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As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems. Analysis of more than 1,500 microbial genomes sheds light on the processing of carbon released as permafrost thaws.

Fucoidans are multifunctional marine macromolecules that are subjected to numerous and various downstream processes during their production. These processes were considered the most important abiotic factors affecting fucoidan chemical skeletons, quality, physicochemical properties, biological properties and industrial applications. Since a universal protocol for fucoidans production has not been established yet, all the currently used processes were presented and justified. The current article complements our previous articles in the fucoidans field, provides an updated overview regarding the different downstream processes, including pre-treatment, extraction, purification and enzymatic modification processes, and shows the recent non-traditional applications of fucoidans in relation to their characters.

Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales ). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). 1yUdaVB8pb7ryNSffJakk6 Video abstract

The current study delves into the transformative effects of intensive grinding to nanoscale upon oxidized phosphate rocks (PRs) of various grades, high (HMP), medium (MMP) and low (LMP) micro-sizes. Hence, the consequences of these transformative changes on phosphorous dissolution rate of these fractions using acetic acid, were carefully evaluated. The produced high (HNP) and medium (MNP) grades of nano-sized fractions revealed significant changes in their chemical composition, mineralogical, morphological and geometrical properties. Whereas the low grade, LNP, was moderately changed. HNP and MNP exhibited a remarkable increase in structural disorder (slight broadening of reflections) and Loss on Ignition (LOI) contents (10.62 and 13 wt.%, orderly), surpassing their counterparts (HMP: 6.04 and MMP: 10.92 wt.%). Despite the reduction in their P 2 O 5 contents, HNP (31.23 wt.% and MNP (24.22 wt.%), astoundingly outperformed their micro-sized equivalents (HMP: 35.70 wt.%, MMP: 27.92 wt.%) in P dissolution. Therefore, HNP and MNP emerge as promising high-reactive P fertilizers for direct agricultural use and have a great potential as a source of P/Ca liquid fertilizer after nutrients balancing. So, eco-friendly grinding offers a potential approach to maximize PRs’ agronomic potential, but long-term environmental impacts should be evaluated.

Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.

Fucoidans are marine sulfated biopolysaccharides that have heterogenous and complicated chemical structures. Various sugar monomers, glycosidic linkages, molecular masses, branching sites, and sulfate ester pattern and content are involved within their backbones. Additionally, sources, downstream processes, and geographical and seasonal factors show potential effects on fucoidan structural characteristics. These characteristics are documented to be highly related to fucoidan potential activities. Therefore, numerous chemical qualitative and quantitative determinations and structural elucidation methods are conducted to characterize fucoidans regarding their physicochemical and chemical features. Characterization of fucoidan polymers is considered a bottleneck for further biological and industrial applications. Consequently, the obtained results may be related to different activities, which could be improved afterward by further functional modifications. The current article highlights the different spectrometric and nonspectrometric methods applied for the characterization of native fucoidans, including degree of purity, sugar monomeric composition, sulfation pattern and content, molecular mass, and glycosidic linkages.

Tongkat ali commonly known as Malaysian Ginseng ( Eurycoma longifolia ) is a herbal root worldwide available in nutraceuticals, either as a crude powder or capsules blended with other herbal products. Herein, a multiplexed metabolomics approach based on nuclear magnetic resonance (NMR) and solid-phase microextraction combined with gas chromatography–mass spectrometry (SPME–GC–MS) was applied for authentic tongkat ali extract vs some commercial products quality control analysis. NMR metabolite fingerprinting identified 15 major metabolites mostly ascribed to sugars, organic and fatty acids in addition to quassinoids and cinnamates. Following that, multivariate analysis as the non-supervised principal component analysis (PCA) and supervised orthogonal partial least squares-discriminant analysis (OPLS-DA) were applied revealing that differences were related to fatty acids and 13,21-dihydroeurycomanone being more enriched in authentic root. SPME–GC–MS aroma profiling led to the identification of 59 volatiles belonging mainly to alcohols, aldehydes/furans and sesquiterpene hydrocarbons. Results revealed that aroma of commercial products showed relatively different profiles being rich in vanillin, maltol, and methyl octanoate. Whereas E -cinnamaldehyde, endo -borneol, terpinen-4-ol, and benzaldehyde were more associated to the authentic product. The present study shed the light for the potential of metabolomics in authentication and standardization of tongkat ali and identification of its true flavor composition.

