Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

The impact of land use change on mycorrhizal fungi and their associations with rodents: insights from a temperate forest in Mexico

Ecosystem functioning is influenced by biological diversity, ecological interactions, and abiotic conditions. Human interactions with ecosystems can cause major changes in how they function when involving changes in the vegetation cover and structure (i.e., land use change). This study examines how land use change affects the diversity of arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) in soil and rodent scats in temperate forest sites. We collected soil and rodent scat samples at five paired sites (i.e., disturbed vs. undisturbed) in Michoacan, Mexico. We identified 112 putative mycorrhizal fungi species using DNA barcoding based on partial internal transcribed region 1 (ITS) sequences. We found a higher richness of EMF in undisturbed soil samples compared to disturbed soil samples and a higher AMF diversity in rodent scat samples from disturbed than undisturbed sites. Scat samples had a high incidence of both AMF (75%) and EMF (100%). We found significant differences in the diversity of both AMF and EMF depending on the rodent species associated with them. We also found a higher diversity of EMF in scats in the wet season than in the dry season. We also report, for the first time, associations between Sigmodon hispidus and numerous AMF and EMF species. Overall, our study highlights the role of rodents as important dispersal vectors of mycorrhizal fungi, particularly for EMF that could be essential to build up mycorrhizal fungi spore banks in disturbed forests.

Anticancer drugs alter active nitrogen-cycling communities with effects on the nitrogen removal efficiency of a continuous-flow aerobic granular sludge system

There is increasing awareness of the presence of anticancer drugs (ACDs) in wastewater. Nonetheless, how ACDs affect the performance of wastewater treatment systems and their microbial populations remains largely unclear. This study investigated the effects of three common ACDs (cyclophosphamide, tamoxifen, and methotrexate) at varying concentrations on physicochemical parameters and drug removal efficiency in an aerobic granular sludge (AGS) system operated in a continuous-flow reactor. Additionally, it examined the abundance of active microbial communities, including nitrifiers (amoA gene from ammonia-oxidizing bacteria and archaea) and denitrifiers (napA, narG, nirK, nirS, nosZ genes), as well as the biodiversity of active prokaryotic communities. The concentration level of ACDs determines variations in biomass density, granule integrity, and removal efficiencies of organic matter (OM) and total nitrogen. Both medium and high ACD concentrations negatively impact these physicochemical parameters. The findings revealed that AGS functioning within a continuous system could help remove ACDs, but removal efficiencies depended on the specific drug and concentration applied. At medium and high ACD concentrations a marked reduction in the abundance of active bacterial and archaeal communities, including nitrifiers and denitrifiers, was observed, alongside a decline in microbial diversity and a transformation in community composition. Specific bacterial genera, which are crucial for OM degradation, nitrification and denitrification were identified as particularly sensitive to anticancer drugs. Our findings highlight the need for monitoring and managing anticancer drugs in wastewater systems, as they can substantially alter treatment performance, nitrogen-cycling communities, and bacterial community composition.

Conserved genetic basis for microbial colonization of the gut

Despite the fundamental importance of gut microbes, the genetic basis of their colonization remains largely unexplored. Here, by applying cross-species genotype-habitat association at the tree-of-life scale, we identify conserved microbial gene modules associated with gut colonization. Across thousands of species, we discovered 79 taxonomically diverse putative colonization factors organized into operonic and non-operonic modules. They include previously characterized colonization pathways such as autoinducer-2 biosynthesis and novel processes including tRNA modification and translation. In vivo functional validation revealed YigZ (IMPACT family) and tRNA hydroxylation protein-P (TrhP) are required for E. coli intestinal colonization. Overexpressing YigZ alone is sufficient to enhance colonization of the poorly colonizing MG1655 E. coli by >100-fold. Moreover, natural allelic variations in YigZ impact inter-strain colonization efficiency. Our findings highlight the power of large-scale comparative genomics in revealing the genetic basis of microbial adaptations. These broadly conserved colonization factors may prove critical for understanding gastrointestinal (GI) dysbiosis and developing therapeutics.

Unraveling the tempo and mode of horizontal gene transfer in bacteria

Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facilitating adaptive innovations, and shaping pangenomes. Recent experimental and theoretical results have shown how HGT shapes the flow of genetic information within and between populations, expanding the range of possibilities for microbial evolution. These advances set the stage for a new wave of research seeking to predict how HGT shapes microbial evolution within natural communities, especially during rapid ecological shifts. In this article, we highlight these developments and outline promising research directions, emphasizing the necessity of quantifying the rates of HGT within diverse ecological contexts.

