Fulvic Acid Enhances Nitrogen Fixation and Retention in Paddy Soils through Microbial-Coupled Carbon and Nitrogen Cycling.

Fulvic acid, the most soluble and active humic substance, is widely used as an agent to remediate contaminated soils and improve soil fertility. However, the influence of fulvic acid (FA), as a microbial carbon source, on carbon and nitrogen cycles in paddy soils remains elusive. Therefore, to investigate it, an incubation experiment was conducted. Gas analyses indicated that the carbon dioxide and methane emissions were enhanced in FA treatment, which increased up to 94.08-fold and 5.06-fold, respectively. 15N-labeling experiments revealed that nitrogen fixation capability was promoted (1.2-fold) to reduce the carbon and nitrogen imbalance due to fulvic acid amendment. Metagenomic analysis further revealed that gene abundances of degradation of lignin-like compounds, gallate degradation, methanogenesis, nitrogen fixation, and urea hydrolysis increased, while the bacterial ammonia oxidation and anaerobic ammonium oxidation decreased, caused by FA application. Metabolic reconstruction of metagenome-assembled genomes revealed that Azospirillaceae, Methanosarcinaceae, and Bathyarchaeota, with higher abundance in FA treatment, were the key microorganisms to maintain the carbon and nitrogen balance. The metabolic pathways of fulvic acid degradation and coupled nitrogen fixation and retention were constructed. Collectively, our results provided novel insights into the theoretical basis of the use of humic substances for reducing nitrogen fertilization and climate change.

Case report: Fatal hemoptysis after effective treatment with tislelizumab and anlotinib in pulmonary sarcomatoid carcinoma.

Pulmonary sarcomatoid carcinoma (PSC), a rare non-small cell lung cancer (NSCLC) subtype, poses diagnostic and treatment difficulties. Current research explores targeted therapies and immunotherapy to improve patient outcomes. This case report details a male patient diagnosed with PSC via pathology. Tests revealed high levels of PD-L1, a marker suggesting potential benefit from immune checkpoint inhibitors. However, despite bronchoscopic intervention, his advanced stage IIIB cancer (cT3N2bM0) progressed quickly, with progression-free survival (PFS) under 3 months. Following progression, the patient received tislelizumab (anti-PD-1 antibody) and anlotinib (an anti-angiogenic drug) as second-line therapy. This combination showed promise, achieving near-partial remission after the first cycle. Subsequent scans documented continued tumor shrinkage until the patient experienced fatal hemoptysis. This case highlights the potential benefits of combining tislelizumab with anlotinib for PSC. However, it also represents the first reported case of fatal hemoptysis with this specific treatment regimen. This finding emphasizes the need for increased awareness of this potential complication, especially in patients with centrally located PSC treated with anti-angiogenic agents like anlotinib.

Taxonomic Diversity, Predicted Metabolic Pathway, and Interaction Pattern of Bacterial Community in Sea Urchin Anthocidaris crassispina.

Bacterial assemblages associated with sea urchin are critical to their physiology and ecology within marine ecosystems. In this study, we characterized the bacterial communities in wild sea urchin Anthocidaris crassispina captured in Daya Bay, South China Sea. A total of 363 amplicon sequence variants belonging to nine phyla and 141 genera were classified from intestine, body surface, and surrounding seawater samples. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacteria phyla found in this study. A network analysis of bacterial interspecies interactions revealed varying complexity, stability, connectivity, and relationship patterns across the samples, with the most intricate network observed in the surrounding seawater. Metagenomic predictions highlighted the distinct bacterial metabolic pathways, with significant differences between intestine and seawater samples. Notably, pathways associated with polysaccharide degradation, including chitin derivatives, starch, and CoM biosynthesis, were markedly abundant, underscoring the gut microbiota's key role in digesting algae. In addition, other metabolic pathways in intestine samples were linked to immune response regulation of sea urchins. Overall, this study provides a comprehensive overview of the bacterial community structure and potential functional roles in A. crassispina.

Regularity and correlation analysis of regional lymph node metastasis in nonoperative patients with non-small cell lung cancer based on positron emission tomography/computed tomography images.

BACKGROUND: Definitive concurrent chemoradiotherapy (CCRT) is the standard treatment for locally advanced, inoperable non-small cell lung cancer (NSCLC). Previous studies have mainly focused on examining local failure and recurrence patterns after surgery and the principles of lymph node metastasis (LNM) in surgical candidates with NSCLC. However, these studies were just only able to guide postoperative radiotherapy (PORT) and the patterns of LNM in patients with resected NSCLC was inadequate to represent that in locally advanced inoperable NSCLC patients for guiding target volume delineation of CCRT. In this study, we aimed to analyze the metastasis regularities and establish the correlations between different lymph node levels in NSCLC patients without any intervention using positron emission tomography/computed tomography (PET/CT) images. METHODS: Overall, 358 patients with N1-N3 NSCLC admitted in our hospital between 2018 and 2022 were retrospectively analyzed. The diagnosis of metastatic lymph nodes was reviewed and determined using the European Organization for Research and Treatment of Cancer standard and the standardized value of the PET/CT examination. Univariate and multivariate analysis were performed to investigate the correlations between the different levels were evaluated by using of the chi-square test and logistic regression model. RESULTS: The lymph nodes with the highest metastasis rates in patients with left lung cancer were in order as follows: 10L, 4L, 5, 4R, and 7; while in those with right lung cancer they were 10R, 4R, 7, 2R, and 1R. Notably, we found left lung patients were more likely to have contralateral hilar, mediastinal and supraclavicular lymph nodes involved, and the right lung group exhibited a higher propensity for ipsilateral mediastinum and supraclavicular lymph node invasion. Furthermore, correlation analysis revealed there were significant correlative patterns in the LNM across different levels. CONCLUSIONS: This study elucidated the patterns of primary LNM in patients with NSCLC who had not undergone surgery (without any treatment interventions) and the correlations between lymph node levels. These findings were expected to provide useful reference for target volume delineation in definitive concurrent chemoradiotherapy in locally advanced NSCLC patients.

The early prognostic value of the 1-4-day BCM/PA trend after admission in neurocritical patients.

The purpose of this study was to investigate early stage dynamic changes in relevant indicators in neurocritical patients to identify biomarkers that can predict a poor prognosis at an early stage (1-4 days after admission). This study retrospectively collected clinical data, inflammatory indicators, and nutritional indicators from 77 patients at the neurology intensive care unit. The 3-month modified Rankin scale score was used as the outcome indicator. A linear mixed model was used to analyze changes in inflammatory indicators and nutritional indicators in neurocritical patients over time from 1-4 days after admission. Logistic regression was used to determine the independent risk factors for a poor prognosis in neurocritical patients and to construct a predictive model. The predictive efficacy of the model was verified using leave-one-out cross-validation and decision curve analysis methods. The analysis results showed that 1-4 days after admission, the inflammatory indicators of white blood cell and absolute monocyte counts and the nutritional indicators of body cell mass(BCM), fat-free mass, body cell mass/phase angle (BCM/PA), intracellular water, extracellular water, and skeletal muscle index increased overall, while the nutritional indicators of albumin and visceral fat area decreased overall. The logistic multivariate regression model showed that the Charlson comorbidity index (CCI) (odds ratio (OR) = 2.526, 95% CI [1.202, 5.308]), hemoglobin (Hb)(on admission)-Hb(min) (OR = 1.049, 95% CI [1.015, 1.083), BCM(on admission) (OR = 0.794, 95% CI [0.662, 0.952]), and the change in BCM/PA 1-4 days after admission (OR = 1.157, 95% CI [1.070, 1.252]) were independent risk factors for a poor prognosis in neurocritical patients. The predictive analysis showed that the predictive power of Model 1 with BCM/PA (area under the curve (AUC) = 0.95, 95% CI (0.90, 0.99)) was 93%, 65%, 141%, and 133% higher than that of Model 2 without BCM/PA, the CCI, the APACHE II score, and the NRS2002 score (all P < 0.05), respectively. The CCI, Hb(on admission)-Hb(min), BCM(on admission), and an increase in BCM/PA 1-4 days after admission were independently associated with a poor prognosis in neurocritical patients. Of these variables, BCM/PA may be a valid indicator for early stage prediction of a poor prognosis in neurocritical patients.

