High-throughput Sequencing Analysis Research Articles

Contribution of pectin-degrading bacteria to the quality of cigar fermentation: an analysis based on microbial communities and physicochemical components

ObjectiveThis study aims to investigate the effects of pectin-degrading bacteria on the microbial community and physicochemical properties during the fermentation process of cigar tobacco, evaluating its potential in reducing green bitterness and enhancing aroma.MethodsBy isolating and screening pectin-degrading bacteria, high-throughput sequencing and physicochemical analysis were employed to compare the microbial flora and physicochemical component differences in different treatment groups of cigar tobacco. Furthermore, correlation analysis was performed to examine the relationships between these variables.ResultsThe results showed that the strains YX-2 and DM-3, isolated from the cigar tobacco variety “Yunxue No. 1,” exhibited strong pectin-degrading abilities. Phylogenetic analysis revealed that strain YX-2 is highly homologous to Bacillus flexus, while strain DM-3 is highly homologous to Bacillus siamensis. After fermentation, the addition of strains YX-2 and DM-3 significantly reduced the pectin content in the tobacco leaves, increased the total sugar and reducing sugar content, reduced green bitterness, and markedly enhanced the total aroma components. Notably, DM-3 exhibited outstanding performance in the production of Maillard reaction products. Microbial community analysis showed that the addition of pectin-degrading bacteria significantly increased the diversity of both bacteria and fungi, especially in the TDM3 group, where the relative abundance of Pseudomonas was notably elevated. Correlation analysis revealed that Pseudomonas had a significant positive correlation with both reducing sugar and total sugar, and a significant negative correlation with pectin, indicating its important role in sugar metabolism and pectin degradation. Additionally, fungal genera such as Cercospora were significantly negatively correlated with total sugar and total nitrogen, while Eurotium was closely associated with pectin degradation and reducing sugar accumulation.ConclusionThis study found that the addition of Pectin-degrading bacteria YX-2 and DM-3 significantly optimized the microbial community structure during the cigar tobacco fermentation process and improved the physicochemical properties of the tobacco leaves, with notable effects in reducing green bitterness and enhancing aroma.

Nonselective beta blockade enhances gut microbiome diversity in a rodent model of trauma, hemorrhage, and chronic stress

BACKGROUND Traumatic injury leads to gut dysbiosis with changes in microbiome diversity and conversion toward a “pathobiome” signature characterized by a selective overabundance of pathogenic bacteria. The use of non-selective beta antagonism in trauma patients has been established as a useful adjunct to reduce systemic inflammation. We sought to investigate whether beta-adrenergic blockade following trauma would prevent the conversion of microbiome to a “pathobiome” phenotype. METHODS Sprague-Dawley rats (n = 6–8/group) were subjected to routine daily handling (naïve), lung contusion with hemorrhagic shock (LCHS), or LCHS with daily chronic stress (LCHS/CS), each with or without administration of intraperitoneal propranolol (BB) (10 mg/kg/day). Fecal microbiome was measured on Days 0, 7, and 14 using high-throughput 16S rRNA sequencing and QIIME2 bioinformatics analyses. Alpha- and beta-diversity and microbiome composition were assessed with significance defined as *p < 0.05. RESULTS Use of propranolol following LCHS or LCHS/CS demonstrated a significant increase in the number of bacterial species (Chao1 index), as well as overall richness and evenness (Shannon index) compared with their untreated counterparts at Day 7. By Day 14, these differences were no longer apparent between BB and untreated groups subjected to LCHS/CS. There was an abundance of commensal bacteria such as Oscillospiraceae and Clostridia in LCHS and LCHS/CS treated with BB after 7 days which persisted at 14 days. CONCLUSION These findings suggest a role for beta-antagonism in altering the diversity of the gut microbiome and the need for further studies to elucidate the cellular and molecular mechanisms underlying this intriguing connection of microbiome with trauma and beta-blockade.

