Elevated CO Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO Enrichment (FACE) Experiment.

Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO on seed resistomes remains poorly understood. Here, a free-air CO enrichment system was used to examine the impact of elevated CO on seed-associated ARGs and seed endophytic bacteria and fungi.

Gut microbiota genome features associated with brain injury in extremely premature infants.

Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants.

Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.

Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data.

Screening great ape museum specimens for DNA viruses.

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens.

Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions.

Microbial growth is central to soil carbon cycling. However, how microbial communities grow under climate change is still largely unexplored. Here we use a unique field experiment simulating future climate conditions (increased atmospheric CO and temperature) and drought concomitantly and investigate impacts on soil microbial activity.

Soil microbiomes show consistent and predictable responses to extreme events.

Increasing extreme climatic events threaten the functioning of terrestrial ecosystems. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils.

The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration.

Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome.

A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum.

Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations.

Correction: FeS colloids - formation and mobilization pathways in natural waters.

[This corrects the article DOI: 10.1039/C9EN01427F.].

Microbial nitrogen transformations in tundra soil depend on interactive effects of seasonality and plant functional types.

Unlabelled: Nitrogen (N) cycling in organic tundra soil is characterised by pronounced seasonal dynamics and strong influence of the dominant plant functional types. Such patterns in soil N-cycling have mostly been investigated by the analysis of soil N-pools and net N mineralisation rates, which, however, yield little information on soil N-fluxes. In this study we investigated microbial gross N-transformations, as well as concentrations of plant available N-forms in soils under two dominant plant functional types in tundra heath, dwarf shrubs and mosses, in subarctic Northern Sweden.

". Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres.

Unlabelled: Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper ( L.) and ginseng plants ( C.

Priorities to inform research on tire particles and their chemical leachates: A collective perspective.

Concerns over the ecological impacts of urban road runoff have increased, partly due to recent research into the harmful impacts of tire particles and their chemical leachates. This study aimed to help the community of researchers, regulators and policy advisers in scoping out the priority areas for further study. To improve our understanding of these issues an interdisciplinary, international network consisting of experts (United Kingdom, Norway, United States, Australia, South Korea, Finland, Austria, China and Canada) was formed.

A metalloprotease secreted by an environmentally acquired gut bacterium hinders colonization in .

Although the importance of the microbiome in the context of tick biology and vector competence has recently come into a broader research focus, the field is still in its infancy and the complex ecological interactions between the tick residential bacteria and pathogens are obscure. Here, we show that an environmentally acquired gut bacterium has the potential to impair colonization within the tick vector through a secreted metalloprotease. Oral introduction of either LTG-1 isolate or its purified enhancin (Enhancin) protein significantly reduces burden in the guts of ticks.

Quantification of guanidine in environmental samples using benzoin derivatization and LC-MS analysis.

The recent discovery of guanidine-dependent riboswitches in many microbes raised interest in the biological function and metabolism of this nitrogen-rich compound. However, very little is known about the concentrations of guanidine in the environment. Several methods have been published for quantifying guanidine and guanidino compounds in human urine and blood, often relying on derivatization followed by fluorescence detection.

Mechanism of bacterial predation via ixotrophy.

Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate.

Sulfur-oxidizing symbionts colonize the digestive tract of their lucinid hosts.

Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus.

Photoaging enhances the leaching of di(2-ethylhexyl) phthalate and transformation products from polyvinyl chloride microplastics into aquatic environments.

Increasing chemical pollution is a threat to sustainable water resources worldwide. Plastics and harmful additives released from plastics add to this burden and might pose a risk to aquatic organisms, and human health. Phthalates, which are common plasticizers and endocrine-disrupting chemicals, are released from polyvinyl chloride (PVC) microplastics and are a cause of concern.

Cooperative binding of bivalent ligands yields new insights into the guanidine-II riboswitch.

Riboswitches are involved in regulating the gene expression in bacteria. They are located within the untranslated regions of bacterial messenger RNA and function as switches by adjusting their shape, depending on the presence or absence of specific ligands. To decipher the fundamental aspects of bacterial gene control, it is therefore important to understand the mechanisms that underlie these conformational switches.

Characterization of O uncoupling in biodegradation reactions of nitroaromatic contaminants catalyzed by rieske oxygenases.

Rieske oxygenases are known as catalysts that enable the cleavage of aromatic and aliphatic C-H bonds in structurally diverse biomolecules and recalcitrant organic environmental pollutants through substrate oxygenations and oxidative heteroatom dealkylations. Yet, the unproductive O activation, which is concomitant with the release of reactive oxygen species (ROS), is typically not taken into account when characterizing Rieske oxygenase function. Even if considered an undesired side reaction, this O uncoupling allows for studying active site perturbations, enzyme mechanisms, and how enzymes evolve as environmental microorganisms adapt their substrates to alternative carbon and energy sources.

The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches.

In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal.