Origin, dynamics, and implications of extracellular DNA pools in marine sediments

Analysing carbapenemases in hospital wastewater: Insights from intracellular and extracellular DNA using qPCR and digital PCR

The widespread dissemination of carbapenem-resistant bacteria in wastewater systems, particularly from clinical sources, poses a significant public health risk. This study assessed the concentrations and distributions of extracellular DNA (exDNA) and intracellular DNA (iDNA) harboring carbapenemase genes in wastewater from six tertiary care hospitals in Germany. We collected a total of 36 samples, comprising six biological replicates from each hospital, and analysed them using quantitative real-time PCR (qPCR) and digital PCR (dPCR). The analysis targeted seven carbapenemase genes: blaNDM, blaKPC, blaIMP, blaVIM, blaOXA-23-like, blaOXA-48-like, and blaOXA-58-like across both DNA fractions. Our results revealed significant variability in the concentrations of exDNA and iDNA across the sampling sites, with iDNA typically present at higher concentrations. Using NanoDrop One spectrophotometry and the Qubit dsDNA kit, exDNA concentrations ranged from 2.7 to 7.7 ng/mL, while Qubit recorded lower values between 1.1 and 4.0 ng/mL. Conversely, iDNA concentrations were markedly higher, spanning from 42.3 to 191.7 ng/mL with NanoDrop and 12.0 to 46.5 ng/mL with Qubit, highlighting the variability between DNA types and quantification methods. Despite its lower concentrations, exDNA comprised up to 18.2 % of total DNA, highlighting its potential role in the horizontal transfer of antimicrobial resistance genes (ARGs). The study detected target ARGs in both DNA fractions at all sites, with notable differences in their concentrations; iDNA consistently exhibited higher levels of ARGs, with the highest concentrations reaching 10.57 ± 0.20 log gene copies per liter (GC/L) for blaVIM in iDNA and 6.96 ± 0.72 log GC/L for blaIMP in exDNA. dPCR demonstrated greater sensitivity than qPCR, especially effective for detecting low-abundance targets like blaOXA-23-like in the exDNA fraction. Additionally, qPCR's susceptibility to inhibition and contamination emphasizes the superior robustness of dPCR. This research highlights the need for improved monitoring and the implementation of advanced treatment technologies to mitigate ARG dissemination in wastewater.

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.

Development and validation of an experimental life support system to study coral reef microbial communities

In the present study, we developed and validated an experimental life support system (ELSS) designed to investigate coral reef associated bacterial communities. The microcosms in the ELSS consisted of coral reef sediment, synthetic seawater, and specimens of five benthic reef species. These included two hard corals Montipora digitata and Montipora capricornis, a soft coral Sarcophyton glaucum, a zoanthid Zoanthus sp., and a sponge Chondrilla sp.. Physicochemical parameters and bacterial communities in the ELSS were similar to those observed at shallow coral reef sites. Sediment bacterial evenness and higher taxonomic composition were more similar to natural-type communities at days 29 and 34 than at day 8 after transfer to the microcosms, suggesting microbial stabilization after an initial recovery period. Biotopes were compositionally distinct but shared a number of ASVs. At day 34, sediment specific ASVs were found in hosts and visa versa. Transplantation significantly altered the bacterial community composition of M. digitata and Chondrilla sp., suggesting microbial adaptation to altered environmental conditions. Altogether, our results support the suitability of the ELSS developed in this study as a model system to investigate coral reef associated bacterial communities using multi-factorial experiments.

Taxonomic and abundance biases affect the record of marine eukaryotic plankton communities in sediment DNA archives

Environmental DNA (eDNA) preserved in marine sediments is increasingly being used to study past ecosystems. However, little is known about how accurately marine biodiversity is recorded in sediment eDNA archives, especially planktonic taxa. Here, we address this question by comparing eukaryotic diversity in 273 eDNA samples from three water depths and the surface sediments of 24 stations in the Nordic Seas. Analysis of 18S-V9 metabarcoding data reveals distinct eukaryotic assemblages between water and sediment eDNA. Only 40% of Amplicon Sequence Variants (ASVs) detected in water were also found in sediment eDNA. Remarkably, the ASVs shared between water and sediment accounted for 80% of total sequence reads suggesting that a large amount of plankton DNA is transported to the seafloor, predominantly from abundant phytoplankton taxa. However, not all plankton taxa were equally archived on the seafloor. The plankton DNA deposited in the sediments was dominated by diatoms and showed an underrepresentation of certain nano- and picoplankton taxa (Picozoa or Prymnesiophyceae). Our study offers the first insights into the patterns of plankton diversity recorded in sediment in relation to seasonality and spatial variability of environmental conditions in the Nordic Seas. Our results suggest that the genetic composition and structure of the plankton community vary considerably throughout the water column and differ from what accumulates in the sediment. Hence, the interpretation of sedimentary eDNA archives should take into account potential taxonomic and abundance biases when reconstructing past changes in marine biodiversity.

Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates

In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7-161.6 m2/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: <11 Kb, <6 Kb, and <3 Kb) and assessed the impact of Ca2+ and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca2+, and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca2+ led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.

