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

Human activities accelerated the degradation of saline seepweed red beaches by amplifying top‐down and bottom‐up forces

Salt marshes dominated by saline seepweed (Suaeda heteroptera) provide important ecosystem services such as sequestering carbon (blue carbon), maintaining healthy fisheries, and protecting shorelines. These salt marshes also constitute stunning red beach landscapes, and the resulting tourism significantly contributes to the local economy. However, land use change and degradation have led to a substantial loss of the red beach area. It remains unclear how human activities influence the top‐down and bottom‐up forces that regulate the distribution and succession of these salt marshes and lead to the degradation of the red beaches. We examined how bottom‐up forces influenced the germination, emergence, and colonization of saline seepweed with field measurements and a laboratory experiment. We also examined whether top‐down forces affected the red beach distribution by conducting a field survey for crab burrows and density, laboratory feeding trials, and waterbird investigations. The higher sediment accretion rate induced by human activities limited the establishment of new red beaches. The construction of tourism facilities and the frequent presence of tourists reduced the density of waterbirds, which in turn increased the density of crabs, intensifying the top‐down forces such as predators and herbivores that drive the degradation of the coastal red beaches. Our results show that sediment accretion and plant–herbivory changes induced by human activities were likely the two primary ecological processes leading to the degradation of the red beaches. Human activities significantly shaped the abundance and distribution of the red beaches by altering both top‐down and bottom‐up ecological processes. Our findings can help us better understand the dynamics of salt marshes and have implications for the management and restoration of coastal wetlands

A tripartite filter design for seamless pedestrian navigation using recursive 2-means clustering and Tukey update

Mobile devices are desired to guide users seamlessly to diverse destinations indoors and outdoors. The positioning fixing subsystems often provide poor quality measurements with gaps in an urban environment. No single position fixing technology works continuously. Many sensor fusion variations have been previously trialed to overcome this challenge, including the particle filter that is robust and the Kalman filter which is fast. However, a lack exists, of context aware, seamless systems that are able to use the most fit sensors and methods in the correct context. A novel adaptive and modular tripartite navigation filter design is presented to enable seamless navigation. It consists of a sensor subsystem, a context inference and a navigation filter blocks. A foot-mounted inertial measurement unit (IMU), a Global Navigation Satellite System (GNSS) receiver, Bluetooth Low Energy (BLE) and Ultrawideband (UWB) positioning systems were used in the evaluation implementation of this design. A novel recursive 2-means clustering method was developed to track multiple hypotheses when there are gaps in position fixes. The closest hypothesis to a new position fix is selected when the gap ends. Moreover, when the position fix quality measure is not reliable, a fusion approach using a Tukey-style particle filter measurement update is introduced. Results show the successful operation of the design implementation. The Tukey update improves accuracy by 5% and together with the clustering method the system robustness is enhanced

A perspective on meta-boundaries

The judicious design of electromagnetic boundary provides a crucial route to control light-matter interactions, and it is thus fundamental to basic science and practical applications. General design approaches rely on the manipulation of bulk properties of superstrate or substrate and on the modification of boundary geometries. Due to the recent advent of metasurfaces and low-dimensional materials, the boundary can be flexibly featured with a surface conductivity, which can be rather complex but provide an extra degree of freedom to regulate the propagation of light. In this perspective, we denote the boundary with a non-zero surface conductivity as the meta-boundary. The meta-boundaries are categorized into four types, namely isotropic, anisotropic, biisotropic and bianisotropic meta-boundaries, according to the electromagnetic boundary conditions. Accordingly, the latest development for these four kinds of meta-boundaries are reviewed. Finally, an outlook on the research tendency of meta-boundaries is provided, particularly on the manipulation of light-matter interactions by simultaneously exploiting meta-boundaries and metamaterials

GNSS trajectory anomaly detection using similarity comparison methods for pedestrian navigation

The urban setting is a challenging environment for GNSS receivers. Multipath and other anomalies typically increase the positioning error of the receiver. Moreover, the error estimate of the position is often unreliable. In this study, we detect GNSS trajectory anomalies by using similarity comparison methods between a pedestrian dead reckoning trajectory, recorded using a foot-mounted inertial measurement unit, and the corresponding GNSS trajectory. During a normal walk, the foot-mounted inertial dead reckoning setup is trustworthy up to a few tens of meters. Thus, the differing GNSS trajectory can be detected using form similarity comparison methods. Of the eight tested methods, the Hausdorff distance (HD) and the accumulated distance difference (ADD) give slightly more consistent detection results compared to the rest

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

Low-velocity-favored transition radiation

When a charged particle penetrates through an optical interface, photon emissions emerge - a phenomenon known as transition radiation. Being paramount to fundamental physics, transition radiation has enabled many applications from high-energy particle identification to novel light sources. A rule of thumb in transition radiation is that the radiation intensity generally decreases with the particle velocity v; as a result, low-energy particles are not favored in practice. Here we find that there exist situations where transition radiation from particles with extremely low velocities (e.g. v/c<0.001) exhibits comparable intensity as that from high-energy particles (e.g. v/c=0.999), where c is light speed in free space. The comparable radiation intensity implies an extremely high photon extraction efficiency from low-energy particles, up to eight orders of magnitude larger than that from high-energy particles. This exotic phenomenon of low-velocity-favored transition radiation originates from the excitation of Ferrell-Berreman modes in epsilon-near-zero materials. Our findings may provide a promising route towards the design of integrated light sources based on low-energy electrons and specialized detectors for beyond-standard-model particles.Comment: 13 pages, 4 figure