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

Effects of nitrogen-driven eutrophication on the horizontal transfer of extracellular antibiotic resistance genes in water-sediment environments

Excessive nitrogen and other nutrients can trigger the eutrophication of freshwater bodies. Antibiotic resistance genes (ARGs) are now recognized as environmental pollutants, with extracellular ARGs (eARGs) being the dominant form in sediments. However, research on the propagation characteristics of eARGs remains limited. This study investigated the transfer characteristics of kanamycin resistance (KR) genes in the pEASY-T1 plasmid to intracellular DNA (iDNA) and extracellular DNA (eDNA) in water and sediment microenvironments under increasing nitrogen concentrations, as well as the community structure of free-living (FL) and particle-attached (PA) bacteria. The results revealed KR genes relative abundance in free extracellular DNA (f-eDNA) and adsorbed extracellular DNA (a-eDNA) of the water initially decreased and then increased with rising nitrogen concentrations. Its abundance in iDNA of the sediments decreased significantly with increasing nitrogen content, with relative abundance ranging from 5.09 × 10-4 to 1.14 × 10-3 copies/16SrRNA. The transfer from eDNA to iDNA in the water showed a rising and then falling trend as nitrogen concentration rose. The transfer of iDNA from the water to iDNA in sediments exhibited the opposite pattern. Additionally, copper (Cu) and zinc (Zn) were identified as key factors influencing the abundance of KR genes in the water, but total phosphorus (TP) was the primary determinant of KR gene distribution in sediments according to random forest analysis. These findings reveal novel mechanisms of eARG propagation in eutrophic environments, providing a theoretical foundation for managing antibiotic resistance in aquatic ecosystems.

Application of a real-time reverse transcription polymerase chain reaction for rapid detection of Escherichia coli in drinking water: an EU representative study

The microbiological quality of water intended for human consumption in the EU is regulated by the recast Drinking Water Directive 2020/2184 (DWD), which sets strict parametric values for intestinal enterococci and Escherichia coli (E. coli), allowing no more than zero colony-forming units per 100 mL. Detection and enumeration of E. coli typically rely on culture-based reference methods or the most probable number approach, which require 1-2 days to produce results-potentially delaying timely action during contamination events. In contrast, molecular techniques can deliver results within hours. The DWD permits the use of alternative methods if they are as reliable as the reference method and developing and validating such methods requires multiple laboratory trials in line with ISO standard 16140-2. Following this, we conducted a representative EU study to validate a molecular method based on real-time reverse transcription polymerase chain reaction for rapid E. coli detection in drinking water. In a concerted action, the first of its kind for drinking water, nineteen laboratories across ten Member States participated. To ensure consistency, drinking water was artificially contaminated with E. coli. The alternative method showed slightly lower sensitivity than the reference method (91.1 % vs. 97.2 %) but delivered much faster results, making it a valuable screening tool. It can support rapid decision-making during contamination events, reducing the risk of waterborne outbreaks and protecting public health. For reliable routine performance, appropriate training in this alternative method is strongly recommended.

Biocides as drivers of antibiotic resistance: A critical review of environmental implications and public health risks

The widespread and indiscriminate use of biocides poses significant threats to global health, socioeconomic development, and environmental sustainability by accelerating antibiotic resistance. Bacterial resistance development is highly complex and influenced significantly by environmental factors. Increased biocide usage in households, agriculture, livestock farming, industrial settings, and hospitals produces persistent chemical residues that pollute soil and aquatic environments. Such contaminants contribute to the selection and proliferation of resistant bacteria and antimicrobial resistance genes (ARGs), facilitating their dissemination among humans, animals, and ecosystems. In this review, we conduct a critical assessment of four significant issues pertaining to this topic. Specifically, (i) the role of biocides in exerting selective pressure within the environmental resistome, thereby promoting the proliferation of resistant microbial populations and contributing to the global spread of antimicrobial resistance genes (ARGs); (ii) the role of biocides in triggering transient phenotypic adaptations in bacteria, including efflux pump overexpression, membrane alterations, and reduced porin expression, which often result in cross-resistance to multiple antibiotics; (iii) the capacity of biocides to disrupt bacteria and make the genetic content accessible, releasing DNA into the environment that remains intact under certain conditions, facilitating horizontal gene transfer and the spread of resistance determinants; (iv) the capacity of biocides to disrupt bacterial cells, releasing intact DNA into the environment and enhancing horizontal gene transfer of resistance determinants; and (iv) the selective interactions between biocides and bacterial biofilms in the environment, strengthening biofilm cohesion, inducing resistance mechanisms, and creating reservoirs for resistant microorganisms and ARG dissemination. Collectively, this review highlights the critical environmental and public health implications of biocide use, emphasizing an urgent need for strategic interventions to mitigate their role in antibiotic resistance proliferation.

Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers

BACKGROUND

As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.

RESULTS

Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing.

CONCLUSIONS

Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.

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.

Environmental DNA barcoding reveals general biodiversity patterns in the large tropical rift Lake Albert

Lake Albert, Africa's seventh-largest lake and a biodiversity hotspot, faces significant environmental challenges, including unregulated anthropogenic pressure and a lack of comprehensive biological studies. To address the scarcity of biodiversity data, we utilized environmental DNA (eDNA) metabarcoding to assess the lake's eukaryotic and metazoan communities. Surface water samples were collected at three distinct locations: close to the southern inflow of the Semliki River, the central part of the lake, and close to the northern inflow of the Victoria Nile and outflow of the Albert Nile. We aimed to study ecological patterns across the lake, focusing on sequence variant richness and community composition, testing for differences among locations and between shoreline and pelagic zones. Consistent with previous morphology-based observations, our results revealed differences in community composition among the three sites, with cyclopoid copepods dominating the communities. Distance from shore was a significant factor influencing community composition, confirming expectations about the effects of nutrient and oxygen availability gradients. However, the lack of comprehensive reference sequence data limited accurate taxonomic assignments. Despite these limitations, our study demonstrates that eDNA metabarcoding is highly useful for assessing biodiversity in underexplored tropical freshwater ecosystems. We advocate for urgent efforts to generate reference sequences from tropical regions to enhance the utility of eDNA for biodiversity monitoring and conservation. Our findings underscore the potential of eDNA in providing insights into ecological patterns of entire communities and emphasize the need for comprehensive studies addressing the full taxonomic spectrum in tropical freshwater ecosystems.

Method evaluation for viruses in activated sludge: Concentration, sequencing, and identification

Activated sludge (AS) in wastewater treatment plants is one of the largest artificial microbial ecosystems on earth and it makes enormous contributions to human societies. Viruses are an important component in AS with a high abundance. However, their communities and functionalities have not been as widely explored as those of other microorganisms, such as bacteria. This gap is mainly due to technical challenges in effective viral concentration, extraction, and sequencing. In this study, we compared four kinds of concentration methods, two sequencing approaches, and four identification bioinformatic tools to evaluate the whole analysis workflow for viruses in AS. Results showed flocculation, filtration, and resuspension (FFR) could get the longest DNA lengths and ultracentrifugation obtained the highest DNA yields for viruses in AS. Based on the results of present study, FFR and tangential flow filtration with the membrane pore size of 100 kDa were most recommended to concentrate viruses in AS samples with huge volumes. Besides, different concentration methods could get different viral catalogs and thus multiple methods should be combined to get the whole picture of viruses in the system. In addition, geNomad was the most recommended identification tool for viruses in the present study and the long-read sequencing could improve the assembly statistics of viruses when compared with the short-read sequencing. For the 8192 viral operational taxonomic units in this study, 95.1 % of them were phages and belonged to the same lineage at the order level of Caudovirales. Virulent phages dominated the AS system and Pseudomonadota were the main host. Taken together, this study provides new insights into methods selection for virus research of AS.

Unveiling the role of uranium in enhancing the transformation of antibiotic resistance genes

Transformation represents one of the most important pathways for the horizontal transfer of antibiotic resistance genes (ARGs), which enables competent bacteria to acquire extracellular ARGs from the surrounding environment. Both heavy metals and irradiation have been demonstrated to influence the bacterial transformation process. However, the impact of ubiquitously occurring radioactive heavy metals on the transformation of ARGs remains largely unknown. Here, we showed that a representative radioactive nuclide, uranium (U), at environmental concentrations (0.005-5 mg/L), improved the transformation frequency of resistant plasmid pUC19 into Escherichia coli by 0.10-0.85-fold in a concentration-dependent manner. The enhanced ARGs transformation ability under U stress was demonstrated to be associated with reactive oxygen species (ROS) overproduction, membrane damage, and up-regulation of genes related to DNA uptake and recombination. Membrane permeability and ROS production were the predominant direct and indirect factors affecting transformation ability, respectively. Our findings provide valuable insight into the underlying mechanisms of the impacts of U on the ARGs transformation process and highlight concerns about the exacerbated spread of ARGs in radioactive heavy metal-contaminated ecosystems, especially in areas with nuclear activity or accidents.

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

Active antibiotic-resistant bacteria (ARB) play a major role in spreading antimicrobial resistance (AMR) in the environment; however, they have remained largely unexplored. Herein, we coupled bio-orthogonal noncanonical amino acid tagging with high-throughput fluorescence-activated single-cell sorting (FACS) and sequencing to characterize the phenome and genome of active ARB in complex environmental matrices. Active ARB, conferring resistance to six antibiotics throughout wastewater treatment, were distinguished and quantified. The percentage and concentration of active ARB ranged from 0.28% to 45.3% and from 1.1 × 104 to 2.09 × 107 cells/mL, respectively. Notably, the final effluents retained up to 4.79 × 104 cells/mL of active ARB. Targeted FACS and genomic sequencing revealed a distinct taxonomic composition of active ARB compared with that of the overall population. The coexistence of antibiotic resistome and mobilome in active ARB was also identified, including three high-quality metagenomic assembly genomes assigned to pathogenic bacteria, highlighting the substantial health risks due to their activity, phenotypic resistance, mobility, and pathogenicity. This study advances our understanding of previously overlooked active ARB in the environment by linking their resistance phenotype to their genotype. This high-throughput method will enable efficient quantitative surveillance of active AMR, providing valuable insights into risk control and management.

Prophage induction by non-antibiotic compounds promotes transformation of released antibiotic resistance genes from cell lysis

Prophages are prevalent among bacterial species, including strains carrying antibiotic resistance genes (ARGs). Prophage induction can be triggered by the SOS response to stressors, leading to cell lysis. In environments polluted by chemical stressors, ARGs and prophage co-harboring strains might pose an unknown risk of spreading ARGs through chemical pollutant-mediated prophage induction and subsequent cell lysis. In this study, we investigated the effects of common non-antibiotic water pollutants, triclosan and silver nanoparticles, on triggering prophage induction in clinical isolates carrying ARGs and the subsequent uptake of released ARGs by the naturally competent bacterium Acinetobacter baylyi. Our results demonstrate that both triclosan and silver nanoparticles, at environmentally relevant concentrations and those found in commercial products, significantly enhance prophage induction among various clinical isolates. Transmission electron microscopy imaging and plaque assays confirmed the production of infectious phage particles under non-antibiotic pollutants-mediated prophage induction. In addition, the rate of ARG transformation to A. baylyi significantly increased after the release of extracellular ARGs from prophage induction-mediated cell lysis. The mechanism of non-antibiotic pollutants-mediated prophage induction is primarily associated with excessive oxidative stress, which provokes the SOS response. Our findings offer insights into the role of non-antibiotic pollutants in promoting the dissemination of ARGs by triggering prophage induction.

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.

Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting

While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.

IMPORTANCE

The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.

Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes

Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.

Revealing the Viable Microbial Community of Biofilm in a Sewage Treatment System Using Propidium Monoazide Combined with Real-Time PCR and Metagenomics

Microbial community composition, function, and viability are important for biofilm-based sewage treatment technologies. Most studies of microbial communities mainly rely on the total deoxyribonucleic acid (DNA) extracted from the biofilm. However, nucleotide materials released from dead microorganisms may interfere with the analysis of viable microorganisms and their metabolic potential. In this study, we developed a protocol to assess viability as well as viable community composition and function in biofilm in a sewage treatment system using propidium monoazide (PMA) coupled with real-time quantitative polymerase chain reaction (qPCR) and metagenomic technology. The optimal removal of PMA from non-viable cells was achieved by a PMA concentration of 4 μM, incubation in darkness for 5 min, and exposure for 5 min. Simultaneously, the detection limit can reach a viable bacteria proportion of 1%, within the detection concentration range of 102-108 CFU/mL (colony forming unit/mL), showing its effectiveness in removing interference from dead cells. Under the optimal conditions, the result of PMA-metagenomic sequencing revealed that 6.72% to 8.18% of non-viable microorganisms were influenced and the composition and relative abundance of the dominant genera were changed. Overall, this study established a fast, sensitive, and highly specific biofilm viability detection method, which could provide technical support for accurately deciphering the structural composition and function of viable microbial communities in sewage treatment biofilms.

