkermansia, Roseburia, and Bacteroides plebeius DSM 17135), but negatively with other taxa (Fusicatenibacter, Bifidobacterium, UBA1819, Ruminococcus gnavus group, Bifidobacterium longum subsp. Longum, and Parabacteroides distasonis) and specific metabolic pathways (purine metabolism, transcription factors, and type II diabetes mellitus). The postoperative patterns of α- and β-diversity mirrored baseline values. Conclusions and Relevance: This study documents significant changes in the gut microbiome of pediatric patients after AT, including variations in α- and β-diversities, bacterial communities, and inferred metabolic functions. These changes suggest a potential association between the surgical intervention and microbiome alterations, although further studies are necessary to discern the specific contributions of AT amidst possible confounding factors such as antibiotic use. [ABSTRACT FROM AUTHOR]

Introduction: Symbiotic microorganisms in insects regulate multiple physiological functions, widely participating in nutrient metabolism, immune regulation, and crucial regulatory roles in development. However, little is known about how microbial factors might respond to the preparation of insect diapause. Methods: The gut bacterial communities of Loxostege sticticalis larvae induced at different photoperiod of long (LD16:8, nondiapause) and short (LD12:12, prediapause) daylength were compared, by 16S rRNA Illumina MiSeq. Results: A total number of 42 phylum, 78 classes, 191 orders, 286 families, 495 genera, and 424 species were identified in the intestinal bacterial community of L. sticticalis larvae. Alpha diversity and beta diversity analyses revealed significant differences between nondiapause and prediapause larvae. In non-diapause larvae, the dominant intestinal bacteria were Firmicutes and Proteobacteria. In specific, in 3rd and 4th instar larvae, the main intestinal bacteria were Staphylococcus, while in 5th instar, it was JC017. For the prediapause larvae, the dominant phylum in 3rd instar larvae was Firmicutes, with the dominant genus of Staphylococcus, while in 4th and 5th instar larvae was Bacteroidota, with the dominant genus 4th instar was Staphylococcus, and in 5th instar was JC017. KEGG functional prediction analysis revealed that functional bacterial groups involved in metabolism had the highest abundance values. Specifically, the amino acid metabolism of metabolism-related functional genes in the 3rd instar prediapause larvae was significantly lower than that in the 4th and 5th instar prediapause larvae and the non-diapause treatment. However, the carbohydrate metabolism in 3rd instar prediapause larvae was significantly higher than that in 4th and 5th instar prediapause larvae and nondiapause treatments. The dominant bacterial phylum in the prediapause larvae at different stages of L. sticticalis was varied, and there were significant differences in community diversity and richness. Discussion: These results suggest a complex interaction between the hosts' physiological state and its gut microbiota, indicating that bacterial communities may assist insects in adapting to diapause preparation by regulating their metabolic levels. This study lays the foundation for further understanding the physiological mechanisms by which intestinal microorganisms regulate overwintering dormancy in the L. sticticalis. [ABSTRACT FROM AUTHOR]

The study aimed to investigate the effects of dietary supplementation with compound probiotics on the fecal microbiota of British shorthair cats. Twenty-four British Shorthair cats were selected, and fresh fecal samples were collected before supplementation, 10 days after, and 20 days after the supplementation with the compound probiotics. Fecal bacterial diversity, composition, and the impact on the host's physiological functions were analyzed using 16S rDNA sequencing technology. The results showed that compared to before supplementation, there were no changes in the average body weight and daily food intake of the cats, and no difference in fecal scores. However, after supplementation with the compound probiotics, the diversity of the fecal microbiota in cats significantly improved, with greater changes in the early stage and a tendency to stabilize in the later stage. The relative abundance of Lactobacillus, Bifidobacterium, and Enterococcus in the feces increased, and the Firmicutes/Bacteroidetes ratio increased. Predictions of physiological function interactions revealed that the addition of the probiotic mixture promoted physiological processes such as short-chain fatty acid production, glucuronic acid degradation, and inositol degradation in the host, while weakening processes such as the urea cycle. The study indicates that the addition of the compound probiotics to the diet maintained the balance of the gut microbiota, promoted the proliferation of probiotics, and is beneficial to the intestinal health of the British shorthair cats. [ABSTRACT FROM AUTHOR]

Planktonic microorganisms have been recognized as important components in biogeochemical cycling in lakes. However, research into the impact of phyllosphere microorganisms, particularly those involved in carbon cycling, on CO2 fluxes in macrophyte-dominated lakes within the context of global environmental changes remains scarce. Here, by employing high-throughput sequencing techniques, we experimentally tested how nutrient enrichment, top-down effects of fish and increases in dissolved organic carbon (DOC) affect CO2 exchange flux at the water-air interface by altering the community structure and functioning of phyllosphere bacteria on macrophytes. We found that our mesocosm ecosystems exhibited a net absorption of CO2, but nutrient enrichment significantly decreased the absorption ability. Mantel tests and multiple regression modeling also showed that eutrophication-associated parameters (total nitrogen, total phosphorus and ammonium nitrogen), pH, and extinction coefficient were the key drivers influencing abundance of phyllosphere functional microorganisms. In addition, these experimental treatments significantly altered the composition, diversity and co-occurrence networks of carbon cycling-associated phyllosphere microorganisms, which impacted the CO2 flux. Structural equation models and linear regression further showed that the Shannon Index of phyllosphere functional microorganisms related to carbon cycling (rather than plant volume inhabited - PVI) had a significant positive impact on CO2 fixation. This means that environmental changes—especially eutrophication—may hinder carbon sequestration by decreasing the diversity of phyllosphere microorganisms rather than reducing the abundance of submerged macrophytes. This study increases our understanding of carbon cycling processes in aquatic environments from a management perspective by emphasizing the importance of protecting the diversity of phyllosphere microorganisms in macrophyte-dominated lakes. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Wildlife / Yesheng Dongwu Xuebao is the property of Chinese Journal of Wildlife Editorial Office 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.)

