Novel isolates expand the physiological diversity of and illuminate its macroevolution.

is a diverse picocyanobacterial genus and the most abundant phototroph on Earth. Its photosynthetic diversity divides it into high-light (HL)- or low-light (LL)-adapted groups representing broad phylogenetic grades-each composed of several monophyletic clades. Here, we physiologically characterize four new strains isolated from below the deep chlorophyll maximum in the North Pacific Ocean.

Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone.

Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development.

Community context influences the conjugation efficiency of .

In urinary tract infections (UTIs), different bacteria can live in a polymicrobial community consisting of different species. It is unknown how community members affect the conjugation efficiency of uropathogenic . We investigated the influence of individual species often coisolated from urinary infections (UTI) on the conjugation efficiency of isolates in artificial urine medium.

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses.

Development of a genetic system for LR2-5, model host for haloarchaeal viruses.

Unlabelled: Archaeal viruses are among the most enigmatic members of the virosphere, and their diverse morphologies raise many questions about their infection mechanisms. The study of molecular mechanisms underlying virus-host interactions hinges upon robust model organisms with a system for gene expression and deletion. Currently, there are only a limited number of archaea that have associated viruses and have a well-developed genetic system.

From Nontargeted to Targeted Analysis: Feature Selection in the Differentiation of Truffle Species ( spp.) Using H NMR Spectroscopy and Support Vector Machine.

The price of different truffle types varies according to their culinary value, sometimes by more than a factor of 10. Nonprofessionals can hardly distinguish visually the species within the white or black truffles, making the possibility of food fraud very easy. Therefore, the identification of different truffle species ( spp.

Opening the Random Forest Black Box of H NMR Metabolomics Data by the Exploitation of Surrogate Variables.

The untargeted metabolomics analysis of biological samples with nuclear magnetic resonance (NMR) provides highly complex data containing various signals from different molecules. To use these data for classification, e.g.

Food Monitoring: Limitations of Accelerated Storage to Predict Molecular Changes in Hazelnuts ( L.) under Realistic Conditions Using UPLC-ESI-IM-QTOF-MS.

Accelerated storage is routinely used with pharmaceuticals to predict stability and degradation patterns over time. The aim of this is to assess the shelf life and quality under harsher conditions, providing crucial insights into their long-term stability and potential storage issues. This study explores the potential of transferring this approach to food matrices for shelf-life estimation.

Identification of metabolites from complex mixtures by 3D correlation of H NMR, MS and LC data using the SCORE-metabolite-ID approach.

Not only in metabolomics studies, but also in natural product chemistry, reliable identification of metabolites usually requires laborious steps of isolation and purification and remains a bottleneck in many studies. Direct metabolite identification from a complex mixture without individual isolation is therefore a preferred approach, but due to the large number of metabolites present in natural products, this approach is often hampered by signal overlap in the respective H NMR spectra. This paper presents a method for the three-dimensional mathematical correlation of NMR with MS data over the third dimension of the time course of a chromatographic fractionation.

Genomic and Metabolomic Analysis of the Endophytic Fungus sp. VM-40 Isolated from the Medicinal Plant .

The genus is well-known to comprise many pathogenic fungi that affect cereal crops worldwide, causing severe damage to agriculture and the economy. In this study, an endophytic fungus designated sp. VM-40 was isolated from a healthy specimen of the traditional European medicinal plant .

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms.

Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle.

Marine picocyanobacteria and , the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin.

Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses.

Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be "genomic fossils." Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses.

Updated Virophage Taxonomy and Distinction from Polinton-like Viruses.

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world.

Draft genomes of three closely related low light-adapted Prochlorococcus.

Objectives: The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here.

Analysis of Hazelnuts ( L.) Stored for Extended Periods by H NMR Spectroscopy Monitoring Storage-Induced Changes in the Polar and Nonpolar Metabolome.

Storage is a critical step in the post-harvest processing of hazelnuts, as it can lead to mold, rancidity, and off-flavor. However, there is a lack of analytical methods to detect improper or extended storage. To comprehensively investigate the effects of hazelnut storage, samples were stored under five different conditions for up to 18 months.

Archaeal Host Cell Recognition and Viral Binding of HFTV1 to Its Host.

Viruses are highly abundant and the main predator of microorganisms. Microorganisms of each domain of life are infected by dedicated viruses. Viruses infecting archaea are genomically and structurally highly diverse.

Novel integrative elements and genomic plasticity in ocean ecosystems.

Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus.

AC Kelvin Probe Force Microscopy Enables Charge Mapping in Water.

Mapping charged chemical groups at the solid-liquid interface is important in many areas, ranging from colloidal systems to biomolecular interactions. However, classical methods to measure surface charges either lack spatial resolution or─like Kelvin-probe force microscopy (KPFM)─cannot be applied in aqueous solutions because a DC bias voltage is used. Here, we show that using AC Kelvin probe force microscopy (AC-KPFM), in which the DC bias is replaced with an AC voltage of sufficiently high frequency, the surface potential of spatially fixated, charged surface groups can be mapped in aqueous solution.

Phosphonate production by marine microbes: Exploring new sources and potential function.

SignificancePhosphonates are a class of phosphorus metabolites characterized by a highly stable C-P bond. Phosphonates accumulate to high concentrations in seawater, fuel a large fraction of marine methane production, and serve as a source of phosphorus to microbes inhabiting nutrient-limited regions of the oligotrophic ocean. Here, we show that 15% of all bacterioplankton in the surface ocean have genes phosphonate synthesis and that most belong to the abundant groups and SAR11.

Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean.

Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S.

MOSGA 2: Comparative genomics and validation tools.

Due to the highly growing number of available genomic information, the need for accessible and easy-to-use analysis tools is increasing. To facilitate eukaryotic genome annotations, we created MOSGA. In this work, we show how MOSGA 2 is developed by including several advanced analyses for genomic data.

Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate.

Virophages can parasitize giant DNA viruses and may provide adaptive anti-giant virus defense in unicellular eukaryotes. Under laboratory conditions, the virophage mavirus integrates into the nuclear genome of the marine flagellate and reactivates upon superinfection with the giant virus CroV. In natural systems, however, the prevalence and diversity of host-virophage associations has not been systematically explored.