The impact of flooding from the Minjiang River on the succession of harmful algal blooms (HABs) caused by diatoms in China's offshore waters

This study examines diatom assemblages in the Matsu Archipelago, an area influenced by Minjiang River runoff. It focuses on harmful algal blooms (HABs) that occurred between August 2021 and July 2022. Utilizing 18S rRNA metabarcoding and microscopic analysis, we observed a significant diatom bloom during early summer runoff, peaking at 5 × 105 cells L-1. The research reveals dynamic community changes during the runoff season, with dominant genera including Pseudo-nitzschia, Chaetoceros, and Skeletonema. Skeletonema cell density correlated with NO3 levels, Chaetoceros had a slight PO4 affinity, and Pseudo-nitzschia showed a negative correlation with Skeletonema. Pseudo-nitzschia, which prefers high light and pH conditions, had notably high concentrations in the flood season and in the autumn. In both, it was dominated by potential toxin-producing species - P. multistriata and P. pungens during the flooding, and P. cuspidate in the autumn. These findings highlight the intricate relationship between diatom dynamics and environmental factors, providing essential insights for managing HABs, especially Pseudo-nitzschia species, amidst environmental changes.

Assessing eDNA capture method from aquatic environment to optimise recovery of human mt-eDNA

Previous studies have shown that environmental DNA (eDNA) from human sources can be recovered from natural bodies of water, and the generation of DNA profiles from such environmental samples may assist in forensic investigations. However, fundamental knowledge gaps exist around the factors influencing the probability of detecting human eDNA and the design of optimal sampling protocols. One of these is understanding the particle sizes eDNA signals are most strongly associated with and the most appropriate filter size needed for efficiently capturing eDNA particles. This study assessed the amount of mitochondrial eDNA associated with different particle sizes from human blood and skin cells recovered from freshwater samples. Samples (300 mL) were taken from experimental 10 L tanks of freshwater spiked with 50 µL of human blood or skin cells deposited by vigorously rubbing hands together for two minutes in freshwater. Subsamples were collected by passing 250 mL of experimental water sample through six different filter pore sizes (from 0.1 to 8 µm). This process was repeated at four time intervals after spiking over 72 hours to assess if the particle size of the amount of eDNA recovered changes as the eDNA degrades. Using a human-specific quantitative polymerase chain reaction (qPCR) assay targeting the HV1 mitochondrial gene region, the total amount of mitochondrial eDNA associated with different particle size fractions was determined. In the case of human blood, at 0 h, the 0.45 µm filter pore size captured the greatest amount of mitochondrial eDNA, capturing 42 % of the eDNA detected. The pattern then changed after 48 h, with the 5 µm filter pore size capturing the greatest amount of eDNA (67 %), and 81 % of eDNA at 72 h. Notably, a ten-fold dilution proved to be a valuable strategy for enhancing eDNA recovery from the 8 µm filter at all time points, primarily due to the PCR inhibition observed in hemoglobin. For human skin cells, the greatest amounts of eDNA were recovered from the 8 µm filter pore size and were consistent through time (capturing 37 %, 56 %, and 88 % of eDNA at 0 hours, 48 hours, and 72 hours respectively). There is a clear variation in the amount of eDNA recovered between different cell types, and in some forensic scenarios, there is likely to be a mix of cell types present. These results suggest it would be best to use a 5 µm filter pore size to capture human blood and an 8 µm filter pore size to capture human skin cells to maximize DNA recovery from freshwater samples. Depending on the cell type contributing to the eDNA, a combination of different filter pore sizes may be employed to optimize the recovery of human DNA from water samples. This study provides the groundwork for optimizing a strategy for the efficient recovery of human eDNA from aquatic environments, paving the way for its broader application in forensic and environmental sciences.

Quantitative assessment of reef foraminifera community from metabarcoding data

Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.

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.

eDNA Adsorption onto Microplastics: Impacts of Water Chemistry and Polymer Physiochemical Properties

Adsorption of biomacromolecules onto polymer surfaces, including microplastics (MPs), occurs in multiple environmental compartments, forming an ecocorona. Environmental DNA (eDNA), genetic material shed from organisms, can adsorb onto MPs which can potentially either (1) promote long-range transport of antibiotic resistant genes or (2) serve to gain insights into the transport pathways and origins of MPs by analyzing DNA sequences on MPs. However, little is known about the capacity of MPs to adsorb eDNA or the factors that influence sorption, such as polymer and water chemistries. Here we investigated the adsorption of extracellular linear DNA onto a variety of model MP fragments composed of three of the most environmentally prevalent polymers (polyethylene, polyethylene terephthalate, and polystyrene) in their pristine and photochemically weathered states. Batch adsorption experiments in a variety of water chemistries were complemented with nonlinear modeling to quantify the rate and extent of eDNA sorption. Ionic strength was shown to strongly impact DNA adsorption by reducing or inhibiting electrostatic repulsion. Polyethylene terephthalate exhibited the highest adsorption capacity when normalizing for MP specific surface area, likely due to the presence of ester groups. Kinetics experiments showed fast adsorption (majority adsorbed under 30 min) before eventually reaching equilibrium after 1-2 h. Overall, we demonstrated that DNA quickly binds to MPs, with pseudo-first- and -second-order models describing adsorption kinetics and the Freundlich model describing adsorption isotherms most accurately. These insights into DNA sorption onto MPs show that there is potential for MPs to act as vectors for genetic material of interest, especially considering that particle-bound DNA typically persists longer in the environment than dissolved DNA.

Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA

Nutrient deficiency, natural enemies and litter autotoxicity have been proposed as possible mechanisms to explain species-specific negative plant-soil feedback (PSF). Another potential contributor to negative PSF is the plant released extracellular self-DNA during litter decay. In this study, we sought to comprehensively investigate these hypotheses by using Arabidopsis thaliana (L.) Heynh as a model plant in a feedback experiment. The experiment comprised a conditioning phase and a response phase in which the conditioned soils underwent four treatments: (i) addition of activated carbon, (ii) washing with tap water, (iii) sterilization by autoclaving, and (iv) control without any treatment. We evaluated soil chemical properties, microbiota by shotgun sequencing and the amount of A. thaliana extracellular DNA in the differently treated soils. Our results showed that washing and sterilization treatments mitigated the negative PSF effect. While shifts in soil chemical properties were not pronounced, significant changes in soil microbiota were observed, especially after sterilization. Notably, plant biomass was inversely associated with the content of plant self-DNA in the soil. Our results suggest that the negative PSF observed in the conditioned soil was associated to increased amounts of soilborne pathogens and plant self-DNA. However, fungal pathogens were not limited to negative conditions, butalso found in soils enhancing A.thaliana growth. In-depth multivariate analysis highlights that the hypothesis of negative PSF driven solely by pathogens lacks consistency. Instead, we propose a multifactorial explanation for the negative PSF buildup, in which the accumulation of self-DNA weakens the plant's root system, making it more susceptible to pathogens.

Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community

Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera were successfully captured using both methods, and sedDNA revealed a previously undetected community of phytoplankton. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of <100 years. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. The taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, also require further research.

Using the Fossil Record to Understand Extinction Risk and Inform Marine Conservation in a Changing World

Understanding the long-term effects of ongoing global environmental change on marine ecosystems requires a cross-disciplinary approach. Deep-time and recent fossil records can contribute by identifying traits and environmental conditions associated with elevated extinction risk during analogous events in the geologic past and by providing baseline data that can be used to assess historical change and set management and restoration targets and benchmarks. Here, we review the ecological and environmental information available in the marine fossil record and discuss how these archives can be used to inform current extinction risk assessments as well as marine conservation strategies and decision-making at global to local scales. As we consider future research directions in deep-time and conservationpaleobiology, we emphasize the need for coproduced research that unites researchers, conservation practitioners, and policymakers with the communities for whom the impacts of climate and global change are most imminent.

Fate, risk and sources of antibiotic resistome and its attenuation dynamics in the river water-sediment system: Field and microcosm study

Antibiotic resistance genes (ARGs) in rivers have received widespread attentions. Deciphering the fate and spread mechanisms of ARGs in river system can contribute to the design of effective strategies for reducing resistome risk in the environment. Although some studies have reported the prevalence and distribution of ARGs in rivers worldwide, few have systematically explored their fates, sources and risks in river water-sediment system. Also, the role of natural sunlight on the attenuation and fate of ARGs in river remains to be demonstrated. To fill the gaps, field investigation and microcosm experiment have been conducted in this study to reveal the fate, risk, source-sink relationship and attenuation dynamics of ARGs in an urban river water-sediment system, by utilizing high-throughput sequencing-based metagenomic assembly analysis and machine-learning-based source tracking tool. In all, 527 unique ARGs belonging to 29 antimicrobial classes were identified in the river. Relatively, the level of ARGs in the sediments were significantly higher (p < 0.05) than that in the waters. Variance partitioning analysis indicated the biotic and abiotic factors co-governed the riverine resistome, totally explaining 76% and 83% variations of ARGs in the waters and sediments, respectively. Microcosm experiment under natural light and dark condition showed that light induced the decay of ARGs in the waters and might promote their transfers from waters to sediments, which were also confirmed by the attenuation dynamics of bacteria in the experimental water-sediment system. Notably, the co-occurrences of ARGs with MGEs and VFs on the same contigs suggested resistome risk in the river, and relatively, the risk scores in the sediments were significantly higher (p < 0.05) than those in the waters. Source apportionment with metagenomic resistome signatures showed the Wenyu River was the most dominant contributor of ARGs in the downstream, with average contributions of 44.5% and 40.8% in the waters and sediments, respectively.

Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.

Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation

Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.

Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil

Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.

Microcosm experiments revealed resistome coalescence of sewage treatment plant effluents in river environment

Sewage treatment plant (STP) effluents are important contributors of antibiotic resistance (AR) pollution in rivers. Effluent discharging into rivers causes resistome coalescence. However, their mechanisms and dynamic processes are poorly understood, especially for the effects of dilution, diffusion, and sunlight-induced attenuation on coalescence. In this study, we have constructed microcosmic experiments based on in-situ investigation to explore these issues. The first batch experiment revealed the effects of dilution and diffusion. The coverage of water coalesced resistomes ranged 66.26∼152.18 × /Gb and was positively correlated with effluent volume (Mann-Kendall test, p < 0.01). Principal coordinate analysis (PCoA) and source tracking analysis demonstrated that dilution and diffusion stepwise reduced AR pollution. The second batch experiment explored the temporal dynamics and sunlight attenuation on coalesced resistomes. Under natural light, the coverage and diversity of water resistomes posed decreasing trends, primarily attributed to drastic erasure of effluent traces. The proportion of effluent-specific ARGs in coalesced resistomes significantly declined over time (Spearman's r = -0.83 and -0.94 in coverage and richness). While under dark condition, the coverage and diversity increased. Sunlight radiation intensified the interactions between water and sediment resistomes, as evidenced by more shared ARGs and less dissimilarities across niches. Network analysis, metagenome-assembled genome (MAG) analysis and variation partitioning analysis (VPA) showed that microbiome controlled resistome coalescence, explaining 56.5% and 58.4% of resistomes in water and sediment, respectively. Biotic and abiotic factors synergistically explained 40% of water resistomes. This study offers a comprehensive understanding of AR transmission and provides theoretical bases for grasping AR pollution and developing effective suppression strategies.

Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes

Wastewater treatment plants (WWTPs) have been reported as major anthropogenic reservoirs for the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment, worldwide. While most studies mainly focus on the intracellular DNA (iDNA), extracellular DNA (exDNA) accounting for a significant proportion of the total DNA in wastewater, was usually neglected. Following the One Health approach, this study focuses on wastewaters of municipal, clinical, and livestock origins (n = 45) that undergo different treatment processes (i.e., conventional activated sludge, ultrafiltration, and ozonation). Water samples were analysed for 12 ARGs as indicators of the different compartments associated with iDNA and exDNA by quantitative real-time PCR (qPCR). Taxonomic profiling of exDNA-fractions, obtained using nucleic acid adsorption particles, was conducted by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Notified exDNA concentrations varied between on-site WWTPs and treatment stages, and ranged from 314.0 ± 70.2 ng/mL in untreated livestock wastewater down to 0.7 ± 0.1 ng/mL in effluents after ultrafiltration. In general, influents exhibited higher concentrations compared to effluents, while wastewater treated by advanced treatment processes (i.e., ultrafiltration and ozonation) showed the lowest exDNA concentrations. Despite the lower concentrations, free-floating exDNA accounted for up to 80.0 ± 5.8% of the total DNA in effluents. Target ARGs were more common in the iDNA (100%, n = 45/45), compared to the exDNA-fractions (51.1%, n = 23/45), whereas exDNA-ARGs were mostly detected in clinical and slaughterhouse wastewaters as well as in the municipal influents. Compared to the iDNA-ARGs, the concentrations of exDNA-ARGs were in general lower. Nevertheless, significant higher concentrations for exDNA-associated genes were measured in clinical wastewaters for blaNDM (4.07 ± 0.15 log gene copies (GC)/L) and blaVIM-2 (6.0 ± 0.2 log GC/L). Overall, our results suggest that depending on the origin of wastewater and its treatment methods, exDNA represents an important reservoir for ARGs, particularly in clinical wastewater.

Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation

The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.

Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance

Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.

Earthworms restructure the distribution of extracellular antibiotics resistance genes of sludge by modifying the structure of extracellular polymeric substances during vermicomposting

The role of earthworms in reducing the antibiotic resistance genes (ARGs) in sludge vermicompost remains unclear. The structure of extracellular polymeric substance (EPS) of sludge may be associated with the horizontal gene transfer behavior of ARGs in the vermicomposting of sludge. Therefore, this study aimed to investigate the effects of earthworms on the structural characteristics of EPS associated with the fate of ARGs in EPS during the vermicomposting of sludge. The results showed vermicomposting could diminish the abundance of ARGs and mobile genetic elements (MGEs) in the EPS of sludge by 47.93 % and 7.75 %, compared to the control, respectively. Relative to the control, vermicomposting also led to the reduction of MGEs abundances in the soluble EPS of 40.04 %, lightly bound EPS of 43.53 %, and tightly bound EPS of 70.49 %, respectively. The total abundances of certain ARGs dramatically diminished 95.37 % in tightly bound EPS of sludge during vermicomposting. In vermicomposting, the main influencing factor of ARGs distribution was the proteins in LB-EPS, accounting for 48.5 % of the variation. This study suggests that the earthworms lower the total abundances of ARGs by regulating the microbial community and modifying the microbial metabolic pathways associated with ARGs and MGEs in the EPS of sludge.

Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota

Benefiting from the rapid developments and wide applications of high-throughput sequencing, great advancements have been made in investigating microbiota, which are highly diverse and play key roles in both element cycling and the energy flow of ecosystems. There have been inherent limitations of amplicon sequencing that could introduce uncertainty and raise concerns about the accuracy and reproducibility of this technology. However, studies focusing on the reproducibility of amplicon sequencing are limited, especially in characterizing microbial communities in deep-sea sediments. To evaluate reproducibility, 118 deep-sea sediment samples were used for 16S rRNA gene sequencing in technical replicates (repeated measurements of the same sample) that demonstrate the variability of amplicon sequencing. The average occurrence-based overlaps were 35.98% and 27.02% between two and among three technical replicates, respectively, whereas their abundance-based overlaps reached 84.88% and 83.16%, respectively. Although variations of alpha and beta diversity indices were found between/among technical replicates, alpha diversity indices were similar across samples, and the average beta diversity indices were much smaller for technical replicates than among samples. Moreover, clustering methods (i.e., operational taxonomic units [OTUs] and amplicon sequence variants [ASVs]) were shown to have little impact on the alpha and beta diversity patterns of microbial communities. Taken together, although there are variations between/among technical replicates, amplicon sequencing is still a powerful tool with which to reveal diversity patterns of microbiota in deep-sea sediments. IMPORTANCE The reproducibility of amplicon sequencing is vital for whether the diversities of microbial communities could be accurately estimated. Thus, reproducibility influences the drawing of sound ecological conclusions. Nevertheless, few studies have focused on the reproducibility of microbial communities that are characterized by amplicon sequencing, and studies focusing on microbiota in deep-sea sediments have been especially lacking. In this study, we evaluated the reproducibility of amplicon sequencing targeting microbiota in deep-sea sediments of cold seep. Our results revealed that there were variations between/among technical replicates and that amplicon sequencing was still a powerful tool with which to characterize the diversities of microbial communities in deep-sea sediments. This study provides valuable guidelines for the reproducibility evaluation of future work in experimental design and interpretation.

RNA Hydrolysis at Mineral-Water Interfaces

As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe₂O₃) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.

Temporal pesticide dynamics alter specific eukaryotic taxa in a coastal transition zone

Land use change and anthropogenic forcing can drastically alter the rates and patterns of sediment transport and modify biodiversity and ecosystem functions in coastal transition zones, such as the coastal ecosystems. Molecular studies of sediment extracted DNAs provide information on currently living organisms within the upper layers or buried from various periods of time, but might also provide knowledge on species dynamics, replacement and turnover. In this study, we evaluated the eukaryotic communities of a marine core that present a shift in soil erosion that was linked to glyphosate usage and correlated to chlordecone resurgence since 2000. We show differences in community composition between samples from the second half of the last century and those from the last two decades. Temporal analyses of the relative abundance, alpha diversity, and beta diversity for the two periods demonstrated different temporal dynamics depending on the considered taxonomic group. In particular, Ascomycetes showed a decrease in abundance over the most recent period associated with changes in community membership but not community structure. Two photosynthetic groups, Bacillariophyceae and Prasinophytes clade VII, showed a different pattern with an increase in abundance since the beginning of the 21st century with a decrease in diversity and evenness to form more heterogeneous communities dominated by a few abundant OTUs. Altogether, our data reveal that agricultural usages such as pesticide use can have long-term and species-dependent implications for microeukaryotic coastal communities on a tropical island.

Salp blooms drive strong increases in passive carbon export in the Southern Ocean

The Southern Ocean contributes substantially to the global biological carbon pump (BCP). Salps in the Southern Ocean, in particular Salpa thompsoni, are important grazers that produce large, fast-sinking fecal pellets. Here, we quantify the salp bloom impacts on microbial dynamics and the BCP, by contrasting locations differing in salp bloom presence/absence. Salp blooms coincide with phytoplankton dominated by diatoms or prymnesiophytes, depending on water mass characteristics. Their grazing is comparable to microzooplankton during their early bloom, resulting in a decrease of ~1/3 of primary production, and negative phytoplankton rates of change are associated with all salp locations. Particle export in salp waters is always higher, ranging 2- to 8- fold (average 5-fold), compared to non-salp locations, exporting up to 46% of primary production out of the euphotic zone. BCP efficiency increases from 5 to 28% in salp areas, which is among the highest recorded in the global ocean.

Are genomic indices effective alternatives to morphology based benthic indices in biomonitoring studies? Perspectives from a major harbour and marine protected area

Ecological assessments are currently being conducted by traditional morpho-taxonomical identification techniques that are time-consuming and often inaccurate. Biomonitoring programs are increasingly being complemented by the more rapid and efficient DNA barcoding approach. We compared the congruency of morpho-taxonomic (AMBI - AZTI's Marine Biotic Index) and genomic (gAMBI) benthic indices in ecological quality status (EcoQS) assignation in Mumbai harbour and Malvan Marine Protected area (MPA). The study, first of its kind to adopt the gAMBI tool in the selected milieu, contributed substantial number of macrobenthic cytochrome c oxidase subunit I gene (COI) sequences that were previously unavailable in the reference library, adding sufficient genetic resources for establishing ecostatus. AMBI and gAMBI values based on presence/absence data related significantly with those derived from abundance data matrices. Taxonomic and genomic indices derived ecostatus corresponded sufficiently well despite minor discrepancies, underscoring the viability of gAMBI as a superior alternative to AMBI in monitoring studies.