Targeting the Gut Microbiota's Role in Host Energy Absorption With Precision Nutrition Interventions for the Prevention and Treatment of Obesity

The field of precision nutrition aims to develop dietary approaches based on individual biological factors such as genomics or the gut microbiota. The gut microbiota, which is the highly individualized and complex community of microbes residing in the colon, is a key contributor to human physiology. Although gut microbes play multiple roles in the metabolism of nutrients, their role in modulating the absorption of dietary energy from foods that escape digestion in the small intestine has the potential to variably affect energy balance and, thus, body weight. The fate of this energy, and its subsequent impact on body weight, is well described in rodents and is emerging in humans. This narrative review is focused on recent clinical evidence of the role of the gut microbiota in human energy balance, specifically its impact on energy available to the human host. Despite recent progress, remaining gaps in knowledge present opportunities for developing and implementing strategies to understand causal microbial mechanisms related to energy balance. We propose that implementing rigorous microbiota-focused measurements in the context of innovative clinical trial designs will elucidate integrated diet-host-gut microbiota mechanisms. These mechanisms are primed to be targets for precision nutrition interventions to optimize energy balance to achieve desired weight outcomes. Given the magnitude and impact of the obesity epidemic, implementing these interventions within comprehensive weight management paradigms has the potential to be of public health significance.

Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism

Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.

Sustainable Land Use Enhances Soil Microbial Respiration Responses to Experimental Heat Stress

Soil microbial communities provide numerous ecosystem functions, such as nutrient cycling, decomposition, and carbon storage. However, global change, including land-use and climate changes, affects soil microbial communities and activity. As extreme weather events (e.g., heatwaves) tend to increase in magnitude and frequency, we investigated the effects of heat stress on the activity (e.g., respiration) of soil microbial communities that had experienced four different long-term land-use intensity treatments (ranging from extensive grassland and intensive grassland to organic and conventional croplands) and two climate conditions (ambient vs. predicted future climate). We hypothesized that both intensive land use and future climate conditions would reduce soil microbial respiration (H1) and that experimental heat stress would increase microbial respiration (H2). However, this increase would be less pronounced in soils with a long-term history of high-intensity land use and future climate conditions (H3), and soils with a higher fungal-to-bacterial ratio would show a more moderate response to warming (H4). Our study showed that soil microbial respiration was reduced under high land-use intensity (i.e., -43% between extensive grassland and conventional cropland) and future climate conditions (-12% in comparison to the ambient climate). Moreover, heat stress increased overall microbial respiration (+17% per 1°C increase), while increasing land-use intensity reduced the strength of this response (-25% slope reduction). In addition, increasing soil microbial biomass and fungal-to-bacterial ratio under low-intensity land use (i.e., extensive grassland) enhanced the microbial respiration response to heat stress. These findings show that intensive land use and climate change may compromise the activity of soil microbial communities as well as their respiration under heatwaves. In particular, soil microbial communities under high-intensity land use and future climate are less able to respond to additional stress, such as heatwaves, potentially threatening the critical ecosystem functions driven by soil microbes and highlighting the benefits of more sustainable agricultural practices.

Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms

Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications.IMPORTANCEAlthough soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction-less than 1%-can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from an in situ soil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.

Morphological spore-based characterisation and molecular approaches reveal comparable patterns in glomeromycotan communities

Traditionally, characterisation and comparison of AMF communities has been carried out by morphological identification of asexual spores in soil. In recent decades, molecular methods such as soil metabarcoding have become more popular than morphological identification of spores, but direct comparisons of the efficiency of both approaches have been rare. In this study, we compared AMF communities in soil samples from vegetable farms using both morphological and molecular methods (internal transcribed spacer, ITS, markers). In addition, we performed a systematic literature search and retrieved nine studies that analysed AMF communities using both approaches in the same soil samples, mostly in agroecosystems. Our results show that AMF communities determined by morphological spore-based identification are different than those determined by molecular genetic markers, but not as often claimed. In some cases, the morphological spore-based characterisation of spores revealed more diverse glomeromycotan communities. Moreover, in several cases the spore-based methods recovered taxa that the molecular methods did not, while in other cases the opposite was observed. The field and literature-based results of this study indicate that for a comprehensive and exhaustive characterisation of AMF communities it is necessary to combine both approaches. However, if the aim is to compare communities under different environmental conditions, both approaches provide comparable patterns.

Foliar fungi-imposed costs to plant productivity moderate shifts in composition of the rhizosphere microbiome

Plants in grasslands navigate a complex landscape of interactions including competition for resources and defense against pathogens. Foliar fungi can suppress plant growth directly through pathogenic interactions, or indirectly via host growth-defense tradeoffs. The exclusion of foliar fungi allows the reallocation of resources from defense to growth and reproduction. In addition, plants also invest photosynthates in rhizodeposition, or root exudates, which play a significant role in shaping the rhizosphere microbial community. However, it remains unclear what impact the exclusion of foliar fungi has on the allocation of resources to rhizodeposition and the composition of the rhizosphere microbial community. Using a 6-year foliar fungicide study in plots planted with 16 species of native prairie plants, we asked whether foliar fungi influence the rhizosphere microbial composition of a common prairie grass (Andropogon gerardii) and a common legume (Lespedeza capatita). We found that foliar fungicide increased aboveground biomass and season-long plant production, but did not alter root biomass, seed production, or rhizosphere microbial diversity. The magnitude of change in aboveground season-long plant production was significantly associated with the magnitude of change in the rhizosphere microbial community in paired foliar fungicide-treated vs. control plots. These results suggest important coupling between foliar fungal infection and plant investment in rhizodeposition to modify the local soil microbial community.