RXLR effector genes mediate regional adaptation of Phytophthora infestans

AbstractLocal adaptation has been a central theme of eco-evolutionary research for decades. It is generally assumed that plant pathogens are locally adapted due to their standing interactions with biotic and abiotic factors in the ecosystem. Effectors, secreted small proteins encoded by pathogens, play critical roles in host–pathogen interactions, by activating host genotype-specific resistance, suppressing plant immunity, and playing other functions. In this study, we investigated the potential involvement of RXLR effector genes in ecological adaptation by examining the simple sequence repeat (SSR), virulence, and effector profiles in Phytophthora infestans isolates collected from two geographic regions differing in ecological environments. Genotypic analyses with SSR markers and virulence assays showed that the pathogen from the two regions shared genetic background but differed in virulence spectrums. High-throughput sequencing and expression analysis of 24 selected P. infestans isolates further showed variations in the RXLR effector repertoire, ranging from 536 to 548 for each isolate and the expression of effector genes was highly associated with the accumulation of homologous sRNA. Regional specific alleles were detected at 94 RXLR effector genes, and a specific accumulation of homologous 25–26 nt sRNAs was found at 67 RXLR effector genes. Two of the regional specific RXLR effector genes were confirmed to be virulence factors. Taken together, these results suggest that genomic and epigenetic variations in RXLR effector genes contribute significantly to the ecological adaptation of P. infestans populations and that regional specific effector genes will help to understand the adaptive landscape of pathogens and efficient use of host resistance genes.

Exploring lncRNA expression in follicular fluid exosomes of patients with obesity and polycystic ovary syndrome based on high-throughput sequencing technology.

Infertility is a reproductive health problem that attracts worldwide attention. Polycystic ovary syndrome (PCOS) is a major cause of female infertility and patients with obesity and PCOS are particularly common in clinical practice. Long non-coding RNA (lncRNAs) are a functional core in cells that regulate gene expression, transcription, and chromatin modification processes, and participate in epigenetics, cell cycle, and cell differentiation. LncRNAs are assumed to play a role in the occurrence and development of PCOS; however, their specific mechanism of action remains to be elucidated. High-throughput sequencing technology has been used to sequence and analyze lncRNAs in exosomes from the follicular fluid of patients with obesity and PCOS and those who underwent assisted reproductive therapy owing to male factors. Specific expression profiles of patients with obesity and PCOS were obtained and functional information analysis combined with a literature review were performed to screen for differentially expressed lncRNAs, which were validated using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). High-throughput sequencing analysis revealed that compared to normal patients with male infertility, patients with obesity and PCOS had a total of 20 lncRNAs with significant expression differences in follicular fluid exosomes. Among them, 17 lncRNAs were upregulated and three were downregulated. Functional analysis showed that differentially expressed genes were mainly enriched in "cell metabolism," "cell adhesion," and other aspects: related gene pathways mainly involved Huntington's disease, Parkinson's disease, spliceosomes, non-alcoholic fatty liver disease, and ribosomes. Verification of differentially expressed lncRNAs revealed that the expression of lncRNAs TPT1-AS1, PTOV1-AS1, PTPRG-AS1, and SNHG14 in follicular fluid exosomes was consistent with the sequencing results. A preliminary differential expression profile of lncRNAs in exosomes of patients with obesity and PCOS was established by transcriptomic analysis of these individuals. Our bioinformatics analysis results may be applicable to further study of the impact mechanism involving obesity and PCOS. These differentially expressed lncRNAs maybe served as potential biomarkers for in-depth studies of the occurrence, development on Follicle quality and function for patients with PCOS in the future.

Improved treatment of coking wastewater and higher biodiversity through immobilization of Comamonas sp. ZF-3 supplemented microbial community.

The aim of this study was to investigate the relationship among pollutant removal performance, microbial community structure and potential gene function of immobilized microorganisms in coking wastewater (CWW) treatment process. The results showed that the immobilized biomass containing strain Comamonas sp. ZF-3 displayed greater resistance to CWW and higher COD, NH4+-N removal efficiency (92%, 60%) than free cells (48%, 7%), meanwhile, the results from GC-MS proved main organic pollutants in CWW including phenolic compounds, heterocyclic compounds and polycyclic aromatic hydrocarbons were basically removed by immobilized microorganisms. During 123 days of degradation experiment, high-throughput 16S rRNA gene sequencing analysis of immobilized carriers showed more stable and diverse microbial community, which was consistent with simultaneous removal of COD and NH4+-N observed in carrier experiment. Among them, Comamonas sp. ZF-3 continuously remained at the highest proportion (23.25%) in immobilized carrier, while Nitrosomonas (1.47%) and Nitrospira (1.90%) were simultaneously detected. Moreover, microbial community of immobilized carriers showed higher relative abundance of potential function in membrane transport and xenobiotics biodegradation and metabolism, which may indirectly displayed biodegradation activity of immobilized functional microorganisms. This work illustrated the survival status and potential gene function of immobilized microorganisms, and provided basis for practical application of immobilized carriers in CWW treatment.