Discovery of 1(2H)-phthalazinone and 1(2H)-isoquinolinone derivatives as potent hematopoietic progenitor kinase 1 (HPK1) inhibitors.

Although immune checkpoint inhibitors (ICIs) have been a revelation for treating several cancers, an unmet need remains to broaden ICI therapeutic scope and increase their response rates in clinical trials. Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T cell activation and has previously been identified as a promising target for immunotherapy. Herein, we report the discovery of a series of HPK1 inhibitors with novel 1(2H)-phthalazinone and 1(2H)-isoquinolinone scaffolds. Among them, compound 24 demonstrated potent in vitro activity (HPK1 IC50 value of 10.4 nM) and cellular activity (pSLP76 EC50 = 41 nM & IL-2 EC50 = 108 nM). Compound 24 exhibited favorable mouse and rat pharmacokinetic profiles with reasonable oral exposure. Compound 24 showed potent in vivo anti-tumor activity in a CT26 syngeneic tumor model with 95 % tumor growth inhibition in combination with anti-PD-1.

Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management.

Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.

Association of bioimpedance analysis parameters trajectories with clinical outcomes in neurocritical patients.

Background and objective: Neurocritical patients often experience uncontrolled high catabolic metabolism state during the acuta phase of the disease. The complex interactions of neuroendocrine, inflammation, and immune system lead to massive protein breakdown and changes in body composition. Bioelectrical impedance analysis (BIA) evaluates the content and proportions of body components based on the principles of bioelectricity. Its parameters reflect the overall health status of the body and the integrity of cellular structure and function, playing an important role in assessing the disease status and predicting prognosis of such patients. This study explored the association of BIA parameters trajectories with clinical outcomes in neurocritical patients. Methods: This study prospectively collected BIA parameters of 127 neurocritical patients in the Department of Neurology admitted to the NICU for the first 1-7 days. All these patients were adults (≥18 years old) experiencing their first onset of illness and were in the acute phase of the disease. The group-based trajectory modeling (GBTM), which aims to identify individuals following similar developmental trajectories, was used to identify potential subgroups of individuals based on BIA parameters. The short-term prognosis of patients in each trajectory group with variations in phase angle (PA) and extracellular water/total body water (ECW/TBW) over time was differentially analyzed, and the logistic regression model was used to analyze the relationship between potential trajectory groups of PA and ECW/TBW and the short-term prognosis of neurocritical patients. The outcome was Glasgow Outcome Scale (GOS) score at discharge. Results: Four PA trajectories and four ECW/TBW trajectories were detected respectively in neurocritical patients. Among them, compared with the other latent subgroups, the "Low PA rapidly decreasing subgroup" and the "High ECW/TBW slowly rising subgroup" had higher incidences of adverse outcomes at discharge (GOS:1-3), in-hospital mortality, and length of neurology intensive care unit stay (all P < 0.05). After correcting for potential confounders, compared with the "Low PA rapidly decreasing subgroup", the risk of adverse outcome (GOS:1-3) was lower in the other three PA trajectories, with OR values of 0.0003, 0.0004, and 0.003 respectively (all P < 0.05). Compared with the "High ECW/TBW slowly rising subgroup", the risk of adverse outcome (GOS:1-3) was lower in the other three ECW/TBW trajectories, with OR values of 0.013, 0.035 and 0.038 respectively (all P < 0.05). Conclusion: Latent PA trajectories and latent ECW/TBW trajectories during 1-7 days after admission were associated with the clinical outcomes of neurocritical patients. The risk of adverse outcomes was highest in the "Low PA rapidly decreasing subgroup" and the "High ECW/TBW slowly rising subgroup". These results reflected the overall health status and nutritional condition of neurocritical patients at the onset of the disease, and demonstrated the dynamic change process in body composition caused by the inflammatory response during the acute phase of the disease. This provided a reference basis for the observation and prognostic evaluation of such patients.

Predictive value of the random forest model based on bioelectrical impedance analysis parameter trajectories for short-term prognosis in stroke patients.