Essential mineral elements such as zinc and iron play a crucial role in maintaining crop growth and development, as well as ensuring human health. Foxtail millet is an ancient food crop rich in mineral elements and constitutes an important dietary supplement for nutrient-deficient populations. The ZIP (ZRT, IRT-like protein) transporters are primarily responsible for the absorption, transportation and accumulation of Zn, Fe and other metal ions in plants. Here, we identified 14 ZIP transporters in foxtail millet (SiZIP) and systematically characterized their phylogenetic relationships, expression characteristics, sequence variations, and responses to various abiotic stresses. As a result, SiZIPs display rich spatiotemporal expression characteristics in foxtail millet. Multiple SiZIPs demonstrated significant responses to Fe, Cd, Na, and K metal ions, as well as drought and cold stresses. Based on homologous comparisons, expression characteristics and previous studies, the functions of SiZIPs were predicted as being classified into several categories: absorption/efflux, transport/distribution and accumulation of metal ions. Simultaneously, a schematic diagram of SiZIP was drawn. In general, SiZIPs have diverse functions and extensively involve in the transport of metal ions and osmotic regulation under abiotic stresses. This work provides a fundamental framework for the transport and accumulation of mineral elements and will facilitate the quality improvement of foxtail millet. [ABSTRACT FROM AUTHOR]

The growth and biological decline of alfalfa may be linked to the rhizosphere microbiome. However, plant–microbe interactions in the rhizosphere of alfalfa and associated microbial community variations with stand age remain elusive. This study explored the successional pattern of rhizosphere microbial communities across different aged alfalfa stands and its relationship with alfalfa decline. Rhizosphere soils were collected from 2- and 6-year-old alfalfa stands. Control soils were collected from interspaces between alfalfa plants in the same stands. Soil bacterial and fungal communities were characterized by 16S and ITS rRNA gene sequencing, respectively. Specific microbial taxa colonized the rhizosphere soils, but not the control soils. The rhizosphere-specific taxa mainly included potentially beneficial genera (e.g., Dechloromonas, Verrucomicrobium) in the young stand and harmful genera (e.g., Peziza, Campylocarpon) in the old stand. Alfalfa roots regulated soil microbial communities by selective promotion or inhibition of distinct taxa. The majority of time-enriched taxa were reported as harmful fungi, whose relative abundances were negatively correlated with plant traits. Time-depleted taxa were mostly known as beneficial bacteria, which had relative abundances positively correlated with plant traits. The relative abundances of functional bacterial genes associated with vancomycin biosynthesis, zeatin biosynthesis, and amino acid metabolism trended lower in rhizosphere soils from the old stand. An upward trend was observed for fungal pathogens and wood saprotrophs with increasing stand age. The results suggest that root activity drives the negative succession of rhizosphere microbial communities during alfalfa decline in old stands. [ABSTRACT FROM AUTHOR]

Copyright of Biotechnology Bulletin is the property of Biotechnology Bulletin Editorial Office 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.)

Early in the SARS-CoV2 pandemic, in this journal, Hou et al. (BMC Med 18:216, 2020) interpreted public genotype data, run through functional prediction tools, as suggesting that members of particular human populations carry potentially COVID-risk-increasing variants in genes ACE2 and TMPRSS2 far more often than do members of other populations. Beyond resting on predictions rather than clinical outcomes, and focusing on variants too rare to typify population members even jointly, their claim mistook a well known artifact (that large samples reveal more of a population's variants than do small samples) as if showing real and congruent population differences for the two genes, rather than lopsided population sampling in their shared source data. We explain that artifact, and contrast it with empirical findings, now ample, that other loci shape personal COVID risks far more significantly than do ACE2 and TMPRSS2—and that variation in ACE2 and TMPRSS2 per se unlikely exacerbates any net population disparity in the effects of such more risk-informative loci. [ABSTRACT FROM AUTHOR]

Macroalgae are vital reservoirs for essential epibiotic microorganisms. Among these are growth-promoting bacteria that support the growth and healthy development of their host macroalgae, and these macroalgae can be utilized in agriculture as biostimulants, offering an alternative to traditional agrochemicals. However, to date, no comparative studies have been conducted on the functional profile and bacterial diversity associated with coastal macroalgae of Peru. In this study, we employed amplicon sequencing of the V3-V4 region of 16S rRNA gene in twelve host macroalgae collected from two rocky shores in central Peru to compare their bacterial communities. The results revealed high bacterial diversity across both sites, but differences in microbial composition were noted. The phyla Bacteroidota and Pseudomonadota were predominant. The functional prediction highlighted 44 significant metabolic pathways associated with the bacterial microbiota when comparing host macroalgae. These active pathways are related to metabolism and genetic and cellular information processing. No direct association was detected between the macroalgal genera and the associated microbiota, suggesting that the bacterial community is largely influenced by their genetic functions than the taxonomic composition of their hosts. Furthermore, some species of Chlorophyta and Rhodophyta were observed to host growth-promoting bacteria, such as Maribacter sp. and Sulfitobacter sp. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Agricultural Science & Technology (1008-0864) is the property of Journal of Agricultural 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.)

Although established biotechnological applications of microalgae e.g., the production of high-value metabolites is based on axenic cultures, exploitation of the mutualistic consortia of microalgae and bacteria quickly comes to foreground, especially in bioremediation and wastewater treatment. This trend shifts the focus from genomic research of certain microalgal species to metagenomic studies of interactions between microalgae and bacteria in natural communities and in artificial consortia. Dissection of the genetic determinants of the robustness and productivity of the consortia become a hot research direction, too. Admirable contribution to this topic had been made by high-throughput sequencing (HTS), while recent breakthrough in this field was entailed by the advent and rapid development of the 3rd generation nanopore sequencing which becomes increasingly accurate while providing unprecedented sequencing performance. Recent progress of the Oxford Nanopore Technologies (ONT) enabled both classical metagenomic analysis of microalgal-bacterial communities based on whole metagenome sequencing as well as taxonomic and genetic profiling based on the amplicon sequencing. The parallel emergence of novel bioinformatic algorithms for processing the metagenomic datasets opened new opportunities for the analysis of structure and physiology of microalgal-bacterial communities. From the practical perspective, the new HTS techniques became a time- and labor-savers in discovery of new microalgae with a high potential for the accumulation of valuable metabolites, biodegradation of hazardous micropollutants, and biosequestration of nutrients from waste streams. Search for prokaryotic species boosting the biotechnological potential of eukaryotic microalgae via mutualistic interactions with them is another important goal. The insights from the both short-read and long-read metagenomics will form a solid foundation for the rational design of microalgal-bacterial consortia for biotechnology. In this review, we briefly outline the benefits of the long-read sequencing for structural and functional investigation of algal-bacterial consortia and summarize recent reports on using this approach for achieving the biotechnology-related goals. [ABSTRACT FROM AUTHOR]

Copyright of Asian Journals of Ecotoxicology 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.)