Fucoidan is a heterogeneous group of polysaccharides isolated from marine organisms, including brown algae and marine invertebrates. The physicochemical characteristics and potential bioactivities of fucoidan have attracted substantial interest in pharmaceutical industries in the past few decades. These polysaccharides are characterized by possessing sulfate ester groups that impart negatively charged surfaces, low/high molecular weight, and water solubility. In addition, various promising bioactivities have been reported, such as antitumor, immunomodulatory, and antiviral effects. Hence, the formulation of fucoidan has been investigated in the past few years in diverse pharmaceutical dosage forms to be able to reach their site of action effectively. Moreover, they can act as carriers for various drugs in value-added drug delivery systems. The current work highlights the attractive biopharmaceutical properties of fucoidan being formulated in oral, inhalable, topical, injectable, and other advanced formulations treating life-quality-affecting diseases. Therefore, the present work points out the current status of fucoidan pharmaceutical formulations for future research transferring their application from in vitro and in vivo studies to clinical application and market availability.

The current study introduces groundbreaking insights into how organic matter (OM) of the black phosphate (RB-Ph) uniquely influences phosphorus (P) solubility during acetic acid (AA) leaching, expanding our understanding in this crucial area. To highlight such role, the OM of the RB-Ph was treated separately by different procedures including calcination at 550 ℃/4 h (CB-Ph), 30% hydrogen peroxide (HB-Ph) and intensive grinding to nano-sizes (NB-Ph). The mineralogical, chemical and morphological characteristics of phosphatic and non-phosphatic components of these phosphatic materials were carefully examined pre- and post-treatment via different techniques. The P dissolution of the precursor RB-Ph and its modified derivatives all over the applied experimental parameters traced the following trend: NB-Ph > RB-Ph > CB-Ph > HB-Ph. Intensive grinding to nanoscale resulted in amorphous components with conspicuous OM content (TOC, 0.410%), significantly enhanced P dissolution rate of NB-Ph (730–980 ppm), despite the noticeable reduction in its P 2 O 5 content to 22.34 wt.%. The precursor RB-Ph, thanks to its high OM content (TOC, 0.543%), also displayed a sufficient P dissolution rate (470–750 ppm) compared to the two other modified derivatives, CB-Ph (410–700 ppm) and HB-Ph (130–610 ppm). Such deep and conspicuous impact of OM on P solubility can be tied to their decomposition, releasing not only organic acids but also the adsorbed P by the OM’s surficial binding sites to the solution. Finally, the optimum conditions of P leaching were attained at 2:1 acid/solid (w/w) ratio and 2 h of retention time of all investigated samples.

The current study investigates the development and characterization of sustainable activated carbons (ACs) via chemo-thermal activation from the hull and core of sugarcane bagasse as a viable and renewable substitute for commercial ACs. Characterize ACs using XRD, FTIR, SEM, etc. The sorption kinetics of methylene blue (MB) onto AC(H) were well described by a pseudo-second-order model. Also, the controlling step in the MB sorption process was related to several intervening diffusion sorts, including intra-particle ones. The MB equilibrium data were also analyzed using linear and non-linear forms of Langmuir, Freundlich, and Temkin isotherms, revealing a better fit of Langmuir, with R 2 values > 0.97 in both modes. With adsorption capacities (q max  = 357.14 and 389.4 mg/g) in linear and non-linear modes, orderly. The activation energy (EDR) of 550.8 and 2500 J/mol in non-linear and linear further supports the dominance of chemisorption, implying the formation of chemical bonds between the MB and the functional groups present in the sorbent material. The spontaneous and exothermic nature of the MB sorption process at 291–323 K was confirmed by the thermodynamic parameters ΔH°, ΔS°, and ΔG°. The design expert program suggested 17 numerical possibilities for the maximum dye removal at the 99% desirability level using ANOVA within the experimental parameter range. The total cost of producing 1.0 g of AC(H) is estimated at 0.041 USD. These findings underscore the potential of AC(H) as a highly efficient adsorbent for MB removal, positioning it as a strong candidate for wastewater treatment applications.