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.

The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches

BACKGROUND

Anthropogenic impacts on freshwater habitats are causing a recent biodiversity decline far greater than that documented for most terrestrial ecosystems. However, knowledge and description of freshwater biodiversity is still limited, especially targeting all size classes to uncover the distribution of biodiversity between different trophic levels. We assessed the biodiversity of the Lower Rhine and associated water bodies in the river's flood plain including the river's main channel, oxbows and gravel-pit lakes, spanning from the level of protists up to the level of larger invertebrate predators and herbivores organized in size classes (nano-, micro, meio- and macrofauna). Morphological diversity was determined by morphotypes, while the molecular diversity (amplicon sequencing variants, ASVs) was assessed through eDNA samples with metabarcoding targeting the V9 region of the 18S rDNA.

RESULTS

Considering all four investigated size classes, the percentage of shared taxa between both approaches eDNA (ASVs with 80-100% sequence similarity to reference sequences) and morphology (morphotypes), was always below 15% (5.4 ± 3.9%). Even with a more stringent filtering of ASVs (98-100% similarity), the overlap of taxa could only reach up to 43% (18.3 ± 12%). We observed low taxonomic resolution of reference sequences from freshwater organisms in public databases for all size classes, especially for nano-, micro-, and meiofauna, furthermore lacking metainformation if species occur in freshwater, marine or terrestrial ecosystems.

CONCLUSIONS

In our study, we provide a combination of morphotype detection and metabarcoding that particularly reveals the diversity in the smaller size classes and furthermore highlights the lack of genetic resources in reference databases for this diversity. Especially for protists (nano- and microfauna), a combination of molecular and morphological approaches is needed to gain the highest possible community resolution. The assessment of freshwater biodiversity needs to account for its sub-structuring in different ecological size classes and across compartments in order to reveal the ecological dimension of diversity and its distribution.

Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity

Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with aw, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as aw decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the 0.409-aw brine (an MgCl2-dominated site) despite the presence of cell-like structures. Extrapolating our data, we predict an aw limit for detectable anabolic activity of 0.540, which is beyond the currently accepted limit of life based on cell division. This work demonstrates the utility of single-cell, metabolism-based techniques for detecting active life and expands the potential habitable space on Earth and beyond.

Relic DNA obscures DNA-based profiling of multiple microbial taxonomic groups in a river-reservoir ecosystem

Numerous studies have investigated the spatiotemporal variability in water microbial communities, yet the effects of relic DNA on microbial community profiles, especially microeukaryotes, remain far from fully understood. Here, total and active bacterial and microeukaryotic community compositions were characterized using propidium monoazide (PMA) treatment coupled with high-throughput sequencing in a river-reservoir ecosystem. Beta diversity analysis showed a significant difference in community composition between both the PMA untreated and treated bacteria and microeukaryotes; however, the differentiating effect was much stronger for microeukaryotes. Relic DNA only resulted in underestimation of the relative abundances of Bacteroidota and Nitrospirota, while other bacterial taxa exhibited no significant changes. As for microeukaryotes, the relative abundances of some phytoplankton (e.g. Chlorophyta, Dinoflagellata and Ochrophyta) and fungi were greater after relic DNA removal, whereas Cercozoa and Ciliophora showed the opposite trend. Moreover, relic DNA removal weakened the size and complexity of cross-trophic microbial networks and significantly changed the relationships between environmental factors and microeukaryotic community composition. However, there was no significant difference in the rates of temporal community turnover between the PMA untreated and treated samples for either bacteria or microeukaryotes. Overall, our results imply that the presence of relic DNA in waters can give misleading information of the active microbial community composition, co-occurrence networks and their relationships with environmental conditions. More studies of the abundance, decay rate and functioning of nonviable DNA in freshwater ecosystems are highly recommended in the future.