In agricultural ecosystems, rhizosphere microbial communities serve as the driving force for the successful cycling and transformation of nutrients and organic matter in soil, exerting a significant impact on the growth, health, and nutritional status of crops. To investigate the diversity of rhizosphere fungi in different habitats in the northern Tianshan Mountains and the driving factors behind their variations, this study employed high-throughput sequencing to analyze the diversity, structures, functions, and driving factors of rhizosphere and non-rhizosphere fungi in alfalfa rhizosphere soils in mountainous and plain habitats. The results revealed that: (1) Soil nitrogen, potassium, organic matter, and enzyme activity in the mountainous alfalfa rhizosphere soil were significantly higher than those in plain alfalfa rhizosphere soil, while electrical conductivity and pH were significantly lower than those in plain alfalfa rhizosphere soil. (2) Significant differences were observed in the fungal communities in mountainous and plain soils, with the operational taxonomic units (OTUs), Chao1, and ACE indices of plain alfalfa rhizosphere soil being significantly higher than those of mountainous alfalfa rhizosphere soil; additionally, the OTUs, Chao1, ACE, and Shannon indices showed significantly higher values in rhizosphere soils than those in non-rhizosphere soils. (3) The dominant fungal phyla in the region were Ascomycota, Mortierellomycota, Basidiomycota, and Blastocladiomycota, with notable differences in their distribution across different habitats. (4) Based on FUNGuild' s fungal functional predictions, pathogenic fungi in mountainous areas were significantly higher than those in plain areas, while arbuscular mycorrhizal fungi were significantly lower in mountainous areas. (5) Redundancy analysis and Mantel tests indicated that soil pH, total nitrogen, total potassium and available potassium were the main driving factors for the differential distribution of fungal community structures in soils. [ABSTRACT FROM AUTHOR]

In this paper, a magnetic sequencing batch reactor (SBR) was constructed, and the influence rule of magnetic particle dosing performance of denitrification was investigated. The diversity, structure, and potential functions of the microbial community were comprehensively explored. The results showed that the particle size and the dosage of Fe3O4 magnetic particles were the main parameters affecting the sedimentation performance of activated sludge. The start-up phase of the SBR reactor with Fe3O4 magnetic particles was 5 days less than the control. Moreover, total nitrogen removal efficiency during the start-up phase was improved, with the maximum value reaching 91.93%, surpassing the control by 9.7% with the Fe3O4 dosage of 1.2 g L−1. In addition, the activated sludge concentration and dehydrogenase activity were improved, compared to the control. High-throughput sequencing showed that the denitrifying bacterium Saccharimonadales dominated the reactor and was enriched by magnetic particles. According to predicted functions, the abundance of genes for denitrification increased with the addition of magnetic particles, suggesting the capacity of nitrogen removal was enhanced in the microbial community. Overall, the Fe3O4 magnetic particles provide great potential for enhanced wastewater nitrogen removal. [ABSTRACT FROM AUTHOR]

Numerous members of the WOX gene family play pivotal roles during the processes of growth and development in many plants, as has been demonstrated. Cymbidium goeringii, Cymbidium ensifolium, and Cymbidium sinense are ornamental plants with a fascinating floral morphology that are economically important in China. However, there is limited knowledge about the members of the WOX gene family and their functions in these three Cymbidium species. Hence, the WOX genes in three Cymbidium species were identified on the ground of the genomes data of C. goeringii, C. ensifolium, and C. sinense in this study. These identified WOX genes were further studied for their physicochemical properties, evolutionary relationship, gene structure, protein structure, and cis-acting elements of promoters, as well as the expression pattern of the WOX genes in different tissues of C. goeringii. The findings revealed that eight WOX genes in C. goeringii, twelve WOX genes in C. ensifolium, and nine WOX genes were identified. These WOX genes were further subdivided into WUS, ancient, and intermediate clades. The length of the coding region ranged from 149 to 335 aa, and it was predicted that all WOX genes would be located on the cell nucleus. The promoter cis-acting elements primarily comprised stress response, phytohormone response, plant growth and development, and transcription factor elements. Furthermore, both the transcriptomic data and RT-qPCR analysis showed that most WOX genes may be involved in multiple developmental stages of C. goeringii. To sum up, these results may serve as a theoretical foundation for further study of the function analysis of WOX genes in orchids. [ABSTRACT FROM AUTHOR]

Intercropping, a well-established agroecological technique designed to bolster ecological stability, has been shown to have a significant impact on soil health. However, the specific effects of tea/Trachelospermum jasminoides intercropping on the physicochemical properties and functional microbial community structure in practical cultivation have not been thoroughly investigated. In this study, we utilized high-throughput sequencing technology on the 16S/ITS rDNA genes to assess the impact of tea intercropping with T. jasminoides on the composition, diversity, and potential functions of the soil microbial community in tea gardens. The results indicated that the tea/T. jasminoides intercropping system significantly increased pH levels, soil organic matter, available nitrogen, phosphorus, potassium, and enzyme activity, ultimately augmenting soil nutrient levels. Furthermore, an in-depth analysis of the bacterial co-occurrence network and topological structure portrayed a more intricate and interconnected soil bacterial community in tea gardens. Remarkably, the abundance of beneficial genera, including Burkholderia, Mesorhizobium, Penicillium, and Trichoderma, underwent a substantial increase, whereas the relative abundance of pathogenic fungi such as Aspergillus, Fusarium, and Curvularia experienced a marked decline. Functional predictions also indicated a notable enhancement in the abundance of microorganisms associated with nitrogen and carbon cycling processes. In summary, the intercropping of tea and T. jasminoides holds the potential to enrich soil nutrient content, reshape the microbial community structure, bolster the abundance of functional microorganisms, and mitigate the prevalence of pathogenic fungi. Consequently, this intercropping system offers a promising solution for sustainable tea garden management, overcoming the limitations of traditional cultivation methods and providing valuable insights for sustainable agriculture practices. [ABSTRACT FROM AUTHOR]