Effects of Zn(II) on the simultaneous nitrification and denitrification (SND) process: performance and microbial community

Simultaneous nitrification and denitrification (SND) is considered an attractive alternative to traditionally biological nitrogen removal technology. Knowing the effects of heavy metals on the SND process is essential for engineering. In this study, the responses of SND performance to Zn(II) exposure were investigated in a biofilm reactor. The results indicated that Zn(II) at low concentration (≤ 2 mg·L−1) had negligible effects on the removal of nitrogen and COD in the SND process compared to that without Zn(II), while the removal of ammonium and COD was strongly inhibited with an increasing in the concentration of Zn(II) at 5 or 10 mg·L−1. Large amounts of EPS, especially PN, were secreted to protect microorganisms from the increasing Zn(II) damage. High-throughput sequencing analysis indicated that Zn(II) exposure could significantly reduce the microbial diversity and change the structure of microbial community. The RDA analysis further confirmed that Azoarcus-Thauera-cluster was the dominant genus in response to low exposure of Zn(II) from 1 to 2 mg·L−1, while the genus Klebsiella and Enterobacter indicated their adaptability to the presence of elevated Zn(II). According to PICRUSt, the abundance of key genes encoding ammonia monooxygenase (EC: 1.14.99.39) was obviously reduced after exposure to Zn(II), suggesting that the influence of Zn(II) on nitrification was greater than that of denitrification, leading to a decrease in ammonium removal of SND system. This study provides a theoretical foundation for understanding the influence of Zn(II) on the SND process in a biofilm system, which should be a source of great concern.

Enhanced electricity generation and energy storage in a microbial fuel cell with a bimetallic-modified capacitive anode

Microbial fuel cells (MFCs) are energy conversion devices that utilize microorganisms attached to the electrode as catalysts for the oxidation of organic waste, thereby generating electricity. In this study, a two-step hydrothermal method was employed to prepare a CF/NiO/Fe3O4 capacitive composite anode by directly growing NiO on a carbon felt substrate as a metal framework to support the in-situ growth of Fe3O4. In this paper, electrochemical tests such as cyclic voltammetry and AC impedance were used to investigate the electrochemical performance of the modified anode. The two electrodes were characterized by SEM, EDS, XRD, FTIR, BET, TEM and SAED test. The MFCs with the CF/NiO/Fe3O4 anode exhibited significant improvements in generation of power and storage of energy performance, reaching a maximum power density of 9.29 W/m3, which has increased by 1.54-fold compared to CF/NiO anode. After charging/discharging for 60 min, the CF/NiO/Fe3O4 anode had a sum charge of 8532.07C /m2, which was a significant increase of 1868.82C/m2 compared to the CF/NiO anode. High-throughput sequencing analysis suggested that the proportion of electricity-generating microorganisms on the CF/NiO/Fe3O4 surface of the anode reached 86.03 %, which was higher than that on CF/NiO anode surface. The protein contents of the CF/NiO/Fe3O4 reached 71.03 mg/cm3. The application of capacitive materials in MFCs would allow the constructed MFCs to generate and store bioelectricity simultaneously.

Application of high-hydrostatic pressure to extend shelf life of miso-marinated Escolar loins during cold storage

The changes in the microbiological and chemical qualities of escolar meat following high-pressure processing (HPP) (300–600 MPa, 5 min) along with miso marinade for 15 days with refrigeration were evaluated. Miso marinade and HPP treatment of escolar meat had synergistic inactivating effects on microorganisms that were more pronounced at higher pressures. In addition, when stored at 4°C, the combination of miso marinade and HPP treatment significantly delayed microbial growth and total volatile basic nitrogen (TVBN) production and inhibited pH changes. Using TVBN < 25 mg/100 g as the criterion for freshness, miso marinade and HPP treatment (300–600 MPa) extended the refrigerated storage period from 3 days without treatment and 6 days with miso marinade alone to 15 days. In addition, high-throughput sequencing analysis showed that the combination of miso marinade and HPP treatment significantly altered the microbiome of the fish during refrigeration, thereby slowing the spoilage process. This study demonstrated that miso marinade along with HPP treatment can improve color and texture, inhibit microbial growth, delay quality deterioration, and prolong the shelf life of fish meat. Therefore, high pressure together with miso marinade is an effective hurdle technique for improving the quality and freshness of aquatic products.

Characteristics of the IgM Repertoires in the Peripheral Blood of Early Rheumatoid Arthritis Patients.

Rheumatoid arthritis is a common autoimmune disease, but little is known about the characteristics of the B cell repertoires in the peripheral blood. In this study, the peripheral IgM repertoires of early rheumatoid arthritis (ERA) patients were analyzed by high-throughput sequencing and bioinformatics analyses. Clonal expansion was observed in IgM repertoires of ERA patients. Interestingly, a subset of the dominant clones in ERA repertoires showed self- and poly-reactivity to several autoantigens. The clones were also present in IgM repertoires of healthy adults but they were not expanded, suggesting that may stem from the natural auto-reactive B cell repertoire. Additionally, the ERA repertoires exhibited a greater extent of somatic hypermutations, particularly in the ERA dominant clones, resulting in an enrichment of amino acids important for antigen-antibody interaction. The in-depth analysis of B-cell repertoires improved our knowledge of the IgM repertoires in early rheumatoid arthritis, offering potential insights into the disease's pathogenesis.

S0-dependent bio-reduction for antimonate detoxification from wastewater by an autotrophic bioreactor with internal recirculation.

Elemental sulfur (S0) autotrophic reduction is a promising approach for antimonate [Sb(V)] removal from water; however, it is hard to achieve effective removal of total antimony (TSb). This study established internal recirculation in an S0 autotrophic bioreactor (SABIR) to enhance TSb removal from Sb(V)-contaminated water. Complete Sb(V) reduction (10mg/L) with bare residual Sb(III) (< 0.26mg/L) was achieved at hydraulic retention time (HRT) = 8h. Shortening HRT adversely affected the removal efficiencies of Sb(V) and TSb; meanwhile, an increased reflux ratio was conducive to Sb(V) and TSb removal at the same HRT. Sulfur disproportionation occurred in the SABIR and was the primary source for SO42- generation and alkalinity consumption. The alkalinity consumption decreased with the shortening HRT and increased with an increased reflux ratio at the same HRT. The generated SO42- was significantly higher (50-100 times) than the theoretical value for Sb(V) reduction. Coefficient of variation (CV), first-order kinetic models, and osmolality analyses showed that internal recirculation did not significantly affect the stability of SABIR but contributed to enhancing TSb removal by increasing mass transfer and reflowing generated sulfide back to the SABIR. SEM-EDS, Raman spectroscopy, XRD and XPS analyses identified that the precipitates in the SABIR were Sb2S3 and Sb-S compounds. In addition, high-throughput sequencing analysis revealed the microbial community structure's temporal and spatial distribution in the SABIR. Dominant genera, including unclassified-Proteobacteria (18.72-38.99%), Thiomonas (0.94-4.87%) and Desulfitobacterium (1.18-2.75%) might be responsible for Sb(V) bio-reduction and removal. This study provides a strategy to remove Sb from water effectively and supports the theoretical basis for the practical application of the SABIR in Sb(V)-contaminated wastewater.

Palmitoleic Acid Inhibits Hepatotoxic Effects by Reducing Trimethylamine-N-Oxide (TMAO) Formation in High L-Carnitine-Treated Mice.

This study investigated the effects of palmitoleic acid (POA) consumption on liver function, intestinal microbiota, and trimethylamine-N-oxide (TMAO) levels in the serum of mice treated with 3% L-carnitine drinking water. The purpose was to highlight the impact of POA on liver injury associated with high L-carnitine intake. A correlation analysis was carried out. The physiological and biochemical results showed that the administration of POA could alleviate liver injury induced by high L-carnitine ingestion, as reflected by a reduction in liver function indices (ALT, AST, AKP, and TBA activities) and modulation of antioxidant enzyme activities (SOD, GSH-Px, MDA, and RAHFR). The study also monitored the levels of total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C). Additionally, to assess the impact of POA on intestinal microbiota, we conducted a 16S rRNA high-throughput sequencing analysis. The findings indicated that POA administration resulted in lower levels of TMAO in treated mice. Furthermore, POA could regulate the composition of intestinal microbiota in L-carnitine mice, particularly affecting Bacteroides vulgatus, Parabacteroides distasonis, Alistipes shahii, Lachnospiraceae NK4A136 group, and Parasutterella secunda, which were closely related to liver injury. In summary, POA could repair liver damage caused by high intake of L-carnitine by regulating the distribution of intestinal flora and subsequently decreasing serum TMAO levels.

Altitude Distribution Patterns and Driving Factors of Rhizosphere Soil Microbial Diversity in the Mountainous and Hilly Region of Southwest, China

The distribution characteristics of the microbial community in rhizosphere soils of different altitudinal gradients were explored to uncover ecological factors affecting microbial community composition. In this study, the community variations of bacteria and fungi in the rhizosphere soil of Chrysanthemum indicum L. were analyzed. Samples were distributed along an altitudinal gradient of 300–1500 m above sea level in the Fuling watershed of the Three Gorges Reservoir area, China. The analysis was conducted using Illumina MiSeq high-throughput sequencing and bioinformatics analyses. Through correlation analysis with ecological factors, the altitude distribution pattern and driving factors of soil microbial diversity in the mountainous and hilly region of Chongqing were explored. According to the results, the richness and diversity of rhizosphere soil bacteria increased with altitude, while fungi were the richest and most diverse at an altitude of 900 m. The composition of the microbial community differed among different altitudes. Actinobacteria, Proteobacteria, Acidobacteriota, Chloroflexi, Bacteroidota, Ascomycota, unclassified_k_Fungi, Basidiomycota, and Mortierellomycota dominated the microbial community in rhizosphere soil. Correlation analysis showed that the distribution of rhizosphere soil microbial communities correlated with soil ecological factors at different altitudes. Moisture, pH, total nitrogen, total potassium, available potassium, urease, and catalase were significantly positively correlated with rhizosphere soil bacterial α-diversity, while their correlations with fungi were not significant. Variation partition analysis showed that the combined effects of soil physical and chemical factors, enzyme activity, and microbial quantity regulated bacterial community structure and composition. Their combined contributions (19.21%) were lower than the individual effects of soil physical and chemical factors (48.49%), enzyme activity (53.24%), and microbial quantity (60.38%). The effects of ecological factors on fungal communities differed: While the soil physical and chemical factors (44.43%) alone had a clear effect on fungal community structures, their combined contributions had no apparent effect. The results of this study not only contribute to a deeper understanding of the impact mechanism of altitude gradient on the diversity of rhizosphere soil microbial communities, but also provide a scientific basis for the protection and management of mountainous and hilly ecosystems. It lays a foundation for the future exploration of the relationship between microbial communities and plant–soil interactions.

Effects of fermented Chinese herbal medicine feed additives on growth performance and intestinal microbiota of piglets.

Fermented Chinese medicine (FCM), as a functional feed additive, has been widely recognized to play a significant role in protecting the intestinal health of piglets and enhancing productive performance. However, the relationship between the active components of FCM, gut microbiota, and their beneficial effects on animal performance remains unclear. In this study, metabolomics analysis revealed a significant increase in the main contents of lactic acid and propionic acid in FCM, while most glycosides and their derivatives decreased after three days of microbial fermentation. Subsequently, piglets were fed a basic diet supplemented with 1% FCM, while the control group received only the basic diet. The results indicated a significant increase in feed intake and average daily gain within 14 days (P<0.05) due to FCM supplementation. Additionally, FCM significantly improved feed efficiency from 1.76 to 1.50 (P<0.05), and piglets in the FCM group exhibited significantly lower frequencies of diarrhea and coughing, which indicated improved health condition by FCM. Moreover, high-throughput sequencing analysis revealed higher abundances of Lactobacillus agilis, Megasphaera elsdenii, Ligilactobacillus, and Veillonellaceae in FCM group. In summary, FCM increased the content of active metabolites through microbial fermentation and regulated the intestinal microbiota to improve the health of piglets. FCM offers a promising potential for enhancing production performance and economic efficiency in the livestock industry.

Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling.

