Expanding anaerobic alkane metabolism in the domain of Archaea

Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea1. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4–6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hou, J., Sievert, S. M., Wang, Y., Seewald, J. S., Natarajan, V. P., Wang, F., & Xiao, X. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. Microbiome, 8(1), (2020): 102, doi:10.1186/s40168-020-00851-8.Background Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys. Results Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9–10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased. Conclusions This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a “fluid-shaped” microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a “mineral-shaped” community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years.This work was supported by the China Ocean Mineral Resources R&D Association (grant No. DY135-B2-12), the Natural Science Foundation of China (grant No. 41530967, 41921006, 91751205), the Senior User Project of RV KEXUE (KEXUE2019GZ06), and by the US National Science Foundation grant OCE-1136727 and the WHOI Investment in Science Fund to S.M.S

A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism

Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide–reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca.) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia

Bio-mineralization of virus-like particles by metal-organic framework nanoparticles enhances the thermostability and immune responses of the vaccines.

peer reviewedVirus-like particle (VLPs) vaccines have been extensively studied due to their good immunogenicity and safety; however, they highly rely on cold-chain storage and transportation. Nanotechnology of bio-mineralization as a useful strategy has been employed to improve the thermal stability and immunogenicity of VLPs. A zeolitic imidazole framework (ZIF-8), a core-shell structured nanocomposite, was applied to encapsulate foot-and-mouth disease virus (FMDV) VLPs. It was found that the ZIF-8 shell enhanced the heat resistance of VLPs and promoted their ability to be taken up by cells and escape from lysosomes. The VLPs-ZIF-8 easily activated antigen-presenting cells (APCs), triggered higher secretion levels of cytokines, and elicited stronger immune responses than VLPs alone even after being treated at 37 °C for 7 days. This platform has good potential in the development of VLP-based vaccine products without transportation

Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea Iron Reducing Bacterium Shewanella piezotolerans WP3

Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as genes for two sets of flagellum systems, structural RNA modification, eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and synthesis. And WP3 contains 55 open reading frames encoding putative c-type cytochromes which are substantial to its wide environmental adaptation ability. The mtr-omc gene cluster involved in the insoluble metal reduction in the Shewanella genus was identified and compared. The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature

Fluorescent immunochromatographic assays (FICA) for quantitative detection of the foot-and-mouth disease virus serotype O antibodies

Foot-and-mouth disease (FMD) is a transboundary animal disease, and a disease of great economic significance in the animal husbandry industry. The prevention and control of such epidemic diseases is particularly important. Effective diagnosis is indispensable to accomplish the mission. The common diagnostic methods are based on live virus or inactivated virus, which may cause leakage of virus easily. Some other methods are also time-consuming, labor-consuming or need sophisticated instruments. Considering the biosafety and practicality, the aim of this thesis is to develop simple quantitative real-time diagnostic assay for FMD with high sensitivity, specificity, and stability. Here, the fluorescent immunochromatographic assays (FICAs) were selected, owing to their simple, rapid, convenient, and safe performance. Rare earth fluorescent nanoparticles exhibit several unique fluorescent properties which make them suitable candidates for detecting biomolecules. Virus-like-particles (VLPs) are capsid proteins of virions, and they are assembled from structural proteins; they are noninfectious, owing to lack of genetic materials. The activated rare earth nanoparticles are integrated with conventional immunochromatography to quantitatively detect foot-and-mouth disease virus (FMDV) antibodies. First, noninfectious FMDV VLPs are utilized as capture antigen, and fluorescent europium microparticles (EuMSs) are applied as fluorescent labels. The labeled staphylococcal protein-A (SPA) are referred to as fluorescent sensors. The fluorescence signal intensity at test line and control line is associated with the concentration of the target antibody. The EuMSs-based assay showed 30-fold more sensitive through observation in five minutes and 68-fold more sensitive through portable equipment than colloidal gold assay. Next, to reduce the cost of the fluorescent nanoparticles and enhance the stability of the assembled strips, we prepared upconversion nanoparticles (UCNPs). Rare earth salts reacted under argon atmosphere according to the solvent thermal method, and then they are modified with citric acid using a ligand exchange method. The carboxyl-modified UCNPs were coupled with protein G to form the UCNPs sensor. The UCNPs-based strips showed higher stability at 4 ℃ for about one year. These assays have been evaluated with real serum samples without cross-interference. Therefore, such assays have great prospects for rapid, sensitive, and quantitative determination of foot-and-mouth disease virus serotype O (O-FMDV) antibodies

The first genome assembly of the amphibian nematode parasite (Aplectana chamaeleonis)

Cosmocercoid nematodes are common parasites of the digestive tract of amphibians. Genomic resources are important for understanding the evolution of a species and the molecular mechanisms of parasite adaptation. So far, no genome resource of Cosmocercoid has been reported. In 2020, a massive Cosmocercoid infection was found in the small intestine of a toad, causing severe intestinal blockage. We morphologically identified this parasite as A. chamaeleonis. Here, we report the first A. chamaeleonis genome with a genome size of 1.04 Gb. The repeat content of this A. chamaeleonis genome is 72.45%, and the total length is 751 Mb. This resource is fundamental for understanding the evolution of Cosmocercoid and provides the molecular basis for Cosmocercoid infection and control

比利时

peer reviewedUltrasensitive and quantitative real-time detection of infectious disease has long been a challenge in prevention and diagnosis of epidemic disease. It’s essential to develop a quantitative point-of-care (POC) diagnostic approach. Herein, a fluorescent platform was designed, which was a sandwich type and applied noninfectious virus-like-particles (VLPs) as capture antigen, making the process safer and more efficient. The fluorescent europium microparticles (EuMSs) conjugated with staphylococcal protein-A (SPA), then antibody was bind with SPA and target antibody was further captured by VLPs at test line. The excessive labelled-SPA was captured by rabbit IgG at control line. Specifically, the fluorescent signal intensity at test line and control line was relative to the concentration of the target antibody. Moreover, the fluorescent assay can not only be monitored through fluorescent signal output within 15 min but also be observed under UV light with 5 min. The limit of detection (LOD) for quantitative detection of serotype O antibody against foot-and-mouth disease virus (O-FMDV) in serum was over 60 times more sensitive than conventional colored gold-colloids. Owing to the advantages of sensitivity and specificity, the fluorescent immunochromatographic test strips (ICTSs) would be a potential tool for rapid and sensitive probe for quantitative determination of O-FMDV antibody

Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis

Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA’s enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life