Drivers of soil health across European Union - Data from the literature review.

Soil health in Europe has reached a critical point: it is estimated that 60-70% of European soils are unhealthy. Changes in land use, its intensity and the quality of management have significant impacts on soil health and soil related ecosystem services. A systems analysis of soil health dynamics requires an understanding of the drivers inducing changes in land use and management.

Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores.

Discovery of Eremiobacterota with nifH homologues in tundra soil.

We describe the genome of an Eremiobacterota population from tundra soil that contains the minimal set of nif genes needed to fix atmospheric N. This putative diazotroph population, which we name Candidatus Lamibacter sapmiensis, links for the first time Eremiobacterota and N fixation. The integrity of the genome and its nif genes are well supported by both environmental and taxonomic signals.

Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA.

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world.

Metagenome-assembled genomes from mineral tundra soils in Rásttigáisá, northern Norway.

Microbial communities in tundra soils remain largely unknown despite their important roles in the cycling of greenhouse gases. Here, we report 59 non-redundant metagenome-assembled genomes (MAGs) recovered from mineral tundra soils in Rásttigáisá, northern Norway. The MAGs were obtained by clustering contigs according to tetranucleotide frequency and differential coverage and were manually curated to remove contigs with outlying GC content and/or mean coverage.

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics.

Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats.

Local eukaryotic and bacterial stream community assembly is shaped by regional land use effects.

With anticipated expansion of agricultural areas for food production and increasing intensity of pressures stemming from land-use, it is critical to better understand how species respond to land-use change. This is particularly true for microbial communities which provide key ecosystem functions and display fastest responses to environmental change. However, regional land-use effects on local environmental conditions are often neglected, and, hence, underestimated when investigating community responses.

Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution.

Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota.

Localized coevolution between microbial predator and prey alters community-wide gene expression and ecosystem function.

Closely interacting microbial species pairs (e.g., predator and prey) can become coadapted via reciprocal natural selection.

Pangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum.

Background: Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L.

Marination increased tyramine levels in rainbow trout fillet strips packaged under modified atmosphere.

Marinades are increasingly used to manufacture raw fish products. In corresponding meats, marinating is known to have a major effect on the composition of the microbiome, but the effect of marinating on fish is not known as well. This knowledge gap prompted our study of the microbial ecology and amine formation in marinated and unmarinated modified atmosphere commercially packaged rainbow trout fillet strips.

The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types.

Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic.

Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities.

Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean.

Microbiome assembly in thawing permafrost and its feedbacks to climate.

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks.

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.

Background: In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (NO). However, the microorganisms involved in the cycling of NO in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of NO, we aimed at investigating differences in community structure across different soil ecosystems in the tundra.

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load.

Background: Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) are present in high numbers in antibiotic-naive infants' gut microbiomes, and infant mortality caused by resistant infections is high. The role of antibiotics in shaping the infant resistome has been studied, but there is limited knowledge on other factors that affect the antibiotic resistance burden of the infant gut.

Longitudinal Metatranscriptomic Analysis of a Meat Spoilage Microbiome Detects Abundant Continued Fermentation and Environmental Stress Responses during Shelf Life and Beyond.

Microbial food spoilage is a complex phenomenon associated with the succession of the specific spoilage organisms (SSO) over the course of time. We performed a longitudinal metatranscriptomic study on one modified-atmosphere-packaged (MAP) beef product to increase understanding of the longitudinal behavior of a spoilage microbiome during shelf life and beyond. Based on the annotation of the mRNA reads, we recognized three stages related to the active microbiome that were descriptive of the sensory quality of the beef: acceptable product (AP), early spoilage (ES), and late spoilage (LS).

Growth and metabolic characteristics of fastidious meat-derived Lactobacillus algidus strains.

Lactobacillus algidus is a meat spoilage bacterium often dominating the bacterial communities on chilled, packaged meat. Yet, L. algidus strains are rarely recovered from meat, and only few studies have focused on this species.

Metabolomics and bacterial diversity of packaged yellowfin tuna (Thunnus albacares) and salmon (Salmo salar) show fish species-specific spoilage development during chilled storage.

Microbial (colony counts, 16S rRNA gene amplification), chemical (pH, H NMR spectroscopy) and sensory changes in raw Atlantic Salmon (Salmo salar) and tuna (Thunnus albacares) fillets stored under vacuum at 3 °C were evaluated over a period of 12 days. Both species of fish are globally important and among the ten most consumed fishes in the world. Although the sensory analyses showed a decrease in the quality of both fish species, only the salmon fillets were considered spoiled at the end of the storage period.

Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes.

Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the effects of low concentrations of antibiotics on multispecies microbial communities. Here, we address this question by investigating the effects of low antibiotic concentration on community composition and horizontal transfer of an antibiotic resistance plasmid in a 62-strain bacterial community in response to manipulation of the spatial environment and presence of predation.

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.

The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers.

Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution.

Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems.

Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent.

Wastewater treatment plants (WWTPs) collect wastewater from various sources for a multi-step treatment process. By mixing a large variety of bacteria and promoting their proximity, WWTPs constitute potential hotspots for the emergence of antibiotic resistant bacteria. Concerns have been expressed regarding the potential of WWTPs to spread antibiotic resistance genes (ARGs) from environmental reservoirs to human pathogens.

Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef.

Understanding the factors influencing meat bacterial communities is important as these communities are largely responsible for meat spoilage. The composition and structure of a bacterial community on a high-O modified-atmosphere packaged beef product were examined after packaging, on the use-by date and two days after, to determine whether the communities at each stage were similar to those in samples taken from different production lots. Furthermore, we examined whether the taxa associated with product spoilage were distributed across production lots.

Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics.

Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods.