Evolutionary diversification and succession of soil huge phages in glacier foreland.

Background: Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.

Results: Here, we conduct a size-fractioned (< 0.

Increasing pesticide diversity impairs soil microbial functions.

Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels.

Open-set deep learning-enabled single-cell Raman spectroscopy for rapid identification of airborne pathogens in real-world environments.

Pathogenic bioaerosols are critical for outbreaks of airborne disease; however, rapidly and accurately identifying pathogens directly from complex air environments remains highly challenging. We present an advanced method that combines open-set deep learning (OSDL) with single-cell Raman spectroscopy to identify pathogens in real-world air containing diverse unknown indigenous bacteria that cannot be fully included in training sets. To test and further enhance identification, we constructed the Raman datasets of aerosolized bacteria.

Using Large Language Models to Assist Antimicrobial Resistance Policy Development: Integrating the Environment into Health Protection Planning.

Increasing antimicrobial resistance (AMR) poses a substantial threat to global health and economies, which has led many countries and regions to develop AMR National Action Plans (NAPs). However, inadequate logistical capacity, funding, and essential information can hinder NAP policymaking, especially in low-to-middle-income countries (LMICs). Therefore, major gaps exist between aspirations and actions, such as fully operationalized environmental AMR surveillance programs in NAPs.

Extracellular Vesicles Are Prevalent and Effective Carriers of Environmental Allergens in Indoor Dust.

The global incidence of allergic diseases is rising and poses a substantial threat to human health. Allergenic proteins released by various allergenic species play a critical role in the pathogenesis of allergic diseases and have been widely detected in the environmental matrix. However, the release, presence and interaction of environmental allergens with human body remain to be elucidated.

Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.

Background: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils.

Adaptive expression of phage auxiliary metabolic genes in paddy soils and their contribution toward global carbon sequestration.

Habitats with intermittent flooding, such as paddy soils, are crucial reservoirs in the global carbon pool; however, the effect of phage-host interactions on the biogeochemical cycling of carbon in paddy soils remains unclear. Hence, this study applied multiomics and global datasets integrated with validation experiments to investigate phage-host community interactions and the potential of phages to impact carbon sequestration in paddy soils. The results demonstrated that paddy soil phages harbor a diverse and abundant repertoire of auxiliary metabolic genes (AMGs) associated with carbon fixation, comprising 23.

Integrating Anthropogenic-Pesticide Interactions Into a Soil Health-Microbial Index for Sustainable Agriculture at Global Scale.

Soil microbiota in intensive agriculture are threatened by pesticides, economic activities, and land-use changes. However, the interactions among these anthropogenic factors remain underexplored. By analyzing 2356 soil metagenomes from around the world, we developed a comprehensive soil health-microbial index that integrates microbial diversity, nutrient cycling potential, metabolic potential, primary productivity, and health risks to assess how the soil microbiota respond to anthropogenic factors.

From grasslands to genes: exploring the major microbial drivers of antibiotic-resistance in microhabitats under persistent overgrazing.

Background: The extensive use of antibiotics in the global livestock industry in recent decades has accelerated the accumulation and dissemination of antibiotic-resistance genes (ARGs) within terrestrial ecosystems. This occurs due to the limited absorption of most antibiotics, leading to their release into the environment through feces and urine. This poses a significant threat to both the environment and human health.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene.

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China.

Impacts of soil type on the temporal dynamics of antibiotic resistance gene profiles following application of composted manure.

Farmland application of composted manure is associated with a risk of dissemination of antibiotic resistance genes (ARGs) in agricultural soils. However, the impact of soil type on the temporal dynamics of ARGs in agricultural soil remains largely unclear. The aims of this study were to study the persistence of composted manure-derived ARGs in six soil types representative for Chinese agriculture and to explore the underlying environmental drivers of soil ARG profiles in a controlled greenhouse experiment.

Soil viral-host interactions regulate microplastic-dependent carbon storage.

Microplastic is globally regarded as an important factor impacting biogeochemical cycles, yet our understanding of such influences is limited by the uncertainties of intricate microbial processes. By multiomics analysis, coupled with soil chemodiversity characterization and microbial carbon use efficiency (CUE), we investigated how microbial responses to microplastics impacted soil carbon cycling in a long-term field experiment. We showed that biodegradable microplastics promoted soil organic carbon accrual by an average of 2.

Antibiotic resistance at environmental multi-media interfaces through integrated genotype and phenotype analysis.

Antibiotic resistance is currently an unfolding global crisis threatening human health worldwide. While antibiotic resistance genes (ARGs) are known to be pervasive in environmental media, the occurrence of antibiotic resistance at interfaces between two or more adjacent media is largely unknown. Here, we designed a microcosm study to simulate plastic pollution in paddy soil and used a novel method, stimulated Raman scattering coupled with deuterium oxide (DO) labelling, to compare the antibiotic resistance in a single medium with that at the interface of multiple environmental media (plastic, soil, water).

Antibiotics and Pesticides Enhancing the Transfer of Resistomes among Soil-Bayberry-Fruit Fly Food Chain in the Orchard Ecosystem.

While substantial amounts of antibiotics and pesticides are applied to maintain orchard yields, their influence on the dissemination and risk of antibiotic resisitome in the orchard food chain remains poorly understood. In this study, we characterized the bacterial and fungal communities and differentiated both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the soil, Chinese bayberry (matured and fallen), and fruit fly gut, collected from five geographic locations. Our results showed that fruit fly guts and soils exhibit a higher abundance of ARGs and VFGs compared with bayberry fruits.

High-Throughput Single-Cell Metabolic Labeling, Sorting, and Sequencing of Active Antibiotic-Resistant Bacteria in the Environment.

Active antibiotic-resistant bacteria (ARB) play a major role in spreading antimicrobial resistance (AMR) in the environment; however, they have remained largely unexplored. Herein, we coupled bio-orthogonal noncanonical amino acid tagging with high-throughput fluorescence-activated single-cell sorting (FACS) and sequencing to characterize the phenome and genome of active ARB in complex environmental matrices. Active ARB, conferring resistance to six antibiotics throughout wastewater treatment, were distinguished and quantified.

Climate change exacerbates the environmental impacts of agriculture.

Agriculture's global environmental impacts are widely expected to continue expanding, driven by population and economic growth and dietary changes. This Review highlights climate change as an additional amplifier of agriculture's environmental impacts, by reducing agricultural productivity, reducing the efficacy of agrochemicals, increasing soil erosion, accelerating the growth and expanding the range of crop diseases and pests, and increasing land clearing. We identify multiple pathways through which climate change intensifies agricultural greenhouse gas emissions, creating a potentially powerful climate change-reinforcing feedback loop.

Unveiling the overlooked small-sized microbiome in river ecosystems.

Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information.