BACKGROUND: The short-term prognosis of stroke patients is mainly influenced by the severity of the primary disease at admission and the trend of disease development during the acute phase (1-7 days after admission). OBJECTIVE: The aim of this study is to explore the relationship between the bioelectrical impedance analysis (BIA) parameter trajectories during the acute phase of stroke patients and their short-term prognosis, and to investigate the predictive value of the prediction model constructed using BIA parameter trajectories and clinical indicators at admission for short-term prognosis in stroke patients. METHODS: A total of 162 stroke patients were prospectively enrolled, and their clinical indicators at admission and BIA parameters during the first 1-7 days of admission were collected. A Group-Based Trajectory Model (GBTM) was employed to identify different subgroups of longitudinal trajectories of BIA parameters during the first 1-7 days of admission in stroke patients. The random forest algorithm was applied to screen BIA parameter trajectories and clinical indicators with predictive value, construct prediction models, and perform model comparisons. The outcome measure was the Modified Rankin Scale (mRS) score at discharge. RESULTS: PA in BIA parameters can be divided into four separate trajectory groups. The incidence of poor prognosis (mRS: 4-6) at discharge was significantly higher in the "Low PA Rapid Decline Group" (85.0%) than in the "High PA Stable Group " (33.3%) and in the "Medium PA Slow Decline Group "(29.5%) (all P < 0.05). In-hospital mortality was the highest in the "Low PA Rapid Decline Group" (60%) compared with the remaining trajectory groups (P < 0.05). Compared with the prediction model with only clinical indicators (Model 1), the prediction model with PA trajectories (Model 2) demonstrated higher predictive accuracy and efficacy. The area under the receiver operating characteristic curve (AUC) of Model 2 was 0.909 [95% CI 0.863, 0.956], integrated discrimination improvement index (IDI), 0.035 (P < 0.001), and net reclassification improvement (NRI), 0.175 (P = 0.031). CONCLUSION: PA trajectories during the first 1-7 days of admission are associated with the short-term prognosis of stroke patients. PA trajectories have additional value in predicting the short-term prognosis of stroke patients.

Combined metabolomics and proteomics to reveal the mechanism of S. oneidensis MR-1 degradation malathion enhanced by FeO/C.

Iron oxide @ biochar (FeO/C) promotes bacterial growth and facilitates electron transfer, thereby effectively promoting malathion degradation by Shewanella oneidensis MR-1 (S. oneidensis MR-1). This study elucidated the underlying mechanism of FeO/C-enhanced malathion degradation by S. oneidensis MR-1 through a combination of metabolomics and proteomics analysis. The kinetic fitting results from the degradation experiment indicated that 0.1 g/L FeO/C exerted the most significant enhancement effect on malathion degradation by S. oneidensis MR-1. Observations from Scanning Electron Microscopy and Laser Scanning Confocal Microscopy, along with physiological and biochemical analysis, showed that FeO/C enhanced the growth and oxidative response of S. oneidensis MR-1 under malathion stress. In addition, metabolomics and proteomics analysis revealed an increase in certain electron transfer related metabolites, such as coenzymes, and the upregulation of proteins, including coenzyme A, sdhD, and petC. Overall, spectroscopic analysis suggested that Fe2+, which was reduced from Fe3+ by S. oneidensis MR-1 in FeO/C, promoted electron transfer in S. oneidensis MR-1 to enhance the degradation of malathion. This study offers enhanced strategies for efficient removal of malathion contaminants.

Metabolic potential of Nitrososphaera-associated clades.

Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.

HBB as a Novel Biomarker for the Diagnosis and Monitoring of Lung Cancer Regulates Cell Proliferation via ERK1/2 Pathway.

Objective: Recent studies have revealed that hemoglobin beta (HBB) plays an important role not only in blood disorders but also in malignancies. The aim of this study is to investigate the clinical significance, diagnostic value, and biological function of HBB in lung cancer. Methods: HBB expression was examined in lung cancer tissues and plasma samples using quantitative real-time polymerase chain reaction, and its relationship with clinical pathological characteristics was analyzed. Receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic value of HBB in lung cancer. The proliferation of A549 and SPCA1 cells was analyzed using a cell counting kit-8 assay and protein expressions were detected by western blot. Results: The expressions of HBB were found to be down-regulated in both lung cancer tissues and plasma samples. Notably, plasma HBB levels were significantly elevated in postoperative samples when compared to their preoperative counterparts. Across 66 cases of lung cancer tissues, a correlation was observed between HBB levels and both gender and tumor, node, metastasis staging. ROC curve analysis further confirmed the high diagnostic potential of HBB expression in lung cancer. Moreover, the combination of HBB and carcinoembryonic antigen (CEA) had greater significance than HBB or CEA alone in the diagnosis of lung cancer. Knocking out or overexpressing HBB could affect lung cancer cell proliferation through the ERK1/2 signaling pathway. Conclusion: HBB can serve as a novel biomarker for the diagnosis and monitoring of lung cancer, regulating cell proliferation via the ERK1/2 pathway and playing a pivotal role in the oncogenesis and progression of the disease.

