Substantial Deep-Soil Carbon Losses Outweigh Topsoil Gains in European Beech Forests Since the 1980s.

Soils are a major reservoir for organic carbon (C), with subsoils (> 20-30 cm soil depth) storing most of this C. Predicting the response of deep-soil C to global change remains a critical research priority; yet long-term field observations for forests are scarce. In this study, we assessed decadal C dynamics in mineral soils to 90 cm depth of 62 temperate mature stands of European beech (Fagus sylvatica) in Austria using data from sampling campaigns in 1984, 2012, and 2022.

Uptake of tire-wear derived compounds by lettuce grown in three soils.

Tire-wear derived compounds have recently been detected in commercially grown leafy vegetables, raising concern about their uptake and accumulation in crops under realistic agricultural conditions. Lettuce (Lactuca sativa L.) cultivated in three agricultural soils, which varied in sand content (25-82 %), clay content (4-27 %), cation exchange capacity (11 meq/100 g-21 meq/100 g), and organic matter content (1.

Microbial iron oxide respiration coupled to sulfide oxidation.

Microorganisms have driven Earth's sulfur cycle since the emergence of life, yet the sulfur-cycling capacities of microorganisms and their integration with other element cycles remain incompletely understood. One such uncharacterized metabolism is the coupling of sulfide oxidation with iron(III) oxide reduction, a ubiquitous environmental process hitherto considered to be strictly abiotic. Here we present a comprehensive genomic analysis of sulfur metabolism across prokaryotes, and reveal bacteria that are capable of oxidizing sulfide using extracellular solid phase iron(III).

The bacterial community of the freshwater bryozoan Cristatella Mucedo and its secondary metabolites production potential.

While marine bryozoans were shown to be a promising source of bioactive compounds with the potential to be developed into drugs, their freshwater counterparts remain understudied. Considering that bioactive compounds isolated from bryozoans may originate from bacterial communities associated with the hosts, we explored the bacterial community of the freshwater bryozoan Cristatella mucedo using genomics and metabolomics. 16 S rRNA gene amplicon sequencing of the bacterial community associated with C.

Evolutionarily conserved grammar rules viral factories of amoeba-infecting members of the hyperdiverse phylum.

Despite sharing fewer than 10 core genes, the hyperdiverse phylum (ranging from poxviruses to giant viruses) universally assembles viral factories (VFs) resembling biomolecular condensates. Regardless, it is unclear how these viruses achieve such a level of functional conservation without clear conserved genetic information. We demonstrate that the VFs produced by amoeba-infecting viruses have liquid-like properties and identify a conserved molecular grammar governing viral factory scaffold protein: charge-patterned intrinsically disordered regions that drive phase separation independently of sequence homology.

Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.

Background: Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.

Eyes in the wild: Thelazia callipaeda in wild carnivores of Croatia.

Background: Thelazia callipaeda is an emerging zoonotic nematode that infects the eyes of domestic and wild mammals across Europe and is transmitted by drosophilid flies of the genus Phortica. Despite increasing reports across the continent, its distribution in wildlife in southeastern Europe remains poorly understood. To our knowledge, this study represents the first comprehensive parasitological and molecular investigation of T.

Unusual Plastoquinones in Non-Phototrophic Nitrifying Bacteria.

Isoprenoid quinones are important compounds in most organisms. They are essential in electron and proton transport in respiratory and photosynthetic electron transport chains, and additional functions include oxidative stress defence. The biologically most relevant quinones are naphthoquinones including menaquinone and benzoquinones including ubiquinone and plastoquinone.

Hemotropic pathogens in aborted fetuses of domestic ruminants: transplacental transmission and implications for reproductive loss.

Objective: Hemotropic pathogens of the genera , , , and hemotropic are significant infectious agents in domestic ruminants, most commonly associated with vector-borne transmission. However, their potential for transplacental transmission and their contribution to reproductive disorders remains poorly understood. This study aimed to investigate the presence of hemopathogens in aborted fetuses of cattle, sheep, and goats in Croatia, and to evaluate their potential role in transplacental transmission.

Comparative genome analysis reveals broad phylogenetic and functional diversity within the order Nitrospirales.

Nitrification, a key process in the nitrogen cycle, involves the oxidation of ammonia to nitrite and nitrate by a diverse group of chemolithoautotrophic microorganisms. The order Nitrospirales (referred to in literature as the genus Nitrospira), which includes both nitrite-oxidizing and complete ammonia-oxidizing bacteria, plays a central role in this process. We sequenced the genomes of nine Nitrospirales members, incorporating genomes from previously unsequenced taxonomic Nitrospirales lineages.

Two new psychrotolerant Massilia species inhibit plant pathogens Clavibacter and Curtobacterium.

Three bacterial strains producing blue-violet pigmented colonies on R2A agar were isolated from a wet rock wall and lakes in the deglaciated northern part of James Ross Island, Antarctica. The isolated strains inhibited phytopathogenic Gram-positive bacteria Clavibacter spp., Curtobacterium flacumfaciens, and Paenarthrobacter ilicis.

Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome.

Lactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products.

TreeGrid: A Spatial Planning Tool Integrating Tree Species Traits for Biodiversity Enhancement in Urban Landscapes.

Urbanization, habitat fragmentation, and intensifying urban heat island (UHI) effects accelerate biodiversity loss and diminish ecological resilience in cities, particularly in climate-vulnerable regions. To address these challenges, we developed TreeGrid, a functionality-based spatial tree planning tool designed specifically for urban settings in the Northern Plains of India. The tool integrates species trait datasets, ecological scoring metrics, and spatial simulations to optimize tree placement for enhanced ecosystem service delivery, biodiversity support, and urban cooling.

Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.

[This corrects the article DOI: 10.3389/fmicb.2023.

The adaptation of chlamydiae to facultative host multicellularity.

The phylum Chlamydiota consists of obligate intracellular bacteria comprising the human pathogen Chlamydia trachomatis and a large variety of species infecting animals and protists. Despite their diversity, a feature shared by all known chlamydiae is their biphasic developmental cycle, consisting of intra- and extracellular stages with substantial differences in morphology and physiology. Here, we report the isolation of a social amoeba, Dictyostelium giganteum, naturally infected with a chlamydial symbiont.

Hemolymph microbiota and host immunity of crustaceans and mollusks.

None declared.Conflicts of interestCrustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production.

Warming Weakens Soil Nitrogen Stabilization Pathways Driving Proportional Carbon Losses in Subarctic Ecosystems.

Climate warming poses a significant threat to the nitrogen (N) and carbon (C) retention capacities of subarctic ecosystems, with cascading effects on soil nutrient cycling and long-term ecosystem functioning. Here, we investigated the effects sustained soil warming on the temporal retention and stabilization of N in key ecosystem pools in a subarctic grassland performing a N-tracing experiment in different seasons. Our results reveal that warming reduced N retention across key soil pools, with the largest proportional losses occurring in the non-extractable soil fraction, a critical long-term reservoir of organic matter.

AlphaDesign: a de novo protein design framework based on AlphaFold.

De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.

Advantages of run-reverse motility pattern of bacteria for tracking light and small food sources in dynamic fluid environments.

Marine bacteria are fundamental to the processes and cycles that sustain ocean ecosystems. Their activity at small scales, where they search for food sources in a highly heterogeneous and dynamic environment, for example controls the decomposition of organic matter. To be effective, these microorganisms have evolved sophisticated behaviours, which include extremely rapid swimming speeds, a precise chemosensing ability and particular swimming patterns.

Increased Nitrate Intake From Beetroot Juice Over 4 Weeks Changes the Composition of the Oral, But Not the Intestinal Microbiome.

Inorganic dietary nitrate, metabolized through an endogenous pathway involving nitrate reducing bacteria, improves cardiovascular health, but its effects on the oral and intestinal microbiomes of older adults with treated hypertension are unknown. Our study investigated the effects of nitrate from beetroot juice on the oral and intestinal microbiomes of this population. A randomized, double-blind, placebo-controlled crossover trial was conducted with 15 participants (age range: 56-71 years), who consumed nitrate-rich or nitrate-depleted (placebo) beetroot juice for 4 weeks.

Eco-Corona Formation Enhances Cotransport of Nanoplastics and Organic Contaminants in Porous Media.

The dynamic interactions between nanoplastics and environmental macromolecules, particularly the formation of eco-corona, have received growing attention. There is increasing evidence that eco-corona plays a critical role in determining the fate, transport, and impact of nanoplastics. In this study, we show that even a low mass of eco-corona formed on nanoplastics significantly affects the cotransport of nanoplastics and organic contaminants in porous media.

Mimivirus transcription and translation occur at well-defined locations within amoeba host cells.

Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence hybridization (smFISH) protocol for giant viruses in an host.

A Comprehensive and Ultrasensitive Isotope Calibration Method for Soil Amino Compounds Using Orbitrap Mass Spectrometry.

Bound amino compounds (amino acid and amino sugar polymers) comprise a significant proportion (∼40%) of soil organic nitrogen and therefore represent an essential source of nitrogen for plant and microbial nutrition. The analysis of their content and isotope enrichment still represents a significant challenge due to the low isotope enrichment levels reached under near-native soil conditions and the lack of isotopically labeled standards for some key amino compounds. In this study, we used both a C-labeled and an unlabeled amino acid mixture to establish isotope calibration curves for 16 amino compounds, using the 6-aminoquinolyl--hydroxysccinimidyl carbamate (AQC) derivatization method and ultrahigh-performance liquid chromatography with high-resolution Orbitrap mass spectrometry (UPLC-Orbitrap MS).

Dupilumab treatment has no effect on the nasal microbiome in patients with NSAID-exacerbated respiratory disease: a longitudinal pilot study.

Background: Non-steroidal anti-inflammatory drugs-exacerbated respiratory disease (N-ERD) affects up to 10% of patients suffering from nasal polyps and has a severe impact on quality of life. Dupilumab, a monoclonal antibody targeting the IL-4 receptor α chain, leads to symptom relief and reduction in nasal type 2 mediator levels. Here, we investigated the impact of dupilumab treatment on the composition and diversity of the nasal microbiome.