Microbial communities from freshwater sediments are involved in biogeochemical cycles and they can be modified by physical and chemical changes in the environment. Linking the microbial community structure (MCS) with physicochemistry of freshwater courses allows a better understanding of its ecology and can be useful to assess the ecological impact generated by human activity. The MCS of tributary channels from La Plata River affected by oil refinery (C, D, and E) and one also by urban discharges (C) was studied. For this purpose, 16S rRNA metabarcoding analysis, in silico metagenome functional prediction, and the hydrocarbon degradation potential (in silico predictions of hydrocarbon-degrading genes and their quantification by qPCR) of the MCS were studied. Principal coordinate analysis revealed that the MCS was different between sites, and it was not structured by the hydrocarbon content. Site C showed physicochemical characteristics, bacterial taxa, and an in silico functional prediction related to fermentative/heterotrophic metabolism. Site D, despite having higher concentration of hydrocarbon, presented autotrophic, syntrophic, and methanogenic pathways commonly involved in natural processes in anoxic sediments. Site E showed and intermediate autotrophic/heterotrophic behavior. The hydrocarbon degradation potential showed no positive correlation between the hydrocarbon-degrading genes quantified and predicted. The results suggest that the hydrocarbon concentration in the sites was not enough selection pressure to structure the bacterial community composition. Understanding which is the variable that structures the bacterial community composition is essential for monitoring and designing of sustainable management strategies for contaminated freshwater ecosystems. [ABSTRACT FROM AUTHOR]

Background: Soil salinization has a major impact on crop production and it is expected to increase in area in the coming years. In this scenario, exploring the potential of halophytes and their plant-associated microbiomes as to increase phytoremediation strategies represents a suitable and sustainable strategy. Methods: We conducted a microcosm experiment with the halophyte Atriplex nummularia, cultivating it in two contrasting soils (clay and sandy) at distinct levels of salinity (0, 10 and 20 mS/cm). After 109 days, we assessed its growth and bacteriome composition, through 16S rRNA gene sequencing of the leaf and root endospheres, as well as rhizosphere. Results: A. nummularia showed increased growth under salinity levels of up to 20 mS/cm in both soils. Salinity and soil type had an effect in determining the rhizosphere bacterial communities of A. nummularia, with a stronger signal in the sandy soil. Most interestingly, no differences were found in endophytic bacterial communities, suggesting a strong buffering effect of the plant physiology, even though this halophyte accumulates NaCl. Last, functional prediction based on a subset of differentially abundant taxa in the rhizosphere revealed an increase in plant-growth promotion and salinity tolerance traits in higher salinity, indicating simultaneous selection by salinity and A. nummularia under stress. Conclusion: Collectively, these results provide valuable insights into halophyte-associated bacteria, advancing our understanding of this complex system with potential application in phytoremediation strategies for saline soils. [ABSTRACT FROM AUTHOR]

Although high-performance computing (HPC) systems have been scaled to meet the exponentially growing demand for scientific computing, HPC performance variability remains a major challenge in computer science. Statistically, performance variability can be characterized by a distribution. Predicting performance variability is a critical step in HPC performance variability management. In this article, we propose a new framework to predict performance distributions. The proposed framework is a modified Gaussian process that can predict the distribution function of the input/output (I/O) throughput under a specific HPC system configuration. We also impose a monotonic constraint so that the predicted function is nondecreasing, which is a property of the cumulative distribution function. Additionally, the proposed model can incorporate both quantitative and qualitative input variables. We predict the HPC I/O distribution using the proposed method for the IOzone variability data. Data analysis results show that our framework can generate accurate predictions, and outperform existing methods. We also show how the predicted functional output can be used to generate predictions for a scalar summary of the performance distribution, such as the mean, standard deviation, and quantiles. Our prediction results can further be used for HPC system variability monitoring and optimization. This article has online supplementary materials. [ABSTRACT FROM AUTHOR]

Microbial communities associated with seagrass beds play a crucial role in maintaining the balance of seagrass ecosystems. However, the driving mechanisms behind the structure and functional succession of seagrass microbial communities are still unclear despite the close interaction between seagrass and surrounding microorganisms. To enhance our knowledge of the diversity and functional characteristics of microbial communities in seagrass beds, we employed 16S rRNA gene amplicon sequencing to investigate bacterial communities in seagrass leaves, roots, seawater, and sediments in Caofeidian Zostera marina seagrass beds of Hebei Province, Northern China. Our results highlighted that specific types of bacteria were enriched in different sample compartments, indicating the importance of habitat in influencing microbial diversity and community structure in seagrass bed ecosystems. Notably, the microbial community structure of seagrass leaves and roots showed more similarity to that found in seawater and sediments. Among all the samples, the phylum Pseudomonadota exhibited the highest relative abundance, particularly in sediment samples where they accounted for over 95% of the total bacterial population. In addition, the enrichment of Vibrio, an opportunistic pathogen in several plant samples, alerted us to seagrass and its surrounding marine environments. Finally, functional predictions of microbial communities using PICRUSt2 revealed variations in microbial functions, indicating specific metabolic preferences of microbial communities in different natural environments. The present research sheds light on the mechanisms underlying microbial community succession and their ecological function in seagrass beds. [ABSTRACT FROM AUTHOR]

Introduction: Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods : This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results : Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion : Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population. [ABSTRACT FROM AUTHOR]

Background: The rhizosphere environment regulated by root secretory activity and rhizosphere microbial interactions plays an essential role in resisting soil-borne diseases, while the host species is an important factor that affects the composition of root exudates and rhizosphere microbiomes. However, few studies have been done on the characteristics of root exudates and bacterial communities in terms of composition, diversity, and functional potential when host plants of different species are subjected to the same disease. Results: In this study, we examined the rhizosphere soil bacteria and root exudates of both healthy and diseased tomatoes and peppers employing metabolomics and amplicon techniques. Our findings indicated that variations existed in both root exudates and the bacterial community among different host species and health states. The diversities of both rhizosphere metabolites and bacterial communities were significantly reduced in different diseased plants. Although pepper and tomato resisted the invasion of Ralstonia by recruiting different potentially beneficial bacteria, their rhizosphere bacterial communities had the same functional potential. In comparison to diseased rhizosphere soil, healthy rhizosphere soil had many more functional pathways associated with disease suppression and plant growth. Conclusions: This study highlighted the crucial role of host plants in shaping the rhizosphere environment and revealed the variation characteristics of root exudates and rhizosphere bacteria of different host plants induced by the same disease. [ABSTRACT FROM AUTHOR]

Afforestation plays a pivotal role in ecosystem restoration, exemplified by the Saihanba Mechanized Forest Farm, the world's largest planted forest; however, the assembly mechanisms and interactions of soil microbial communities in such forests remain inadequately understood. This study aimed to elucidate the impact of different afforestation tree species, namely Larix gmelinii var. principis-rupprechtii, Picea asperata, and Pinus sylvestris var. mongolica, on soil bacterial diversity and community structure in comparison to grassland. Sixty soil samples were collected at a 20 cm depth, and high-throughput sequencing was employed to identify bacterial communities and assess their interactions with environmental factors. A total of 6528 operational taxonomic units (OTUs) were identified, with Solirubrobacter, Conexibacter, Bacillus, Massilia, Gaiella, Acidibacter, and Vicinamibacter being the dominant genera. Afforestation significantly impacted soil bacterial alpha diversity, with notable influence from key soil chemical properties, including available phosphorus (AP), cation exchange capacity (CEC), and the carbon-to-nitrogen ratio of soil organic matter (SOM-C/N). The Mantel test highlighted pH, the Normalized Difference Vegetation Index (NDVI), and spatial variable (dbMEM) as primary environmental factors influencing dominant bacterial genera. The bacterial community structure demonstrated deterministic homogeneous selection, wherein SOM-C/N emerged as a significant factor influencing the dissimilarity of soil bacterial communities. Furthermore, plantation soils exhibited a more complex network structure than grassland soil, highlighting the crucial role of bacterial communities in vegetation changes and providing valuable insights into their response to environmental factors during the reforestation process. [ABSTRACT FROM AUTHOR]

The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid‐Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non‐ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non‐ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non‐ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition. [ABSTRACT FROM AUTHOR]

Copyright of Food & Fermentation Industries is the property of Food & Fermentation Industries 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 Feed Research is the property of Editorial Board of Feed Research 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.)

By analyzing the changes of Saccharomyces cerevisiae fortification on the microbial composition and volatile metabolites of Nong-flavour fermented grains, the disturbances of the microbial ecological network, volatile metabolites and the potential metabolic functions of the microbial community were explored. A strain of Saccharomyces cerevisiae Y1 isolated from nong -flavour fermented grains fermented was used to disturb the solid -state fermentation of fermented grains, and the composition of microorganisms and volatile metabolites were studied by high-throughput sequencing technology and headspace solid-phase microextraction-mass spectrometry technology, respectively. The random forest learning algorithm was used to calculate the biomarkers between the experimental group and the blank group, and the differences in the microbial ecological network between the experimental group and the blank group were analyzed based on the construction of a co-occurrence network model. PLS-DA analysis and Spearman correlation were used to analyze the differences of volatile flavor compounds, the correlation of differential metabolites and biomarkers, respectively. Finally, potential functional changes were analyzed by PICRUST2 functional prediction and pathway enrichment. The results showed that 5 bacteria and 15 fungi can be used as biomarkers to characterize the microbial composition of fermented grains disturbed by Saccharomyces cerevisiae, and also increased the complexity of the microbial ecological network. Meanwhile, the composition of volatile metabolites was altered, with 18 differential metabolites, and the content of some volatile metabolites was improved. The vast majority of biomarkers were significantly associated with differential metabolism. In addition, the perturbation effect of Saccharomyces cerevisiae resulted in 180 up-regulated genes and 46 down-regulated genes in the microbial community, most of which were related to the metabolism of substances. These results provide a basis for the application of Saccharomyces cerevisiae in Baijiu fermentation and the optimization of the fermentation process of fermented grains. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Hydrobiology / Shuisheng Shengwu Xuebao 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.)

Microorganisms possess the capability to impact virtually any form of cultural heritage, leading to contamination, degradation, and even combined degradation, where diverse microorganism communities facilitate the decay of wooden materials. This study aims to analyze the microbial diversity of the wooden structure bridge at the Shahe Ancient bridge site in Xi'an. The objective is to investigate the correlation between microbial species and the state of wood degradation, as well as explore the relationship between wood microbial species and the potential influence of the wood preservation environment on its long-term preservation. Simultaneously, the conventional laboratory separation technique was employed to isolate the microorganisms that were contaminated by experimental ancient wood. This was done to assess the inhibitory effect of two fungicides on the dominant microorganisms found in ancient wood, identify the most effective inhibitor, and subsequently establish an experimental foundation for safeguarding ancient bridge wood structures. The primary objective of this research was to establish microbial control criteria for the enduring conservation of historical sites, while also equipping conservators with scientifically-guided data to inform future research and restoration endeavors. [ABSTRACT FROM AUTHOR]

Kaihua paper is a type of precious hand-made paper in China that has been used throughout Chinese history. Due to its extraordinary whiteness and fine texture, it was adopted by the imperial palace in the reign of Emperor Kang Xi and Yong Zheng of the Qing Dynasty of China in the 17th and 18th century. It is stained by a special type of yellowish-brown spot after years of storage, which is called a "peachy spot." The formation of such spots remains unclear, although complicated physicochemical processes or microbial activities might be involved. We performed nondestructive sampling and high-throughput sequencing on peachy spot surfaces, unstained areas, and air samples in the stack room to analysis the the bacterial and fungal communities, and performed prediction of functional genes of the bacterial communities. The results showed that peachy spot formation was mainly related to bacterial communities rather than fungal communities. Significantly more potential acid-producing, acidophilic or cellulase-producing bacteria, such as, Streptococcus, Staphylococcus, and Lysinibacillus, and pigment-producing bacteria, such as Methylobacterium and Rubrobacter, were identified in the peachy spot samples. Prediction of the functional genes of the bacterial community also suggested the production of acidic substance pigments. These findings provide new insights into the pigment formation mechanism in ancient paper and open an opportunity to develop new strategies to preserve the ancient paper documents. [ABSTRACT FROM AUTHOR]

High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil–plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1 m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1 m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10 m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field. [ABSTRACT FROM AUTHOR]

Fulminant myocarditis (FM) is the most serious type of myocarditis. However, the molecular mechanism underlying the pathogenesis of FM has not been fully elucidated. Small extracellular vesicles (sEVs) play important roles in many diseases, but any potential role in paediatric FM has not been reported. Here, the differential signatures of lncRNAs in plasma sEVs were studied in FM children and healthy children using transcriptome sequencing followed by functional analysis. Then immune‐related lncRNAs were screened to study their role in immune mechanisms, the levels and clinical relevance of core immune‐related lncRNAs were verified by qRT‐PCR in a large sample size. Sixty‐eight lncRNAs had increased levels of plasma sEVs in children with FM and 11 had decreased levels. Functional analysis showed that the sEVs‐lncRNAs with different levels were mainly related to immunity, apoptosis and protein efflux. Seventeen core immune‐related sEVs‐lncRNAs were screened, functional enrichment analysis showed that these lncRNAs were closely related to immune activation, immune cell migration and cytokine pathway signal transduction. The results of the study show that sEVs‐lncRNAs may play an important role in the pathogenesis of fulminant myocarditis in children, especially in the mechanism of immune regulation. [ABSTRACT FROM AUTHOR]

The degradation of alpine meadows on the Qinghai–Tibet Plateau is a major issue affecting both the ecology and the economy. Microorganisms play an important role in soil nutrient cycling and the regulation of ecosystem function. This study aimed to investigate the species composition and diversity of microbial communities and understand the response of microbial communities to changes in physicochemical properties resulting from meadow degradation. In this study, the soil bacterial and fungal communities' composition and diversity of alpine meadows of degradation gradient were sequenced by high-throughput sequencing. During the process of grassland degradation, there were 59 bacterial taxa and 29 fungal taxa showing significant differences. The relative abundance of meadow pathogenic fungi significantly increased (p < 0.05). PICRUSt2 analysis showed a decrease in synthesis-related functional gene abundance and an increase in metabolism-related functional gene abundance. FUNGuild analysis showed that symbiotic and saprophytic nutrient fungi decreased significantly (p < 0.05). The soil nutrient cycling was mainly influenced by the beta diversity of microbial communities. Grassland degradation affects soil structure, thereby affecting the diversity of soil microbial composition and functional soil nutrient content. This work reveals the response of microbial communities to the degradation of alpine meadows and their impact on nutrient cycling, providing theoretical support for the protection and sustainable development of alpine meadows. [ABSTRACT FROM AUTHOR]

The microorganisms and functional predictions of leaf biofilms on submerged plants (Vallisneria natans (Val)) and in water samples (surface water (S) and bottom water (B)) in different seasons were evaluated in this study. S and B groups had 3249 identical operational taxonomic units (OTUs) (50.03%), while the Val group only had 1201 (18.49%) unique OTUs. There was significant overlap between microbial communities of S and B groups in the same season, while Val group showed the greater diversity. The dominant microbial clades were Proteobacteria (18.2-47.3%), Cyanobacteria (3.74-39.3%), Actinobacteria (1.64-29.3%), Bacteroidetes (1.31-21.7%), and Firmicutes (1.10-15.72%). Furthermore, there was a significant relationship between total organic carbon and the distribution of microbial taxa (p = 0.047), and TN may have altered the status of Cyanobacteria by affecting its biological nitrogen fixation capacity and reproductive capacity. The correlation network analysis results showed that the whole system consisted of 249 positive correlations and 111 negative correlations, indicating strong interactions between microbial communities. Functional predictions indicated that microbial functions were related to seasonal variation. These findings would guide the use of submerged plants to improve the diversity and stability of wetland microbial communities. [ABSTRACT FROM AUTHOR]

Coffee is an important cash crop worldwide, but it has been plagued by serious continuous planting obstacles. Intercropping with Areca catechu could alleviate the continuous planting obstacle of coffee due to the diverse root secretions of Areca catechu. However, the mechanism of Areca catechu root secretion in alleviating coffee continuous planting obstacle is still unclear. The changes of coffee rhizosphere soil microbial compositions and functions were explored by adding simulated root secretions of Areca catechu, the primary intercropping plant species (i.e., amino acids, plant hormone, organic acids, phenolic acids, flavonoids and sugars) in current study. The results showed that the addition of coffee root exudates altered soil physicochemical properties, with significantly increasing the availability of potassium and organic matter contents as well as promoting soil enzyme activity. However, the addition of plant hormone, organic acids, or phenolic acids led to a decrease in the Shannon index of bacterial communities in continuously planted coffee rhizosphere soil (RS-CP). The inclusion of phenolic acids specifically caused the decrease of fungal Shannon index. Plant hormone, flavonoids, phenolic acids, and sugars increased the relative abundance of beneficial bacteria with reduced bacterial pathogens. Flavonoids and organic acids increased the relative abundance of potential fungal pathogen Fusarium. The polyphenol oxidase, dehydrogenase, urease, catalase, and pH were highly linked with bacterial community structure. Moreover, catalase, pH, and soil-available potassium were the main determinants of fungal communities. In conclusion, this study highlight that the addition of plant hormone, phenolic acids, and sugars could enhance enzyme activity, and promote synergistic interactions among microorganisms by enhancing the physicochemical properties of RS-CP, maintaining the soil functions in coffee continuous planting soil, which contribute to alleviate the obstacles associated with continuous coffee cultivation. [ABSTRACT FROM AUTHOR]

Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest. [ABSTRACT FROM AUTHOR]

The presence of microbial communities on cave walls and speleothems is an issue that requires attention. Traditional cleaning methods using water, brushes, and steam can spread the infection and cause damage to the cave structures, while chemical agents can lead to the formation of toxic compounds and damage the cave walls. Essential oils (EOs) have shown promising results in disrupting the cell membrane of bacteria and affecting their membrane permeability. In this study, we identified the microorganisms forming unwanted microbial communities on the walls and speleothems of Petralona Cave using 16S and 18S rDNA amplicon sequencing approaches and evaluated the efficacy of EOs in reducing the ATP levels of these ecosystems. The samples exhibited a variety of both prokaryotic and eukaryotic microorganisms, including Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, the SAR supergroup, Opisthokonta, Excavata, Archaeplastida, and Amoebozoa. These phyla are often found in various habitats, including caves, and contribute to the ecological intricacy of cave ecosystems. In terms of the order and genus taxonomy, the identified biota showed abundances that varied significantly among the samples. Functional predictions were also conducted to estimate the differences in expressed genes among the samples. Oregano EO was found to reduce ATP levels by 87% and 46% for black and green spots, respectively. Consecutive spraying with cinnamon EO further reduced ATP levels, with reductions of 89% for black and 88% for green spots. The application of a mixture solution caused a significant reduction up to 96% in ATP levels of both areas. Our results indicate that EOs could be a promising solution for the treatment of microbial communities on cave walls and speleothems. [ABSTRACT FROM AUTHOR]

Copyright of Asian Journals of Ecotoxicology 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.)

Background: The jasmonate ZIM domain (JAZ) protein is a key repressor of the jasmonate signal transduction pathway, which plays an important role in plant growth and development and defense responses. In this study, based on the published whole-genome data, we identified members of the JAZ gene family in Populus trichocarpa. Through a series of bioinformatic approaches, their expression patterns under various stress conditions have been analyzed to explore and excavate the endogenous resistance genes of poplar and provide a theoretical basis for breeding new varieties of poplar resistance. Results: A total of 13 PtJAZ genes have been identified in P. trichocarpa and designated as PtJAZ1–PtJAZ13. Those 13 PtJAZ genes were unevenly distributed on nine chromosomes, and they could be divided into four subfamilies. The gene structures and motif composition of the members derived from the same subfamily were similar. Collinearity analysis demonstrated that, compared with Arabidopsis thaliana and Oryza sativa, the most collinear pairs (13) were found in P. trichocarpa and Eucalyptus robusta. Cis-acting element analysis suggested that the promoter regions of PtJAZs contained a large number of hormones and stress response elements, of which abscisic acid (ABA) and methyl jasmonate (MeJA) hormone response elements were the most abundant. The PtJAZ genes not only had diverse expression patterns in different tissues, but they also responded to various abiotic and biotic stress conditions. The co-expression network and GO and KEGG analyses showed that JAZ genes were closely related to insect resistance. Conclusions: In this study, applying bioinformatic methods, 13 PtJAZ gene family members from P. trichocarpa were identified and comprehensively analyzed. By further studying the function of the poplar JAZ gene family, the aim is to select genes with better insect resistance and stress resistance so as to lay a solid foundation for the subsequent breeding of new poplar varieties. [ABSTRACT FROM AUTHOR]

The BYPASS1-related gene (BPS1) encodes a protein with an unknown functional domain that regulates plant organ growth and development by inhibiting the continuous production of a root-derived long-distance signaling molecule called bypass (bps). We conducted a comprehensive study to investigate the BPS gene family in soybean and identified twenty-three BPS genes in Glycine max and twenty BPS genes in Glycine soja (wild soybean). Collinearity analysis revealied the existence of multiple orthologs of soybean BPS genes in wild soybean, indicating incomplete conservation between the BPS genes of soybean and wild soybean. Phylogenetic analysis successfully categorized all BPS genes into five distinct groups. We further scrutinized their chromosomal locations, gene structures, conserved motifs, cis-acting elements, and expression patterns. Leveraging publicly available data on genetic variation, phenotypic variation, and single-cell transcriptome sequencing of root nodules, we discovered a potential association between BPS genes and multiple soybean traits, particularly those related to the root nodule phenotype. This pioneering study provides a systematic and comprehensive examination of the BPS gene family in soybean. The findings establish a robust foundation for future investigations into the functional roles of BPS genes in plant growth and development. [ABSTRACT FROM AUTHOR]

Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability. [ABSTRACT FROM AUTHOR]

The excessive content of heavy metals and the deficiency of beneficial trace elements in cereals have threatened global food security and human health. As important metal transporters, Natural resistance-associated macrophage proteins (Nramps) are involved in the absorption and transport of various metal ions in plants, including beneficial elements and hazardous heavy metals, yet little is known about their roles in foxtail millet. In this study, 12 Nramps were identified in foxtail millet genome and divided into three clades. Expansion and functional differentiation of SiNramp gene family is evident in the high proportion of gene duplication as well as the diversity in protein structure and expression characteristics. The SiNramp genes exhibited different response patterns to Cd stress in different tissues. Based on the integration of ionome, RNA-seq and orthologous analysis, the association of SiNramp genes with the accumulation of different metal ions was investigated, and the possible functions of several SiNramp genes were predicted, such as SiNramp6 and SiNramp12. In general, this study provides a comprehensive theoretical framework for the study of Nramp genes in foxtail millet and other minor gramineous crops, which will lay a foundation for further research on the mechanism of metal transport and accumulation. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science 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.)