Structure-based design of pan-coronavirus inhibitors targeting host cathepsin L and calpain-1.

Respiratory disease caused by coronavirus infection remains a global health crisis. Although several SARS-CoV-2-specific vaccines and direct-acting antivirals are available, their efficacy on emerging coronaviruses in the future, including SARS-CoV-2 variants, might be compromised. Host-targeting antivirals provide preventive and therapeutic strategies to overcome resistance and manage future outbreak of emerging coronaviruses. Cathepsin L (CTSL) and calpain-1 (CAPN1) are host cysteine proteases which play crucial roles in coronaviral entrance into cells and infection-related immune response. Here, two peptidomimetic α-ketoamide compounds, 14a and 14b, were identified as potent dual target inhibitors against CTSL and CAPN1. The X-ray crystal structures of human CTSL and CAPN1 in complex with 14a and 14b revealed the covalent binding of α-ketoamide groups of 14a and 14b to C25 of CTSL and C115 of CAPN1. Both showed potent and broad-spectrum anticoronaviral activities in vitro, and it is worth noting that they exhibited low nanomolar potency against SARS-CoV-2 and its variants of concern (VOCs) with EC50 values ranging from 0.80 to 161.7 nM in various cells. Preliminary mechanistic exploration indicated that they exhibited anticoronaviral activity through blocking viral entrance. Moreover, 14a and 14b exhibited good oral pharmacokinetic properties in mice, rats and dogs, and favorable safety in mice. In addition, both 14a and 14b treatments demonstrated potent antiviral potency against SARS-CoV-2 XBB 1.16 variant infection in a K18-hACE2 transgenic mouse model. And 14b also showed effective antiviral activity against HCoV-OC43 infection in a mouse model with a final survival rate of 60%. Further evaluation showed that 14a and 14b exhibited excellent anti-inflammatory effects in Raw 264.7 mouse macrophages and in mice with acute pneumonia. Taken together, these results suggested that 14a and 14b are promising drug candidates, providing novel insight into developing pan-coronavirus inhibitors with antiviral and anti-inflammatory properties.

Interaction of tetracycline and copper co-intake in inducing antibiotic resistance genes and potential pathogens in mouse gut.

The widespread use of copper and tetracycline as growth promoters in the breeding industry poses a potential threat to environmental health. Nevertheless, to the best of our knowledge, the potential adverse effects of copper and tetracycline on the gut microbiota remain unknown. Herein, mice were fed different concentrations of copper and/or tetracycline for 6 weeks to simulate real life-like exposure in the breeding industry. Following the exposure, antibiotic resistance genes (ARGs), potential pathogens, and other pathogenic factors were analyzed in mouse feces. The co-exposure of copper with tetracycline significantly increased the abundance of ARGs and enriched more potential pathogens in the gut of the co-treated mice. Copper and/or tetracycline exposure increased the abundance of bacteria carrying either ARGs, metal resistance genes, or virulence factors, contributing to the widespread dissemination of potentially harmful genes posing a severe risk to public health. Our study provides insights into the effects of copper and tetracycline exposure on the gut resistome and potential pathogens, and our findings can help reduce the risks associated with antibiotic resistance under the One Health framework.

Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China.

Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern China, which is a major rice production region. The relative abundance of Bathyarchaeia among total archaea ranged from 3 to 68% in paddy soils, and Bathy-6 was the dominant subgroup among the Bathyarchaeia (70-80% of all sequences). Bathyarchaeia showed higher migration ability and wider niche width based on the neutral and null model simulations. Bathy-6 was primarily assembled by deterministic processes. Soil pH and C/N ratio were identified as key factors influencing the Bathyarchaeia composition, whereas C/N ratio and mean annual temperature influenced the relative abundance of Bathyarchaeia. Network analysis showed that specific Bathyarchaeia taxa occupied keystone positions in the archaeal community and co-occurred with some methanogenic archaea, including Methanosarcina and Methanobacteria, and ammonia-oxidizing archaea belonging to Nitrososphaeria. This study provides important insights into the biogeography and niche differentiation of Bathyarchaeia particularly in paddy soil ecosystems.

Comprehensive insights into the differences of fungal communities at taxonomic and functional levels in stony coral Acropora intermedia under a natural bleaching event.

Previous studies have reported the correlations between bacterial communities and coral bleaching, but the knowledge of fungal roles in coral bleaching is still limited. In this study, the taxonomic and functional diversities of fungi in unbleached, partly bleached and bleached stony coral Acropora intermedia were investigated through the ITS-rRNA gene next-generation sequencing. An unexpected diversity of successfully classified fungi (a total of 167 fungal genera) was revealed in this study, and the partly bleached coral samples gained the highest fungal diversity, followed by bleached and unbleached coral samples. Among these fungi, 122 genera (nearly 73.2%) were rarely found in corals in previous studies, such as Calostoma and Morchella, which gave us a more comprehensive understanding of coral-associated fungi. Positively correlated fungal genera (Calostoma, Corticium, Derxomyces, Fusicolla, Penicillium and Vishniacozyma) and negative correlated fungal genera (Blastobotrys, Exophiala and Dacryopinax) with the coral bleaching were both detected. It was found that a series of fungal genera, dominant by Apiotrichum, a source of opportunistic infections, was significantly enriched; while another fungal group majoring in Fusicolla, a probiotic fungus, was distinctly depressed in the bleached coral. It was also noteworthy that the abundance of pathogenic fungi, including Fusarium, Didymella and Trichosporon showed a rising trend; while the saprotrophic fungi, including Tricladium, Botryotrichum and Scleropezicula demostrated a declining trend as the bleaching deteriorating. The rising of pathogenic fungi and the declining of saprotrophic fungi revealed the basic rules of fungal community transitions in the coral bleaching, but the mechanism of coral-associated fungal interactions still lacks further investigation. Overall, this is an investigation focused on the differences of fungal communities at taxonomic and functional levels in stony coral A. intermedia under different bleaching statuses, which provides a better comprehension of the correlations between fungal communities and the coral bleaching.

Analysis of the Genomic Sequences and Metabolites of Bacillus velezensis YA215.

Discovering more novel antimicrobial compounds has become a keen research problem. In this study, YA215 genome was sequenced by the Illumina HiSeq + PacBio sequencing platform. Genome assembly was performed by Unicycler software and the gene clusters responsible for secondary metabolite biosynthesis were predicted by antiSMASH. The genome comprised 3976514 bp and had a 46.56% G + C content. 3809 coding DNA sequences, 27 rRNAs, 86 tRNAs genes, and 79 sRNA were predicted. Strain YA215 was re-identified as Bacillus velezensis based on ANI and OrthoANI analysis. In the COG database, 23 functional groups from 3090 annotations were predicted. In the GO database, 2654 annotations were predicted. 2486 KEGG annotations linked 41 metabolic pathways. Glycosyl transferases, polysaccharide lyases, auxiliary activities, glycoside hydrolases, carbohydrate esterases, and carbohydrate-binding modules were predicted among the 127 annotations in the CAZy database. AntiSMASH analysis predicted that B. velezensis YA215 boasted 13 gene clusters involved in synthesis of antimicrobial secondary metabolites including surfactin, fengycin, macrolactin H, bacillaene, difficidin, bacillibactin, bacilysin, and plantazolicin. Three of the gene clusters (gene cluster 5, gene cluster 9, and gene cluster 10) have the potential to synthesize unknown compounds. The research underscore the considerable potential of secondary metabolites, identified in the genomic composition of B. velezensis YA215, as versatile antibacterial agents with a broad spectrum of activity against pathogenic bacteria.

Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil.

BACKGROUND: The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics). RESULTS: The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response. CONCLUSIONS: The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.