Distinguishing different surface interactions for nucleotides adsorbed onto hematite and goethite particle surfaces through ATR-FTIR spectroscopy and DFT calculations

Geochemical interfaces can impact the fate and transport of aqueous species in the environment including biomolecules. In this study, we investigate the surface chemistry of adsorbed nucleotides on two different minerals, hematite and goethite, using infrared spectroscopy and density functional theory (DFT) calculations. Attenuated total reflectance-Fourier transform infrared spectroscopy is used to probe the adsorption of deoxyadenosine monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxycytidine monophosphate (dCMP), and deoxythymidine monophosphate (dTMP) onto either hematite or goethite particle surfaces. The results show preferential adsorption of the phosphate group to either surface. Remarkably, surface adsorption of the four nucleotides onto either hematite or goethite have nearly identical experimental spectra in the phosphate region (900 to 1200 cm^-1) for each mineral surface yet are distinctly different between the two minerals, suggesting differences in binding of these nucleotides to the two mineral surfaces. The experimental absorption frequencies in the phosphate region were compared to DFT calculations for nucleotides adsorbed through the phosphate group to binuclear clusters in either a monodentate or bidentate bridging coordination. Although the quality of the fits suggests that both binding modes may be present, the relative amounts differ on the two surfaces with preferential bonding suggested to be monodentate coordination on hematite and bidentate bridging on goethite. Possible reasons for these differences are discussed.

Chlorinated nucleotides and analogs as potential disinfection byproducts in drinking water

Identification of emerging disinfection byproducts (DBPs) of health relevance is important to uncover the health risk of drinking water observed in epidemiology studies. In this study, mutagenic chlorinated nucleotides were proposed as potential DBPs in drinking water, and the formation and transformation pathways of these DBPs in chlorination of nucleotides were carefully investigated. A total of eleven chlorinated nucleotides and analogs were provisionally identified as potential DBPs, such as monochloro uridine/cytidine/adenosine acid and dichloro cytidine acid, and the formation mechanisms involved chlorination, decarbonization, hydrolysis, oxidation and decarboxylation. The active sites of nucleotides that reacted with chlorine were on the aromatic heterocyclic rings of nucleobases, and the carbon among the two nitrogen atoms in the nucleobases tended to be transformed into carboxyl group or be eliminated, further forming ring-opening or reorganization products. Approximately 0.2-4.0 % (mol/mol) of these chlorinated nucleotides and analogs finally decomposed to small-molecule aliphatic DBPs, primarily including haloacetic acids, trichloromethane, and trichloroacetaldehyde. Eight intermediates, particularly chlorinated imino-D-ribose and imino-D-ribose, were tentatively identified in chlorination of uridine. This study provides the first set of preliminary evidence for indicating the promising occurrence of chlorinated nucleotides and analogs as potential toxicological-relevant DBPs after disinfection of drinking water.

Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States

Phytoplankton is the essential primary producer in fresh surface water ecosystems. However, excessive phytoplankton growth due to eutrophication significantly threatens ecologic, economic, and public health. Therefore, phytoplankton identification and quantification are essential to understanding the productivity and health of freshwater ecosystems as well as the impacts of phytoplankton overgrowth (such as Cyanobacterial blooms) on public health. Microscopy is the gold standard for phytoplankton assessment but is time-consuming, has low throughput, and requires rich experience in phytoplankton morphology. Quantitative polymerase chain reaction (qPCR) is accurate and straightforward with high throughput. In addition, qPCR does not require expertise in phytoplankton morphology. Therefore, qPCR can be a useful alternative for molecular identification and enumeration of phytoplankton. Nonetheless, a comprehensive study is missing which evaluates and compares the feasibility of using qPCR and microscopy to assess phytoplankton in fresh water. This study 1) compared the performance of qPCR and microscopy in identifying and quantifying phytoplankton and 2) evaluated qPCR as a molecular tool to assess phytoplankton and indicate eutrophication. We assessed phytoplankton using both qPCR and microscopy in twelve large freshwater rivers across the United States from early summer to late fall in 2017, 2018, and 2019. qPCR- and microscope-based phytoplankton abundance had a significant positive linear correlation (adjusted R2 = 0.836, p-value < 0.001). Phytoplankton abundance had limited temporal variation within each sampling season and over the three years studied. The sampling sites in the midcontinent rivers had higher phytoplankton abundance than those in the eastern and western rivers. For instance, the concentration (geometric mean) of Bacillariophyta, Cyanobacteria, Chlorophyta, and Dinoflagellates at the sampling sites in the midcontinent rivers was approximately three times that at the sampling sites in the western rivers and approximately 18 times that at the sampling sites in the eastern rivers. Welch's analysis of variance indicates that phytoplankton abundance at the sampling sites in the midcontinent rivers was significantly higher than that at the sampling sites in the eastern rivers (p-value = 0.013) but was comparable to that at the sampling sites in the western rivers (p-value = 0.095). The higher phytoplankton abundance at the sampling sites in the midcontinent rivers was presumably because these rivers were more eutrophic. Indeed, low phytoplankton abundance occurred in oligotrophic or low trophic sites, whereas eutrophic sites had greater phytoplankton abundance. This study demonstrates that qPCR-based phytoplankton abundance can be a useful numerical indicator of the trophic conditions and water quality in freshwater rivers.

Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences

Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.

Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology

Detection of pathogens, parasites, and other symbionts in environmental samples via eDNA/eRNA (collectively eNA) is an increasingly important source of information about their occurrence and activity. There is great potential for using such detections as a proxy for infection of host organisms in connected habitats, for pathogen monitoring and surveillance, and for early warning systems for disease. However, many factors require consideration, and appropriate methods developed and verified, in order that eNA detections can be reliably interpreted and adopted for surveillance and assessment of disease risk, and potentially inclusion in international standards, such as the World Organisation for Animal Health guidelines. Disease manifestation results from host-symbiont-environment interactions between hosts, demanding a multifactorial approach to interpretation of eNA signals.

Plastic-microbe interaction in the marine environment: Research methods and opportunities

Approximately 9 million metric tons of plastics enters the ocean annually, and once in the marine environment, plastic surfaces can be quickly colonised by marine microorganisms, forming a biofilm. Studies on plastic debris-biofilm associations, known as plastisphere, have increased exponentially within the last few years. In this review, we first briefly summarise methods and techniques used in exploring plastic-microbe interactions. Then we highlight research gaps and provide future research opportunities for marine plastisphere studies, especially, on plastic characterisation and standardised biodegradation tests, the fate of "environmentally friendly" plastics, and plastisphere of coastal habitats. Located in the tropics, Southeast Asian (SEA) countries are significant contributors to marine plastic debris. However, plastisphere studies in this region are lacking and therefore, we discuss how the unique environmental conditions in the SEA seas may affect plastic-microbe interaction and why there is an imperative need to conduct plastisphere studies in SEA marine environments. Finally, we also highlight the lack of understanding of the pathogenicity and ecotoxicological effects of plastisphere on marine ecosystems.

Monochloramine Induces Release of DNA and RNA from Bacterial Cells: Quantification, Sequencing Analyses, and Implications

Monochloramine (MCA) is a widely used secondary disinfectant to suppress microbial growth in drinking water distribution systems. In monochloraminated drinking water, a significant amount of extracellular DNA (eDNA) has been reported, which has many implications ranging from obscuring DNA-based drinking water microbiome analyses to posing potential health concerns. To address this, it is imperative for us to know the origin of the eDNA in drinking water. Using Pseudomonas aeruginosa as a model organism, we report for the first time that MCA induces the release of nucleic acids from both biofilms and planktonic cells. Upon exposure to 2 mg/L MCA, massive release of DNA from suspended cells in both MilliQ water and 0.9% NaCl was directly visualized using live cell imaging in a CellASIC ONIX2 microfluidic system. Exposing established biofilms to MCA also resulted in DNA release from the biofilms, which was confirmed by increased detection of eDNA in the effluent. Intriguingly, massive release of RNA was also observed, and the extracellular RNA (eRNA) was also found to persist in water for days. Sequencing analyses of the eDNA revealed that it could be used to assemble the whole genome of the model organism, while in the water, certain fragments of the genome were more persistent than others. RNA sequencing showed that the eRNA contains non-coding RNA and mRNA, implying its role as a possible signaling molecule in environmental systems and a snapshot of the past metabolic state of the bacterial cells.

The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA

In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Simple Summary

The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance.

Abstract

The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.