Microbiomes inhabiting rearing ponds have been frequently associated with the survival rate of cultured animals. However, specific studies reporting on the structure, composition, and functional genes of bacteria in commercial ponds with different survival rates are still scarce. Thus, using high-throughput sequencing, the present study addressed this gap by investigating microbiomes in commercial ponds with different survival rates of Pacific white shrimp, Litopenaeus vannamei. Water samples were collected from ponds with low survival rates (LSR) and ponds with high survival rates (HSR) and profiled by high-throughput sequencing of the 16S rRNA gene. Then, functional genes of microbiomes were predicted using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software. The results showed that ponds with different survival rates had distinct bacterial communities. At the genus level, 20 genera had different relative abundance in the two pond groups (LDA > 3), of which 11 genera were in HSR ponds and nine genera were in LSR ponds. The top five most abundant bacterial genera found in LSR ponds were Vibrio, Kocuria, Tepidiphilus, unidentified_Alphaproteobacteria, and Pseudoalteromonas, while the five most abundant found in the HSR ponds were Candidatus_Aquiluna, unidentified_Acinobacteria, Ilumatobacter, unidentified_Deltaproteobacteria, and Marivita. PICRUSt analysis revealed that nine metabolic pathways were higher in HSR grow-out ponds and associated with carbohydrate metabolism, chlorophyll biosynthesis, lignin degradation, arginine and glucosamine biosynthesis, and vitamin K2 synthesis, while nine metabolic pathways were found to be significantly higher in LSR grow-out ponds including lipid IVA biosynthesis (conserved structure in diverse Gram-negative pathogens), and L-tryptophan degradation activity (proteolytic agents). To the authors’ knowledge, this is the first study to report the diversity, composition, and metabolic activity of microbiomes in commercial shrimp grow-out ponds and their effect on the survival rate of Pacific white shrimp. Overall, these findings suggest that the specific microbiomes in rearing water may be linked to the impact on improved survival of Pacific white shrimp. [ABSTRACT FROM AUTHOR]

As an important spawning ground for large yellow croaker Larimichthys crocea, Sansha Bay, South China Sea has been a research hotspot. However, studies on the influence of the bacterioplankton community and assessments of its seasonal succession of bacterioplankton in different sea areas in Sansha Bay are still limited. To address the issue, we use 16S rRNA gene amplicon sequencing and functional prediction to investigate the spatial-temporal dynamics of the bacterioplankton community in three distinct areas, i.e., Breeding Area (BA), Yantian Harbor (YH), and Bay Margin (BM) of Sansha Bay. Results show that the structure of the bacterioplankton community in Sansha Bay had a significant seasonal succession. Moreover, the representative zero-radius Operation Taxon Units in different seasons were significantly different among the three selected sea areas. Specifically, during the breeding season, bacterioplankton communities in BA were characterized by compound-degrading bacteria, such as Rhodococcus and Owenweeksia, while in YH and BM, animal parasites or symbionts such as Vibrio and Arcobacter were dominant. Furthermore, the redundancy analysis and Spearman correlation analysis further explained that water temperature, dissolved oxygen, and ammonia nitrogen were the main environmental factors responsible for the difference. In addition, the bioindicator functions screened by Functional Annotation of Prokaryotic Taxa and random forest machine learning mainly relied on compound degradation, nitrite oxidation, and photoheterotrophy. The compound-degradation-corresponded bacterioplankton genera such as Rhodococcus had relatively higher abundance in BM, while Nitrospina corresponding to nitrite oxidation tended to be abundant in YH and BA. Based on the spatial and temporal variation in the composition and function of bacterioplankton, our findings provide a basis for understanding the theory of bacterioplankton community structure in the inner-bay habitat of the large yellow croaker in Sansha Bay. [ABSTRACT FROM AUTHOR]

Data retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases can reveal important information behind molecular biomarkers and their associated oncogenesis. Therefore, this study was based on in silico predictions and in vitro experiments to explore regulatory network associated with breast carcinogenesis. The breast cancer (BC)‐related data sets were retrieved from GEO database, followed by differential analysis and protein–protein interaction (PPI) analysis. Then, Fos proto‐oncogene, AP‐1 transcription factor subunit (FOS)‐associated gene network was constructed, and the key gene‐related genes in BC were screened by LinkedOmics. Finally, FOS expression was determined in BC tissues and cells, and gain‐of‐function assays were performed to define the role of FOS in BC cells. It was noted that seven differentially expressed genes (EGR1, RASSF9, FOSB, CDC20, KLF4, PTGS2, and FOS) were obtained from BC microarray data sets. FOS was the gene with the most nodes in PPI analysis. Poor FOS mRNA expression was identified in BC patients. Furthermore, FOS was mainly located in the extracellular matrix and was involved in cell processes. FOS was downregulated in BC tissues and cells, and FOS overexpression restrained the malignant phenotypes of BC cells. Collectively, ectopic expression of FOS curtails the development of BC. [ABSTRACT FROM AUTHOR]

A bootstrap procedure for constructing prediction bands for a stationary functional time series is proposed. The procedure exploits a general vector autoregressive representation of the time-reversed series of Fourier coefficients appearing in the Karhunen–Loève representation of the functional process. It generates backward-in-time functional replicates that adequately mimic the dependence structure of the underlying process in a model-free way and have the same conditionally fixed curves at the end of each functional pseudo-time series. The bootstrap prediction error distribution is then calculated as the difference between the model-free, bootstrap-generated future functional observations and the functional forecasts obtained from the model used for prediction. This allows the estimated prediction error distribution to account for the innovation and estimation errors associated with prediction and the possible errors due to model misspecification. We establish the asymptotic validity of the bootstrap procedure in estimating the conditional prediction error distribution of interest, and we also show that the procedure enables the construction of prediction bands that achieve (asymptotically) the desired coverage. Prediction bands based on a consistent estimation of the conditional distribution of the studentized prediction error process also are introduced. Such bands allow for taking more appropriately into account the local uncertainty of the prediction. Through a simulation study and the analysis of two datasets, we demonstrate the capabilities and the good finite-sample performance of the proposed method. [ABSTRACT FROM AUTHOR]