Triclosan (TCS) is a lipophilic, broad spectrum antimicrobial agent commonly used in personal care products with a projected continuous escalation in aquatic environments in the post COVID 19 era. There is rich documentation in the literature on the alteration of physiological responses in fish due to TCS exposure; however, studies on gut associated bacteria of fish are still scarce. This is the first attempt to determine changes in bacterial community structure due to exposure of TCS on Labeo rohita, a commercially essential freshwater species, using 16S V3-V4 region ribosomal RNA (rRNA) next-generation sequencing (NGS). Chronic exposure of TCS at environmentally realistic concentrations viz. 1/5th (T1: 0.129 mg/L) and 1/10th (T2: 0.065 mg/L) of LC50 for 28 days resulted in the dose dependent bioconcentration of TCS in the fish gut. Prolonged exposure to TCS leads to disruption of gut bacteria evidenced by down regulation of the host immune system. Additionally, high-throughput sequencing analysis showed alternation in the abundance and diversity of microbial communities in the gut, signifying Proteobacteria and Verrucomicrobia as dominant phyla. Significant changes were also observed in the relative abundance of Chloroflexi and Gammatimonadetes phyla in TCS exposed groups. The study revealed that gut microbiome can be used as a biomarker in assessing the degree of TCS toxicity in commercially important fish species.

Transcriptome-wide analysis for glucocorticoid receptor-mediated mRNA decay reveals various classes of target transcripts

The glucocorticoid receptor (GR) can bind to DNA or RNA, eliciting transcriptional activation/repression or rapid mRNA degradation, respectively. Although GR-mediated transcriptional regulation has been well-characterized, the molecular details of rapid mRNA degradation induced by glucocorticoids (GCs) are not yet fully understood. Here, we demonstrate that GC-induced GR-mediated mRNA decay (GMD) takes place in the nucleus and the cytoplasm, acting on pre-mRNAs and mRNAs. We also performed cross-linking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) analysis for GMD factors (GR, YBX1, and HRSP12) and mRNA sequencing (mRNA-seq) analysis to identify endogenous GMD substrates. Our comprehensive CLIP-seq and mRNA sequencing analyses reveal that a range of cellular transcripts containing a common binding site for GR, YBX1, and HRSP12 are preferential targets for GMD, suggesting possible new functions of GMD in various biological events.

Exploring novel preservation strategies for blue honeysuckle through high-throughput sequencing and bioinformatics analysis

Berries’ metabolic activities continue post-harvest, and their quality and safety are affected by various external and internal factors, with microbial contamination being one of the major influences. Refrigeration is necessary to preserve freshness and increase shelf life; however, understanding the changes in microbial communities on berries during refrigeration still is in its infancy. This study examines the diversity and dynamics of epidermal microbes on blue honeysuckle during refrigeration. Blue honeysuckle was refrigerated at 4 °C for 0, 4, 8, and 12 d, with microbial communities analyzed via Illumina Novaseq sequencing. Species distribution revealed dominant Ascomycota and Basidiomycota in fungi, Proteobacteria and Firmicutes in bacteria, with fluctuating abundance over time. Through tissue isolation, Alternaria alternata and Irpex lacteus were successfully separated and validated as predominant decay-causing fungi. Additionally, lactobacilli were isolated and screened for inhibiting decay-causing fungi, with Enterococcus faecium showing significant efficacy. Factors influencing its activity were evaluated, with temperature and pH impacting efficacy. Enzyme treatments indicated the role of peptides in inhibition. In vivo tests demonstrated preservation efficacy, highlighting bio-preservation potential for quality maintenance during storage. The study's workflow emphasizes exploring microbial ecological interventions that can be implemented in bio-preservation strategies, thereby enhancing understanding and management of post-harvest quality in berries, particularly blue honeysuckle.

Combined cellular phenotyping and high-throughput sequencing analysis reveals the symbiotic relationships between different types of macadamia root systems and arbuscular mycorrhizal fungi

Macadamia nuts, scientifically designated as Macadamia integrifolia, are a highly valuable crop that originated in Australia. This study provides a comprehensive examination of the symbiotic relationships between various macadamia root systems and arbuscular mycorrhizal fungi (AMF). The four principal macadamia-producing regions in Yunnan Province were selected for investigation on the basis of meticulous criteria. To determine the AMF infection rate, the roots were stained. Furthermore, high-throughput sequencing was employed to conduct a comprehensive analysis of the fungal diversity in the rhizosphere soil. The findings were definitive, indicating that both normal and cluster roots are capable of establishing a symbiotic relationship with AMF. Secondary forests exhibited significantly elevated fungal diversity relative to normal roots, while cluster roots demonstrated the lowest diversity and notable regional variation, indicating that the environment exerts a considerable influence on inter-root fungi and AMF. The analysis of the fungal community composition revealed that the predominant groups were Ascomycetes and Basidiomycetes. The FUNGuild function prediction clearly indicated distinct differences in the fungal functions of secondary forests, cluster roots, and normal roots. This study provides a scientific foundation for the sustainable development of macadamia nuts and significantly contributes to a deeper comprehension of the intricate interactions between macadamia and AMF, thereby fostering the long-term stable and healthy growth of the macadamia nut industry.