Diurnal Rhythmicity in the Rhizosphere Microbiome-Mechanistic Insights and Significance for Rhizosphere Function

The rhizosphere is a key interface between plants, microbes and the soil which influences plant health and nutrition and modulates terrestrial biogeochemical cycling. Recent research has shown that the rhizosphere environment is far more dynamic than previously recognised, with evidence emerging for diurnal rhythmicity in rhizosphere chemistry and microbial community composition. This rhythmicity is in part linked to the host plant's circadian rhythm, although some heterotrophic rhizosphere bacteria and fungi may also possess intrinsic rhythmicity. We review the evidence for diurnal rhythmicity in rhizosphere microbial communities and its link to the plant circadian clock. Factors which may drive microbial rhythmicity are discussed, including diurnal change in root exudate flux and composition, rhizosphere physico-chemical properties and plant immunity. Microbial processes which could contribute to community rhythmicity are considered, including self-sustained microbial rhythms, bacterial movement into and out of the rhizosphere, and microbe-microbe interactions. We also consider evidence that changes in microbial composition mediated by the plant circadian clock may affect microbial function and its significance for plant health and broader soil biogeochemical cycling processes. We identify key knowledge gaps and approaches which could help to resolve the spatial and temporal variation and functional significance of rhizosphere microbial rhythmicity. This includes unravelling the factors which determine the oscillation of microbial activity, growth and death, and cross-talk with the host over diurnal time frames. We conclude that diurnal rhythmicity is an inherent characteristic of the rhizosphere and that temporal factors should be considered and reported in rhizosphere studies.

Minor Effects of Warming on Soil Microbial Diversity, Richness and Community Structure

Climate warming has caused widespread global concern. However, how warming affects soil microbial diversity, richness, and community structure on a global scale remains poorly understood. Here we conduct a meta-analysis of 945 observations from 100 publications by collecting relevant data. The results show that field warming experiments significantly modify soil temperature (+1.8°C), soil water content (-3.2%), and soil pH (-0.04). However, field warming does not significantly alter the diversity, richness, and community structure of soil bacteria and fungi. Warming-induced changes in soil variables (i.e., ΔSoil water content, ΔpH), ΔTemperature and experimental duration are important factors influencing the microbial responses to warming. In addition, soil bacterial α-diversity (Shannon index) decreases significantly (-3.4%) when the warming duration is 3-6 years, and bacterial β-diversity increases significantly (35.2%) when warming exceeds 6 years. Meta-regression analysis reveals a positive correlation between the change of bacterial Shannon index and ΔpH. Moreover, warming produces more pronounced effects on fungal Shannon index and β-diversity in experimental sites with moderate mean annual temperature (MAT, 0°C-10°C) than in higher (> 10°C) or lower (< 0°C) MAT. Overall, this study provides a global perspective on the response of soil microorganisms to climate warming and improves our knowledge of the factors influencing the response of soil microorganisms to warming.

Detection of Live Shiga Toxin-Producing Escherichia coli with Long-Read Sequencing

A requirement of any foodborne pathogen testing method is that it only detects live bacteria. Ethidium monoazide (EMA) and propidium monoazide (PMA) are dyes that penetrate the membranes of dead cells and form cross-linkages in the DNA, which prevents its amplification in PCR. This study investigated whether treatment with EMA or PMA would inhibit the sequencing of DNA from dead Escherichia coli. Range finding experiments with qPCR were conducted to determine the optimal concentrations of EMA and PMA needed to inhibit the amplification of DNA from dead cells while not influencing live cells. An EMA concentration that differentiated between live and dead cells could not be established. However, a PMA concentration of 25 µM effectively prevented qPCR amplification of DNA from dead E. coli while not impacting the amplification of live E. coli DNA. Sequencing experiments were conducted with PMA-treated live, untreated live, PMA-treated dead, and untreated dead E. coli. There were no significant differences in the detection of virulence genes of interest between the PMA-treated live, untreated live, and untreated dead E. coli. However, no DNA sequencing data were obtained from the PMA-treated dead E. coli. These results suggest that PMA could be incorporated into sample preparation methods prior to sequencing to selectively detect live cells of foodborne pathogens.

Ex vivo oral biofilm model for rapid screening of antimicrobial agents including natural cranberry polyphenols

The search has been ongoing for safe and effective antimicrobial agents for control and prevention of oral biofilm associated with disease. Clinical trials for oral specific anti-bacterials are costly and often provide inconclusive results. The simple approach of ex vivo testing of these agents has not demonstrated utility, likely due to variability of effects observed even with a single donor. We show how shed oral biofilms, easily obtained from donor saliva, and tested under optimized conditions, respond reproducibly to anti-bacterial challenges measured by reductions in rRNA accumulation in susceptible taxa. Responses are in part donor specific, but many bacteria taxa were shown to be reproducibly susceptible over a group of donors. For two antibiotics, vancomycin and penicillin G tested at pharmacologic levels, a subset of Gram-positive bacteria was inhibited. A natural product with antibacterial properties, diluted Vaccinium macrocarpon (cranberry) juice, was shown to inhibit a range of oral taxa, including Alloprevotella sp__HMT_473, Granulicatella adiacens, Lachnoanaerobaculum umeaense, Lepotrichia sp__HMT_215, Peptostreptococcus stomatis, Prevotella nanceiensis, Stomatobaculum sp__HMT_097, Veillonella parvula, and kill some targets. The model discussed in this study has promise as a rapid, precise, and reproducible ex vivo method to test and identify potential clinically useful antimicrobial agents active against the oral biofilm community.

