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Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales
Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named “Ca. Nitronereus thalassa”, represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, “Ca. Nitronereus thalassa” harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, “Ca. Nitronereus thalassa” appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.
Genomic and transcriptomic insights into complex virus–prokaryote interactions in marine biofilms
Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Although prokaryotes are the dominant members of these biofilms, little is known about their interactions with viruses. By analysing publicly available and newly sequenced metagenomic data, we identified 2446 virus–prokaryote connections in 84 marine biofilms. Most of these connections were between the bacteriophages in the Uroviricota phylum and the bacteria of Proteobacteria, Cyanobacteria and Bacteroidota. The network of virus–host pairs is complex; a single virus can infect multiple prokaryotic populations or a single prokaryote is susceptible to several viral populations. Analysis of genomes of paired prokaryotes and viruses revealed the presence of 425 putative auxiliary metabolic genes (AMGs), 239 viral genes related to restriction–modification (RM) systems and 38,538 prokaryotic anti-viral defence-related genes involved in 15 defence systems. Transcriptomic evidence from newly established biofilms revealed the expression of viral genes, including AMGs and RM, and prokaryotic defence systems, indicating the active interplay between viruses and prokaryotes. A comparison between biofilms and seawater showed that biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater. Overall, our study unveiled active viruses in natural biofilms and their complex interplay with prokaryotes, which may result in the blooming of defence strategists in biofilms. The detachment of bloomed defence strategists may reduce the infectivity of viruses in seawater and result in the emergence of a novel role of marine biofilms.
Flexible micromachined ultrasound transducers (MUTs) for biomedical applications
The use of bulk piezoelectric transducer arrays in medical imaging is a well-established technology that operates based on thickness mode piezoelectric vibration. Meanwhile, advancements in fabrication techniques have led to the emergence of micromachined alternatives, namely, piezoelectric micromachined ultrasound transducer (PMUT) and capacitive micromachined ultrasound transducer (CMUT). These devices operate in flexural mode using piezoelectric thin films and electrostatic forces, respectively. In addition, the development of flexible ultrasound transducers based on these principles has opened up new possibilities for biomedical applications, including biomedical imaging, sensing, and stimulation. This review provides a detailed discussion of the need for flexible micromachined ultrasound transducers (MUTs) and potential applications, their specifications, materials, fabrication, and electronics integration. Specifically, the review covers fabrication approaches and compares the performance specifications of flexible PMUTs and CMUTs, including resonance frequency, sensitivity, flexibility, and other relevant factors. Finally, the review concludes with an outlook on the challenges and opportunities associated with the realization of efficient MUTs with high performance and flexibility.
Sediment resuspension in muddy sediments enhances pyrite oxidation and carbon dioxide emissions in Kiel Bight
Sediment resuspension of blue carbon ecosystems (e.g., seagrass beds) and muddy sediments exposes buried particulate organic carbon to oxygenated waters and remineralization, potentially enhancing carbon dioxide fluxes. However, the kinetics of carbon degradation under oxic and anoxic conditions are poorly constrained. We report the results of incubation experiments with sediments from Kiel Bight to simulate sediment resuspension events induced by natural and anthropogenic resuspension in this area. A numerical model determined that oxic carbon remineralization rates were up to two-fold higher than those under anoxic conditions. A coupled sediment-water column model demonstrated that pyrite oxidation, rather than carbon oxidation, has the potential to induce large carbon dioxide emissions to the atmosphere following anthropogenic sediment disturbance by trawling. Upscaling to muddy areas of Kiel Bight suggests an annual emission of up to ~14 k tonnes of carbon dioxide per year. Pyrite oxidation may contribute to a weakening of the carbon shelf pump and a reduction of anthropogenic carbon dioxide uptake.
Acoustic frequency comb generation on a composite diamond/silicon microcantilever in ambient air
Acoustic frequency combs (AFCs) contain equidistant coherent signals with unconventional possibilities on metrology. Previously, implementation of AFCs on mechanical microresonators with large air damping loss is difficult, which restricted their atmospheric applications. In this work, we explore the potentials of a composite diamond/silicon microcantilever for parametric generation of AFCs in ambient air. We discover that the diamond layer provides a viable route to reduce the linewidth of the primary flexural mode, yielding a 7.1-times increase of the quality factor. We develop a parametric driving scheme that enables generation of AFCs through injection locking and sequential nonlinear dynamic transitions involving subharmonic synchronization (Arnold tongue), and chaotic dynamics. Ultimately, we realize AFCs with a frequency range extending 800 kHz in the air. This work advances the understanding of AFCs and provides a viable route towards their applications in ambient air for high precision metrology.
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