The inoculation of Bacillus paralicheniformis and Streptomyces thermoviolaceus enhances the lignocellulose degradation and microbial communities during spent mushroom substrate composting

The burgeoning global mushroom industry has precipitated challenges related to the efficient and sustainable utilization of spent mushroom substrate (SMS). Composting is regarded as an efficient way for the ecological utilization of SMS. The addition of microbial inoculants can promote the composting process and improve the quality of compost products. This study introduced two bacterial inoculants, Bacillus paralicheniformis HL-05 (BP) and Streptomyces thermoviolaceus LC-10 (ST), into the composting process of SMS. The impact of these inoculants was evaluated through analyses of physicochemical properties, lignocellulose degradation, and high-throughput sequencing to elucidate their ecological roles and optimize the composting process. The results suggest that inoculation with BP and ST significantly prolonged the thermophilic stage by 2–3 days, representing an increase of 22.22–33.33%. Moreover, it boosted the degradation rates of cellulose, hemicellulose, and lignin by 18.37–29.77%, 35.74−50.43%, and 40.32−40.83%, respectively, compared to the control. Furthermore, inoculation rapidly altered the microbial community structure during the rapid temperature-rising stage and strengthened interconnections among composting microorganisms. The microbial inoculation substantially enhanced the proliferation of thermophilic lignocellulose-degrading microorganisms during the thermophilic stage, thereby facilitating the utilization of lignocellulose. This study proposes a novel and effective strategy for SMS composting using microbial inoculants.

Inference and design of antibody specificity: From experiments to models and back.

Exquisite binding specificity is essential for many protein functions but is difficult to engineer. Many biotechnological or biomedical applications require the discrimination of very similar ligands, which poses the challenge of designing protein sequences with highly specific binding profiles. Experimental methods for generating specific binders rely on in vitro selection, which is limited in terms of library size and control over specificity profiles. Additional control was recently demonstrated through high-throughput sequencing and downstream computational analysis. Here we follow such an approach to demonstrate the design of specific antibodies beyond those probed experimentally. We do so in a context where very similar epitopes need to be discriminated, and where these epitopes cannot be experimentally dissociated from other epitopes present in the selection. Our approach involves the identification of different binding modes, each associated with a particular ligand against which the antibodies are either selected or not. Using data from phage display experiments, we show that the model successfully disentangles these modes, even when they are associated with chemically very similar ligands. Additionally, we demonstrate and validate experimentally the computational design of antibodies with customized specificity profiles, either with specific high affinity for a particular target ligand, or with cross-specificity for multiple target ligands. Overall, our results showcase the potential of leveraging a biophysical model learned from selections against multiple ligands to design proteins with tailored specificity, with applications to protein engineering extending beyond the design of antibodies.

Biofouling effect of different landfill leachates on high-density polyethylene pipe material

Pipelines used for collecting and transporting landfill leachates may be affected by biofouling, subsequently posing environmental risks. This study investigates the surface biofouling on high-density polyethylene (HDPE) pipes immersed in leachates acquired from operating (MSW-1) and closed (MSW-2) landfills and from a landfill containing incinerated bottom ash and municipal waste (MSW-3). Water quality monitoring, material characterization, and microbial high-throughput sequencing analysis were conducted to analyze the biofouling effects of different landfill leachates on HPDE pipes. The total fouling masses in the MSW-1, MSW-2, and MSW-3 leachates were 29.2 %, 35.2 %, and 24.5 %, respectively; MSW-2 depicted severe biofouling. The biofouling mass was dominated by living mycobacterial cells (69.93 % of the total biovolume). Proteobacteria was the dominant phylum (30.43 %) and the key bacteria group to cause biofouling. The leachates had a significant impact on the microbial community structure, with Castellaniella and Luteibacter being the endemic genera in MSW-3 and norank_f__Rhodothermaceae being the endemic genera in MSW-1 and MSW-2. Furthermore, Ca2+ was the dominant water-quality parameter to affect the distribution of microbial communities. This study provides valuable insights for pipeline disinfection and sterilization to mitigate bio-clogging in HDPE pipes.