Biogeography, autecology, and phylogeny of Percolomonads based on newly described species

Percolomonads (Heterolobosea) are aquatic heterotrophic flagellates frequently found in saline waters up to hypersaline environments. We isolated and cultivated seven strains of percolomonad flagellates from marine waters and sediments as well as from a hypersaline inland lake in the Atacama Desert. Morphological characterizations, comprising light and scanning electron microscopy, revealed only slight differences between the strains mainly limited to the cell shape, length of flagella, and length of the ventral feeding groove. Phylogenetic analyses of the 18S and 28S rDNA genes showed the formation of three fully supported clades within the Percolomonadida: the Percolomonadidae, the Barbeliidae fam. nov. and the Lulaidae fam. nov. We describe two new families (Barbeliidae fam. nov., Lulaidae fam. nov.), a new genus (Nonamonas gen. nov.), and five new species (Percolomonas adaptabilis sp. nov., Lula levis sp. nov., Barbelia pacifica sp. nov., Nonamonas montiensis gen. et sp. nov., Nonamonas santamariensis gen. et sp. nov.). Salinity experiments showed that P. adaptabilis sp. nov. from the Atlantic was better adapted to high salinities than all other investigated strains. Moreover, comparisons of our cultivation-based approach with environmental sequencing studies showed that P. adaptabilis sp. nov. seems to be globally distributed in marine surface waters while other species seem to be more locally restricted.

Rapid bacterial and fungal successional dynamics in first year after chaparral wildfire

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by "fire-loving" pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeast Geminibasidium, which traded off against the filamentous Ascomycetes Pyronema, Aspergillus, and Penicillium. For bacteria, the Proteobacteria Massilia dominated all year, but the Firmicute Bacillus and Proteobacteria Noviherbaspirillum increased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.

Environmental changes affect the microbial release of hydrogen sulfide and methane from sediments at Boknis Eck (SW Baltic Sea)

Anthropogenic activities are modifying the oceanic environment rapidly and are causing ocean warming and deoxygenation, affecting biodiversity, productivity, and biogeochemical cycling. In coastal sediments, anaerobic organic matter degradation essentially fuels the production of hydrogen sulfide and methane. The release of these compounds from sediments is detrimental for the (local) environment and entails socio-economic consequences. Therefore, it is vital to understand which microbes catalyze the re-oxidation of these compounds under environmental dynamics, thereby mitigating their release to the water column. Here we use the seasonally dynamic Boknis Eck study site (SW Baltic Sea), where bottom waters annually fall hypoxic or anoxic after the summer months, to extrapolate how the microbial community and its activity reflects rising temperatures and deoxygenation. During October 2018, hallmarked by warmer bottom water and following a hypoxic event, modeled sulfide and methane production and consumption rates are higher than in March at lower temperatures and under fully oxic bottom water conditions. The microbial populations catalyzing sulfide and methane metabolisms are found in shallower sediment zones in October 2018 than in March 2019. DNA-and RNA profiling of sediments indicate a shift from primarily organotrophic to (autotrophic) sulfide oxidizing Bacteria, respectively. Previous studies using data collected over decades demonstrate rising temperatures, decreasing eutrophication, lower primary production and thus less fresh organic matter transported to the Boknis Eck sediments. Elevated temperatures are known to stimulate methanogenesis, anaerobic oxidation of methane, sulfate reduction and essentially microbial sulfide consumption, likely explaining the shift to a phylogenetically more diverse sulfide oxidizing community based on RNA.

Environmental nucleic acids: A field-based comparison for monitoring freshwater habitats using eDNA and eRNA

Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received much attention, the potential of environmental RNA as a biomonitoring tool remains under-explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect "metabolically active" parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra-organismal RNA will be important, but viability needs to be examined in a field-based setting. In this study we evaluate (a) whether extra-organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools.

Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding

Background

Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA).

Methods

Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4-12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction).

Results

Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species.

Conclusions

eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral-algal mutualisms.

Why eDNA fractions need consideration in biomonitoring

The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA-based biodiversity data. Finally, future avenues of research towards eDNA fraction-specific analyses are outlined to unravel the full potential of eDNA-based studies targeting micro- and macro-organisms.

Dynamics, gene transfer, and ecological function of intracellular and extracellular DNA in environmental microbiome

Extracellular DNA (eDNA) and intracellular DNA (iDNA) extensively exist in both terrestrial and aquatic environment systems and have been found to play a significant role in the nutrient cycling and genetic information transmission between the environment and microorganisms. As inert DNA sequences, eDNA is able to present stability in the environment from the ribosome enzyme lysis, therein acting as the historical genetic information archive of the microbiome. As a consequence, both eDNA and iDNA can shed light on the functional gene variety and the corresponding microbial activity. In addition, eDNA is a ubiquitous composition of the cell membrane, which exerts a great impact on the resistance of outer stress from environmental pollutants, such as heavy metals, antibiotics, pesticides, and so on. This study focuses on the environmental dynamics and the ecological functions of the eDNA and iDNA from the perspectives of environmental behavior, genetic information transmission, resistance to the environmental contaminants, and so on. By reviewing the status quo and the future vista of the e/iDNAs research, this article sheds light on exploring the ecological functioning of the e/iDNAs in the environmental microbiome.

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments

Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.

Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf

The planktonic diversity throughout the oceans is vital to ecosystem functioning and linked to environmental change. Plankton monitoring tools have advanced considerably with high-throughput in-situ digital cameras and genomic sequencing, opening new challenges for high-frequency observations of community composition, structure, and species discovery. Here, we combine multi-marker metabarcoding based on nuclear 18S (V4) and plastidial 16S (V4–V5) rRNA gene amplicons with a digital in-line holographic microscope to provide a synoptic diversity survey of eukaryotic plankton along the Newfoundland Shelf (Canada) during the winter transition phase of the North Atlantic bloom phenomenon. Metabarcoding revealed a rich eukaryotic diversity unidentifiable in the imaging samples, confirming the presence of ecologically important saprophytic protists which were unclassifiable in matching images, and detecting important groups unobserved or taxonomically unresolved during similar sequencing campaigns in the Northwest Atlantic Ocean. In turn, imaging analysis provided quantitative observations of widely prevalent plankton from every trophic level. Despite contrasting plankton compositions portrayed by each sampling method, both capture broad spatial differences between the northern and southern sectors of the Newfoundland Shelf and suggest complementary estimations of important features in eukaryotic assemblages. Future tasks will involve standardizing digital imaging and metabarcoding for wider use and consistent, comparable ocean observations.

Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?

Environmental DNA (eDNA) analysis is a promising tool for the sensitive and effective monitoring of species distribution and abundance. Traditional eDNA analysis has targeted mitochondrial DNA (mtDNA) fragments due to their abundance in cells; however, the quantification may vary depending on cell type and physiology. Conversely, some recent eDNA studies have targeted multi-copy nuclear DNA (nuDNA) fragments, such as ribosomal RNA genes, in water, and reported a higher detectability and more rapid degradation than mitochondrial eDNA (mt-eDNA). These properties suggest that nuclear eDNA (nu-eDNA) may be useful for the accurate estimation of species abundance relative to mt-eDNA, but which remains unclear. In this study, we compiled previous studies and re-analyzed the relationships between mt- and nu-eDNA concentration and species abundance by comparing the R² values of the linear regression. We then performed an aquarium experiment using zebrafish (Danio rerio) to compare the relationships across genetic regions, including single-copy nuDNA. We found more accurate relationships between multi-copy nu-eDNA and species abundance than mt-eDNA in these datasets, although the difference was not significant upon weighted-averaging the R² values. Moreover, we compared the decay rate constants of zebrafish eDNA across genetic regions and found that multi-copy nu-eDNA degraded faster than mt-eDNA under pH 7, implying a quick turnover of multi-copy nu-eDNA in the field. Although further empirical studies of nu-eDNA applications are necessary to support our findings, this study provides the groundwork for improving the estimation accuracy of species abundance via eDNA analysis.

Functional group substitutions influence the binding of benzophenone-type UV filters with DNA

As a class of possible carcinogens, benzophenone-type UV filters (BPs) widely exist in natural environments and organisms. The crucial step of the carcinogenic process induced by cancerous toxins is binding with DNA to form adducts. Here, the binding of 10 typical BPs, i.e., benzophenone (BP1), 2-hydroxyl benzophenone (BP2), 4-hydroxyl benzophenone (BP3), 2,2'-dihydroxyl benzophenone (BP4), 2,4-dihydroxyl benzophenone (BP5), 4,4'-dihydroxyl benzophenone (BP6), 2,4,4'-trihydroxyl benzophenone (BP7), 2,2',4,4'-tetrahydroxyl benzophenone (BP8), 2-hydroxyl-4-methoxyl benzophenone (BP9), and 2,2'-dihydroxyl-4-methoxyl benzophenone (BP10), with DNA was tested via fluorescence quenching experiments. Only hydroxyl group-substituted BPs could bind to DNA by groove binding mode, and the quenching constants were 0.93 × 10³-5.89 × 10³ L/mol. Substituted BPs were preferentially bound to thymine. Circular dichroism analysis confirmed that BPs could affect DNA base stacking but could not transform its B-form. Based on molecular electrostatic surface potential analyses, molecular dynamics simulations, and energy decomposition calculations, it could be found that the site and number of hydroxyl substitution changed the molecular polarity of BPs, thereby affecting the number and strength of hydrogen bonds between BPs and DNA. The hydroxyl substitution at site 2 was more conducive to binding than at site 4. This study is beneficial in comprehending the carcinogenic mechanisms of BPs.

Cascade Filtration With PCR Detection and Field-Flow-Fractionation Online With ICP-MS for the Characterization of DNA Interaction With Suspended Particulate Matter

The variety of applied antibiotics in animal and human medicine results in the release, development, and spread of relevant numbers of antibiotic resistance genes (ARGs) in the environment. The majority of ARGs are present in intracellular forms (in bacteria). Neglected aspects are extracellular variants of ARGs (eARGs) and their fragments, which have been detected in surface-water samples and sediments. The stability of eARGs is expected to be low; however, binding to particulate matter is likely to improve their stability and also affect their transport and dissemination behavior. Few studies have investigated DNA particle interactions, mostly via indirect characterization of adduct formation in model systems but not in real environmental matrices. Therefore, our study aims at a novel approach for direct characterization of desoxyribonucleic acid (DNA) particle interactions using both cascade filtration and field-flow fractionation. Cascade filtration with quantitative polymerase chain reaction (qPCR) detection indicated retention of ARGs on filters with much larger pore sizes supporting the hypothesis of ARG-particle interactions. However, artifacts from membrane clogging or DNA–membrane interaction cannot be excluded. Consequently, asymmetric flow field-flow fractionation was investigated as an alternative separation technique with the advantage of particle separation in a thin channel, reducing the risk of artifacts. The key method parameters, membrane composition, molecular weight cut off, and carrier composition, were systematically investigated using a calf-thymus DNA-spiked surface-water sample as a model. The results clearly showed a shift in the elution time of clay particles suggesting the presence of DNA–clay adducts. Multi-element detection by inductively coupled plasma mass spectrometry (ICP-MS) enabled monitoring of clay via the Al, Fe, and Si signals and DNA via the P signal. Matching peak profiles for the new fraction in the fractograms of the ARG and DNA-spiked water sample support adduct formation. Further evidence was provided by a novel post-channel filtration approach for the separation of free DNA from DNA–clay adducts.

Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana

The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.

The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments

Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.

Microbial Sources of Exocellular DNA in the Ocean

Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism. IMPORTANCE With advances in metagenomic sequencing, the microbial composition of diverse environmental systems has been investigated, providing new perspectives on potential ecological dynamics and dimensions for experimental investigations. Here, we characterized exocellular free DNA via metagenomics, using a newly developed method that separates free DNA from cells, viruses, and vesicles, and facilitated the independent characterization of each fraction. The fate of this free DNA has both ecological consequences as a nutrient (N and P) source and potential evolutionary consequences as a source of genetic transformation. Here, we document different microbial sources of free DNA at the surface (0 to 200 m) versus depths of 250 to 1,000 m, suggesting that distinct free DNA production mechanisms may be present throughout the oligotrophic water column. Examining microbial processes through the lens of exocellular DNA provides insights into the production of labile dissolved organic matter (i.e., free DNA) at the surface (likely by viral lysis) and processes that influence the fate of sinking, surface-derived organic matter.

DNA in extracellular vesicles: from evolution to its current application in health and disease

Extracellular vesicle (EV) secretion is a highly conserved evolutionary trait in all organisms in the three domains of life. The packaging and release of EVs appears to be a bulk-flow process which takes place mainly under extreme conditions. EVs participate in horizontal gene transfer, which supports the survival of prokaryotic and eukaryotic microbes. In higher eukaryotes, almost all cells secrete a heterogeneous population of EVs loaded with various biomolecules. EV secretion is typically higher in cancer microenvironments, promoting tumor progression and metastasis. EVs are now recognized as additional mediators of autocrine and paracrine communication in health and disease. In this context, proteins and RNAs have been studied the most, but extracellular vesicle DNA (EV-DNA) has started to gain in importance in the last few years. In this review, we summarize new findings related to the loading mechanism(s), localization, and post-shedding function of EV-DNA. We also discuss the feasibility of using EV-DNA as a biomarker when performing a liquid biopsy, at the same time emphasizing the lack of data from clinical trials in this regard. Finally, we outline the potential of EV-DNA uptake and its interaction with the host genome as a promising tool for understanding the mechanisms of cancer evolution.

Protecting DNA in membrane vesicles seems to be a conserved phenomenon for the horizontal genetic flux between prokaryotes and lower eukaryotes.

Capturing and analyzing this vesicular DNA enables quick and non-invasive monitoring of natural ecosystems.

Cancer-derived extracellular vesicles containing DNA open up novel directions in cell-to-cell communication and therefore disease monitoring.

Complex and fluctuating conditions of the tumor microenvironment, mimicking natural ecosystems, could favor EV-DNA release, mediating tumor multi-clonal evolution and providing survival benefits.

DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll

The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO₄²⁻/Cl⁻ and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.

Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

Extracellular DNA: Insight of a Signal Molecule in Crop Protection

Simple Summary

Agriculture systems use multiple chemical treatments to prevent pests and diseases, and to fertilize plants and eliminate weeds around the crop. These practices are less accepted by the consumers each day, mostly because of the associated environmental, health, and ecological impact; thus, new sustainable green technologies are being developed to replace the use of chemical products. Among green technologies for agriculture practices, the use of plant elicitors represents an alternative with great potential, and extracellular DNA has shown beneficial effects on important production traits such as defence mechanisms, plant growth and development, and secondary metabolites production that results in yield increment and better-quality food. In this review, we reunite experimental evidence of the natural effect that extracellular DNA has on plants. We also aim to contribute a step closer to the agricultural application of extracellular DNA. Additionally, we suggest that extracellular DNA can have a biostimulant effect on plants, and can be applied as a highly sustainable treatment contributing to the circular economy of primary production.

Abstract

Agricultural systems face several challenges in terms of meeting everyday-growing quantities and qualities of food requirements. However, the ecological and social trade-offs for increasing agricultural production are high, therefore, more sustainable agricultural practices are desired. Researchers are currently working on diverse sustainable techniques based mostly on natural mechanisms that plants have developed along with their evolution. Here, we discuss the potential agricultural application of extracellular DNA (eDNA), its multiple functioning mechanisms in plant metabolism, the importance of hormetic curves establishment, and as a challenge: the technical limitations of the industrial scale for this technology. We highlight the more viable natural mechanisms in which eDNA affects plant metabolism, acting as a damage/microbe-associated molecular pattern (DAMP, MAMP) or as a general plant biostimulant. Finally, we suggest a whole sustainable system, where DNA is extracted from organic sources by a simple methodology to fulfill the molecular characteristics needed to be applied in crop production systems, allowing the reduction in, or perhaps the total removal of, chemical pesticides, fertilizers, and insecticides application.

Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems

Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.