Relic DNA obscures bacterial diversity and interactions in ballast tank sediment

The dark and anoxic environment of ballast tank sediment (BTS) harbors substantial amounts of relic DNA, yet its impact on microbial diversity estimates in BTS management remains poorly understood. This study employed propidium monoazide (PMA) treatment to eliminate relic DNA and used 16S amplicon high-throughput sequencing to characterize both total and viable bacteria. Our findings revealed that relic DNA is abundant in BTS. When removed, it led to variable reductions in species richness, which fluctuated from a 3.15% increase to a 37.52% decrease. Additionally, 6.27%-15.79% of OTUs were absent in the PMA-treated samples. These findings indicate that relic DNA has diverse effects on microbial diversity estimates. Moreover, relic DNA removal altered the relative abundances of a wide range of taxa, thereby facilitating the detection of rare taxa. Furthermore, the absence of relic DNA resulted in an overestimation of co-occurrence network size, complexity, and competitiveness, which could lead to misinterpretations of community assembly processes. In conclusion, our findings indicate that relic DNA obscures microbial diversity estimates and risk assessments in BTS, highlighting the critical need for monitoring viable bacteria in ballast sediment management.

Propidium Monoazide is Unreliable for Quantitative Live-Dead Molecular Assays

Propidium monoazide (PMA) is a dye that distinguishes between live and dead cells in molecular assays like the Polymerase Chain Reaction (PCR). It works by cross-linking to the DNA of cells that have compromised membranes or extracellular DNA upon photoactivation, making the DNA inaccessible for amplification. Currently, PMA is used to detect viable pathogens and alleviate systemic bias in the microbiome analysis of samples using 16S rRNA gene sequencing. In these applications, treated samples consist of different amounts of dead bacteria and a range of bacterial strains, variables that can affect the performance of PMA and lead to inconsistent findings across various research studies. To evaluate the effectiveness of PMA, we used a sensitive qPCR assay and post-treatment sample concentration to determine PMA cross-linkage and activity accurately under varying sample conditions. We report that PMA is unreliable for viability assays when the concentration and composition of the bacterial mixtures are unknown. PMA is suitable only for qualitatively assessing viability in samples containing a known number of dead microbes or extracellular DNA.

Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails

BACKGROUND

Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.

METHODS

We use phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.

RESULTS

We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of "supercarriers" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.

CONCLUSIONS

The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.

Toward harnessing biodiversity-ecosystem function relationships in fungi

Fungi are crucial for terrestrial ecosystems, yet the role of fungal diversity in ecosystem functions remains unclear. We synthesize fungal biodiversity and ecosystem function (BEF) relationships, focusing on plant biomass production, carbon storage, decomposition, and pathogen or parasite resistance. The observed BEF relationships for these ecosystem functions vary in strength and direction, complicating generalizations. Strong positive relationships are generally observed when multiple ecosystem functions are addressed simultaneously. Often, fungal community composition outperforms species richness in predicting ecosystem functions. For more comprehensive fungal BEF research, we recommend studying natural communities, considering the simultaneous functions of a broader array of fungal guilds across spatiotemporal scales, and integrating community assembly concepts into BEF research. For this, we propose a conceptual framework and testable hypotheses.

From treetops to river bottoms: Exploring the role of phyllosphere fungi in aquatic fungal communities

Fungi play a crucial role in aquatic leaf litter decomposition. Aquatic fungi have long been thought to spend the majority of their lives in the water. Here, we explore the possibility of an amphibious life cycle, where phyllosphere fungi spend part of their life cycle in aquatic systems. We used internal transcribed spacer (ITS) fungal sequencing to follow phyllosphere fungi onto submerged litter, and quantitative stable isotope probing (qSIP) to differentiate active and inactive fungi. We found that around 30% of fungi active on aquatic litter entered the stream with the leaf and that these phyllosphere fungi were as active, if not more active than, as the fungi colonizing from the water column. These results demonstrate that phyllosphere fungi are an important part of aquatic fungal communities.

A Novel Approach Using LuxSit-i Enhanced Toehold Switches for the Rapid Detection of Vibrio parahaemolyticus

Vibrio parahaemolyticus (V. parahaemolyticus) is a significant concern, as it can cause severe infections and hemolytic trauma. Given its prevalence in seawater and coastal seafood, it poses a substantial risk as a foodborne pathogen. Biosensor-based detection technology has been continuously evolving, and toehold switches have emerged as a promising area within it, especially in the detection of RNA viruses. Here, we have developed a cell-free toehold switch sensor for V. parahaemolyticus detection. Traditional toehold switch detection methods usually use green fluorescent protein (GFP) or enzyme LacZ as the output signal, with an incubation time as long as 2 h, and are also mainly applied to the detection of RNA viruses. In this study, we introduced a novel, artificially designed luciferase (LuxSit-i) as an output signal and constructed toehold switches with two different output signals (sfGFP, LuxSit-i), aimed at reducing the incubation time of toehold switches. Moreover, to further improve the detection process, we separately utilize recombinase polymerase amplification (RPA) and nucleic acid sequence-based amplification (NASBA) to amplify dead and live bacterial suspensions for detection and attempt to distinguish between dead and live bacteria. This study provided a convenient, rapid, and accurate method for the on-site detection of V. parahaemolyticus, especially beneficial for resource-limited settings. By eliminating the requirement for specialized facilities and personnel, this system has the potential to be a valuable tool in improving public health responses, especially in developing regions.

Key active mercury methylating microorganisms and their synergistic effects on methylmercury production in paddy soils

Rice contamination with neurotoxic methylmercury (MeHg) from paddy soils is an escalating global concern. Identifying the microorganisms responsible for mercury (Hg) methylation in these soils is essential for controlling Hg contamination in the food chain and mitigating health impacts. Current research often focuses on total Hg-methylating microorganisms, overlooking the contributions of active ones, which can lead to either overestimating or neglecting the specific roles of microorganisms in Hg methylation within paddy soils. In this study, active Hg-methylating microorganisms in paddy soils were identified using a combination of DNA-SIP, Hg isotope labelling, and Hg methylation gene sequencing techniques. Our findings revealed that Geobacter and Anaerolinea are pivotal active Hg-methylating microorganisms across a contamination gradient in paddy soils. Transcriptomic analysis of soils from major rice-producing provinces in China confirmed the widespread and synergistic involvement of these microorganisms. Microbial incubation further validated their interaction significantly enhances Hg methylation, with Me198Hg concentrations increasing 2.8-fold compared to Geobacter alone and 5.2-fold compared to Anaerolinea alone. These findings enhance our understanding of microbial Hg methylation in paddy soils, providing critical insights for accurately predicting soil MeHg load, rice grain MeHg contamination, and human MeHg exposure risks.

Ecological processes shaping highly connected bacterial communities along strong environmental gradients

Along the river-sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River-South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities' tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.

Enhanced eDNA monitoring for detection of viable harmful algal bloom species using propidium monoazide

This study investigated the use of propidium monoazide (PMA) to improve the accuracy of environmental DNA (eDNA) monitoring by selectively detecting intracellular DNA (iDNA) from living cells, while excluding extracellular DNA (exDNA) from dead organisms. eDNA samples were collected from various depths off the coast of Tongyeong, South Korea, and analyzed alongside environmental factors, such as temperature, dissolved oxygen, turbidity, and nutrient levels. The results showed that PMA-treated iDNA provided a more accurate estimate of viable harmful algal bloom species (HABs) than total eDNA and DNase-treated iDNA. Strong correlations were found between iDNA (PMA) and environmental factors, particularly nutrient levels and turbidity, suggesting its effectiveness in biological environments. The iDNA (PMA) concentrations were higher in the surface and bottom layers, indicating that these layers were more indicative of living organisms in marine environments. The application of PMA in eDNA monitoring reduces false positives and enhances the detection accuracy of viable HAB species, representing a promising tool for real-time monitoring and management of marine ecosystems.

Extracellular DNA as a Strategy to Manage Vascular Wilt Caused by Fusarium oxysporum in Tomato (Solanum lycopersicum L.) Based on Its Action as a Damage-Associated Molecular Pattern (DAMP) or Pathogen-Associated Molecular Pattern (PAMP)

Vascular wilt is an important tomato disease that affects culture yields worldwide, with Fusarium oxysporum (F.o) being the causal agent of this infection. Several management strategies have lost effectiveness due to the ability of this pathogen to persist in soil and its progress in vascular tissues. However, nowadays, research has focused on understanding the plant defense mechanisms to cope with plant diseases. One recent and promising approach is the use of extracellular DNA (eDNA) based on the ability of plants to detect their self-eDNA as damage-associated molecular patterns (DAMPs) and pathogens' (non-self) eDNA as pathogen-associated molecular patterns (PAMPs). The aim of this work was to evaluate the effect of the eDNA of F.o (as a DAMP for the fungus and a PAMP for tomato plants) applied on soil, and of tomato's eDNA (as a DAMP of tomato plants) sprayed onto tomato plants, to cope with the disease. Our results suggested that applications of the eDNA of F.o (500 ng/µL) as a DAMP for this pathogen in soil offered an alternative for the management of the disease, displaying significantly lower disease severity levels in tomato, increasing the content of some phenylpropanoids, and positively regulating the expression of some defense genes. Thus, the eDNA of F.o applied in soil was shown to be an interesting strategy to be further evaluated as a new element within the integrated management of vascular wilt in tomato.

Fungal diversity and key functional gene abundance in Iowa bioretention cells: implications for stormwater remediation potential

Stormwater bioretention cells are green stormwater infrastructure systems that can help mitigate flooding and remove contaminants. Plants and bacteria improve nutrient removal and degrade organic contaminants; however, the roles of fungi in bioretention cells are less known. Although mycorrhizal fungi aid in plant growth/improve nutrient uptake, there is a notable lack of research investigating fungal diversity in bioretention cells. Other types of fungi could benefit bioretention cells (e.g., white rot fungi degrade recalcitrant contaminants). This study addresses the knowledge gap of fungal function and diversity within stormwater bioretention cells. We collected multiple soil samples from 27 different bioretention cells in temperate-climate eastern Iowa USA, characterized soil physicochemical parameters, sequenced the internal transcribed spacer (ITS) amplicon to identify fungal taxa from extracted DNA, and measured functional gene abundances for two fungal laccases (Cu1, Cu1A) and a fungal nitrite reductase gene (nirKf). Fungal biodegradation functional genes were present in bioretention soils (mean copies per g: 7.4 × 105nirKf, 3.2 × 106Cu1, 4.0 × 108Cu1A), with abundance of fungal laccase and fungal nitrite reductase genes significantly positively correlated with soil pH and organic matter (Pearson's R: >0.39; rho < 0.05). PERMANOVA analysis determined soil characteristics were not significant explanatory variables for community composition (beta diversity). In contrast, planting specifications significantly impacted fungal diversity; the presence/absence of a few planting types and predominant vegetation type in the cell explained 89% of variation in fungal diversity. These findings further emphasize the importance of plants and media as key design parameters for bioretention cells, with implications for fungal bioremediation of captured stormwater contaminants.

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations

BACKGROUND

Connecting the composition and function of industrial microbiomes is a major aspiration in microbial biotechnology. Here, we address this question in wine fermentation, a model system where the diversity and functioning of fermenting yeast species are determinant of the flavor and quality of the resulting wines.

RESULTS

First, we surveyed yeast communities associated with grape musts collected across wine appellations, revealing the importance of environmental (i.e., biogeography) and anthropic factors (i.e., farming system) in shaping community composition and structure. Then, we assayed the fermenting yeast communities in synthetic grape must under common winemaking conditions. The dominating yeast species defines the fermentation performance and metabolite profile of the resulting wines, and it is determined by the initial fungal community composition rather than the imposed fermentation conditions. Yeast dominance also had a more pronounced impact on wine meta-transcriptome than fermentation conditions. We unveiled yeast-specific transcriptomic profiles, leveraging different molecular functioning strategies in wine fermentation environments. We further studied the orthologs responsible for metabolite production, revealing modules associated with the dominance of specific yeast species. This emphasizes the unique contributions of yeast species to wine flavor, here summarized in an array of orthologs that defines the individual contribution of yeast species to wine ecosystem functioning.

CONCLUSIONS

Our study bridges the gap between yeast community composition and wine metabolite production, providing insights to harness diverse yeast functionalities with the final aim to producing tailored high-quality wines. Video Abstract.

Synergism of endophytic microbiota and plants promotes the removal of polycyclic aromatic hydrocarbons from the Alfalfa rhizosphere

Endophytic bacteria can promote plant growth and accelerate pollutant degradation. However, it is unclear whether endophytic consortia (Consortium_E) can stabilize colonisation and degradation. We inoculated Consortium_E into the rhizosphere to enhance endophytic bacteria survival and promote pollutant degradation. Rhizosphere-inoculated Consortium_E enhanced polycyclic aromatic hydrocarbon (PAH) degradation rates by 11.5-13.1 % compared with sole bioaugmentation and plant treatments. Stable-isotope-probing (SIP) showed that the rhizosphere-inoculated Consortium_E had the largest number of degraders (8 amplicon sequence variants). Furthermore, only microbes from Consortium_E were identified among the degraders in bioaugmentation treatments, indicating that directly participated in phenanthrene metabolism. Interestingly, Consortium_E reshaped the community structure of degraders without significantly altering the rhizosphere community structure, and strengthened the core position of degraders in the network, facilitating close interactions between degraders and non-degraders in the rhizosphere, which were crucial for ensuring stable functionality. The synergistic effect between plants and Consortium_E significantly enhanced the upregulation of aromatic hydrocarbon degradation and auxiliary degradation pathways in the rhizosphere. These pathways showed a non-significant increasing trend in the uninoculated rhizosphere compared with the control, indicating that Consortium_E primarily promotes rhizosphere effects. Our results explore the Consortium_E bioaugmentation mechanism, providing a theoretical basis for the ecological restoration of contaminated soils.

The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.

Bacterial community response to novel and repeated disturbances

Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long-term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.

Modern microbiology: Embracing complexity through integration across scales

Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.

Microbial ecology of northern Gulf of Mexico estuarine waters

Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 µm) and prefilter (>2.7 µm) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.IMPORTANCEEstuarine and coastal waters are diverse ecosystems influenced by tidal fluxes, interconnected wetlands, and river outflows, which are of high economic and ecological importance. Microorganisms play a pivotal role in estuaries as "first responders" and ecosystem architects, yet despite their ecological importance, they remain underrepresented in microbial studies compared to open ocean environments. This leads to substantial knowledge gaps that are important for understanding global biogeochemical cycling and making decisions about conservation and management strategies in these environments. Our study makes key contributions to the microbial ecology of estuarine and coastal habitats in the northern Gulf of Mexico. Our microbial community data support the concept of a globally distributed, core brackish microbiome and emphasize previously underrecognized brackish-water taxa. Given the projected worsening of land loss, oil spills, and natural disasters in this region, our results will serve as important baseline data for researchers investigating the microbial communities found across estuaries.

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics

Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6-800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.

Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management

Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.

Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances

BACKGROUND

Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances.

RESULTS

The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions.

CONCLUSIONS

Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes.

Integrating Multiple Bacterial Phenotypes and Bayesian Network for Analyzing Health Risks of Pathogens in Plastisphere

Plastic pollution represents a critical threat to soil ecosystems and even humans, as plastics can serve as a habitat for breeding and refuging pathogenic microorganisms against stresses. However, evaluating the health risk of plastispheres is difficult due to the lack of risk factors and quantification model. Here, DNA sequencing, single-cell Raman-D2O labeling, and transformation assay were used to quantify key risk factors of plastisphere, including pathogen abundance, phenotypic resistance to various stresses (antibiotic and pesticide), and ability to acquire antibiotic resistance genes. A Bayesian network model was newly introduced to integrate these three factors and infer their causal relationships. Using this model, the risk of pathogen in the plastisphere is found to be nearly 3 magnitudes higher than that in free-living state. Furthermore, this model exhibits robustness for risk prediction, even in the absence of one factor. Our framework offers a novel and practical approach to assessing the health risk of plastispheres, contributing to the management of plastic-related threats to human health.

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau

Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from an ∼1000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines but beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift, with the importance of drift decreasing but that of dispersal limitation increasing with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.

Microbial Proxies for Anoxic Microsites Vary with Management and Partially Explain Soil Carbon Concentration

Anoxic microsites are potentially important but unresolved contributors to soil organic carbon (C) storage. How anoxic microsites vary with soil management and the degree to which anoxic microsites contribute to soil C stabilization remain unknown. Sampling from four long-term agricultural experiments in the central United States, we examined how anoxic microsites varied with management (e.g., cultivation, tillage, and manure amendments) and whether anoxic microsites determine soil C concentration in surface (0-15 cm) soils. We used a novel approach to track anaerobe habitat space and, hence, anoxic microsites using DNA copies of anaerobic functional genes over a confined volume of soil. No-till practices inconsistently increased anoxic microsite extent compared to conventionally tilled soils, and within one site organic matter amendments increased anaerobe abundance in no-till soils. Across all long-term tillage trials, uncultivated soils had ∼2-4 times more copies of anaerobic functional genes than their cropland counterparts. Finally, anaerobe abundance was positively correlated to soil C concentration. Even when accounting for other soil C protection mechanisms, anaerobe abundance, our proxy for anoxic microsites, explained 41% of the variance and 5% of the unique variance in soil C concentration in cropland soils, making anoxic microsites the strongest management-responsive predictor of soil C concentration. Our results suggest that careful management of anoxic microsites may be a promising strategy to increase soil C storage within agricultural soils.

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems

Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications

Mining activities put the Brazilian savannas, a global biodiversity hotspot, in danger of species and soil carbon losses. Experiments employing biosolids have been applied to rejuvenate this degraded ecosystem, but a lingering question yet to be answered is whether the microbiota that inhabits these impoverished soils can be recovered towards its initial steady state after vegetation recovery. Here, we selected an 18-year-old restoration chronosequence of biosolids-treated, untreated mining and native soils to investigate the soil microbiota recovery based on composition, phylogeny, and diversity, as well as the potential factors responsible for ecosystem recovery. Our results revealed that the soil microbiota holds a considerable recovery potential in the degraded Cerrado biome. Biosolids application not only improved soil health, but also led to 41.7 % recovery of the whole microbial community, featuring significantly higher microbiota diversity and enriched groups (e.g., Firmicutes) that benefit carbon storage compared to untreated mining and native soils. The recovered community showed significant compositional distinctions from the untreated mining or native soils, rather than phylogenetic differences, with physiochemical properties explaining 55 % of the overall community changes. This study advances our understanding of soil microbiota dynamics in response to disturbance and restoration by shedding light on its recovery associated with biosolid application in a degraded biodiverse ecosystem.

Soil conditions are a more important determinant of microbial community composition and functional potential than neighboring plant diversity

Replanting is an important tool for ecological recovery. Management strategies, such as planting areas with monocultures or species mixtures, have implications for restoration success. We used 16S and ITS rRNA gene amplicon sequencing and shotgun metagenomics to assess how the diversity of neighboring tree species impacted soil bacterial and fungal communities, and their functional potential, within the root zone of mānuka (Leptospermum scoparium) trees. We compared data from monoculture and mixed tree species plots and confirmed that soil microbial taxonomic and functional community profiles significantly differed (p < 0.001). Compared to the diversity of neighboring tree species within the plot, soil environmental conditions and geographic distance was more important for structuring the microbial communities. The bacterial communities appeared more impacted by soil conditions, while the fungal communities displayed stronger spatial structuring, possibly due to wider bacterial dispersal. The different mechanisms structuring bacterial and fungal communities could have implications for ecological restoration outcomes.

Disinfection of sink drains to reduce a source of three opportunistic pathogens, during Serratia marcescens clusters in a neonatal intensive care unit

OBJECTIVE

Evaluate the effects of five disinfection methods on bacterial concentrations in hospital sink drains, focusing on three opportunistic pathogens (OPs): Serratia marcescens, Pseudomonas aeruginosa and Stenotrophomonas maltophilia.

DESIGN

Over two years, three sampling campaigns were conducted in a neonatal intensive care unit (NICU). Samples from 19 sink drains were taken at three time points: before, during, and after disinfection. Bacterial concentration was measured using culture-based and flow cytometry methods. High-throughput short sequence typing was performed to identify the three OPs and assess S. marcescens persistence after disinfection at the genotypic level.

SETTING

This study was conducted in a pediatric hospitals NICU in Montréal, Canada, which is divided in an intensive and intermediate care side, with individual rooms equipped with a sink.

INTERVENTIONS

Five treatments were compared: self-disinfecting drains, chlorine disinfection, boiling water disinfection, hot tap water flushing, and steam disinfection.

RESULTS

This study highlights significant differences in the effectiveness of disinfection methods. Chlorine treatment proved ineffective in reducing bacterial concentration, including the three OPs. In contrast, all other drain interventions resulted in an immediate reduction in culturable bacteria (4-8 log) and intact cells (2-3 log). Thermal methods, particularly boiling water and steam treatments, exhibited superior effectiveness in reducing bacterial loads, including OPs. However, in drains with well-established bacterial biofilms, clonal strains of S. marcescens recolonized the drains after heat treatments.

CONCLUSIONS

Our study supports thermal disinfection (>80°C) for pathogen reduction in drains but highlights the need for additional trials and the implementation of specific measures to limit biofilm formation.

Bacterial dispersal enhances the elimination of active fecal coliforms during vermicomposting of fruit and vegetable wastes: The overlooked role of earthworm mucus

Earthworms play a pivotal role in the elimination of fecal coliforms during vermicomposting of fruit and vegetable waste (FVWs). However, the specific mechanisms underlying the action of earthworm mucus remain unclear. This study investigated the mechanisms of fecal coliform reduction related to earthworm mucus during FVWs vermicomposting by comparing treatments with and without earthworms. The results show that the secretion of earthworm mucus decreased by 13.93 % during the startup phase, but significantly (P < 0.001) increased by 57.80 % during the degradation phase. Compared to the control without earthworms, vermicomposting led to a significant (P < 0.05) 1.22 -fold increase in the population of active bacteria, with a strong positive correlation between mucus characteristics and dominant bacterial phyla. As the dominant fecal coliforms, Escherichia coli and Klebsiella pneumoniae significantly (P < 0.05) declined by 86.20 % and 93.38 %, respectively, in the vermi-reactor relative to the control. Bacterial dispersal limitation served as a key factor constraining the elimination of E. coli (r = 0.73, P < 0.01) and K. pneumoniae (r = 0.77, P < 0.001) during vermicomposting. This study suggests that earthworm mucus increases the active bacterial abundance and cooperation by weakening the bacterial dispersal limitation, thus intensifying competition and antagonism between fecal coliforms and other bacteria.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops

Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared a similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared with those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All of the examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared with the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence the bacterial and diazotrophic community composition of any of these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced the community composition and function of these biocrusts.

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.

A case study on the application of spore sampling for the monitoring of macrofungi

Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool with a focus on grassland macrofungi. We applied active and passive air sampling methods, complemented by extensive field surveys of waxcap and clavarioid fungi-species groups of high relevance for conservation. Twenty-nine species were recorded during the field surveys, 19 of which were also detectable by ITS2 metabarcoding of the collected samples. An additional 12 species from the studied genera were identified exclusively in air eDNA. We found that the patterns of species detection and read abundance in air samples reflected the abundance and occurrence of fruiting bodies on the field. Dispersal kernels fitted for the three dominant species predicted rapidly decreasing spore concentrations with increasing distance from fruitbodies. Airborne assemblages were dominated by a high diversity of common species, while rare and threatened red-listed species were under-represented, which underscores the difficulty in detecting rare species, not only in conventional surveys. Considering the benefits and drawbacks of air sampling and fruitbody surveys, we conclude that air sampling serves as a cost- and time-efficient tool to characterize local macrofungal communities, providing the potential to facilitate and improve future fungal monitoring efforts.

The power of citizen science to advance fungal conservation

Fungal conservation is gaining momentum globally, but many challenges remain. To advance further, more data are needed on fungal diversity across space and time. Fundamental information regarding population sizes, trends, and geographic ranges is also critical to accurately assess the extinction risk of individual species. However, obtaining these data is particularly difficult for fungi due to their immense diversity, complex and problematic taxonomy, and cryptic nature. This paper explores how citizen science (CS) projects can be lever-aged to advance fungal conservation efforts. We present several examples of past and ongoing CS-based projects to record and monitor fungal diversity. These include projects that are part of broad collecting schemes, those that provide participants with targeted sampling methods, and those whereby participants collect environmental samples from which fungi can be obtained. We also examine challenges and solutions for how such projects can capture fungal diversity, estimate species absences, broaden participation, improve data curation, and translate resulting data into actionable conservation measures. Finally, we close the paper with a call for professional mycologists to engage with amateurs and local communities, presenting a framework to determine whether a given project would likely benefit from participation by citizen scientists.

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

BACKGROUND

As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

RESULTS

We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

CONCLUSIONS

Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.