Marine particle size-fractionation indicates organic matter is processed by differing microbial communities on depth-specific particles.

Passive sinking flux of particulate organic matter in the ocean plays a central role in the biological carbon pump and carbon export to the ocean's interior. Particle-associated microbes colonize particulate organic matter, producing "hotspots" of microbial activity. We evaluated variation in particle-associated microbial communities to 500 m depth across four different particle size fractions (0.2-1.2, 1.2-5, 5-20, >20 µm) collected using in situ pumps at the Bermuda Atlantic Time-series Study site. In situ pump collections capture both sinking and suspended particles, complementing previous studies using sediment or gel traps, which capture only sinking particles. Additionally, the diagenetic state of size-fractionated particles was examined using isotopic signatures alongside microbial analysis. Our findings emphasize that different particle sizes contain distinctive microbial communities, and each size category experiences a similar degree of change in communities over depth, contradicting previous findings. The robust patterns observed in this study suggest that particle residence times may be long relative to microbial succession rates, indicating that many of the particles collected in this study may be slow sinking or neutrally buoyant. Alternatively, rapid community succession on sinking particles could explain the change between depths. Complementary isotopic analysis of particles revealed significant differences in composition between particles of different sizes and depths, indicative of organic particle transformation by microbial hydrolysis and metazoan grazing. Our results couple observed patterns in microbial communities with the diagenetic state of associated organic matter and highlight unique successional patterns in varying particle sizes across depth.

Impacts of water treatments on bacterial communities of biofilm and loose deposits in drinking water distribution systems.

Treated drinking water is delivered to customers through drinking water distribution systems (DWDSs). Although studies have focused on exploring the microbial ecology of DWDSs, knowledge about the effects of different water treatments on the bacterial community of biofilm and loose deposits in DWDS is limited. This study assessed the effects of additional treatments on the bacterial communities developed in 10 months' old pilot DWDSs. The results showed a similar bacterial community in the pipe-wall biofilm, which was dominated by Novosphingobium spp. (20-82 %) and Sphingomonas spp. (11-53 %), regardless of the treatment applied. The bacterial communities that were retained in the distribution systems (including pipe-wall biofilm and loose deposits) were similar to the particle-associated bacteria (PAB) in the corresponding supply water. The additional treatments showed clear effects of the removal and/or introduction of particles. The genera Aeromonas spp., Clostridium spp., Legionella spp., and Pseudomonas spp., which contain opportunistic pathogenic species, were only detected among the PAB in ion exchange system. Our study demonstrated that the biofilm community is consistent across treatments, and the contribution from bacteria in loose deposits is important but can be controlled by removing particles. These findings offer more insight into the origin and development of microbial ecology in DWDSs and suggest paths for further research on the possibility of managing the microbial ecology in distribution systems.

Deciphering the pathogenic risks of microplastics as emerging particulate organic matter in aquatic ecosystem.

Microplastics are accumulating rapidly in aquatic ecosystems, providing habitats for pathogens and vectors for antibiotic resistance genes (ARGs), potentially increasing pathogenic risks. However, few studies have considered microplastics as particulate organic matter (POM) to elucidate their pathogenic risks and underlying mechanisms. Here, we performed microcosm experiments with microplastics and natural POM (leaves, algae, soil), thoroughly investigating their distinct effects on the community compositions, functional profiles, opportunistic pathogens, and ARGs in Particle-Associated (PA) and Free-Living (FL) bacterial communities. We found that both microplastics and leaves have comparable impacts on microbial community structures and functions, enriching opportunistic pathogens and ARGs, which may pose potential environmental risks. These effects are likely driven by their influences on water properties, including dissolved organic carbon, nitrate, DO, and pH. However, microplastics uniquely promoted pathogens as keystone species and further amplified their capacity as hosts for ARGs, potentially posing a higher pathogenic risk than natural POM. Our research also emphasized the importance of considering both PA and FL bacteria when assessing microplastic impacts, as they exhibited different responses. Overall, our study elucidates the role and underlying mechanism of microplastics as an emerging POM in intensifying pathogenic risks of aquatic ecosystems in comparison with conventional natural POM.

Preserved particulate organic carbon is likely derived from the subsurface sulfidic photic zone of the Proterozoic Ocean: evidence from a modern, oxygen-deficient lake.

Biological processes in the Proterozoic Ocean are often inferred from modern oxygen-deficient environments (MODEs) or from stable isotopes in preserved sediment. To date, few MODE studies have simultaneously quantified carbon fixation genes and attendant stable isotopic signatures. Consequently, how carbon isotope patterns reflect these pathways has not been thoroughly vetted. Addressing this, we profiled planktonic productivity and quantified carbon fixation pathway genes and associated organic carbon isotope values (δ13 CPOC ) of size-fractionated (0.2-2.7 and >2.7 µm) particulate matter from meromictic Fayetteville Green Lake, NY, USA. The high-O2 Calvin-Benson-Bassham (CBB) gene (cbbL) was most abundant in the <2.7 µm size fraction in shallow oxic and deep hypoxic waters, corresponding with cyanobacterial and eukaryote algal populations. The low-O2 CBB gene (cbbM) was most abundant near the lower oxycline boundary in the larger size fraction, coincident with purple sulfur bacteria populations. The reverse citric acid cycle gene (aclB) was equally abundant in both size fractions in the deepest photic zone, coinciding with green sulfur bacteria populations. Methane coenzyme reductase A (mcrA), of anaerobic methane cyclers, was most abundant at the lower oxycline boundary in both size fractions, coinciding with Methanoregula populations. δ13 CPOC values overlapped with the high-O2 CBB fixation range except for two negative excursions near the lower oxycline boundary, likely reflecting assimilation of isotopically-depleted groundwater-derived carbon by autotrophs and sulfate-reducers. Throughout aphotic waters, δ13 CPOC values of the large size fraction became 13 C-enriched, likely reflecting abundant purple sulfur bacterial aggregates. Eukaryote algae- or cyanobacteria-like isotopic signatures corresponded with increases in cbbL, cbbM, and aclB, and enrichment of exopolymer-rich prokaryotic photoautotrophs aggregates. Results suggest that δ13 CPOC values of preserved sediments from areas of the Proterozoic Ocean with sulfidic photic zones may reflect a mixture of alternate carbon-fixing populations exported from the deep photic zone, challenging the paradigm that sedimentary stable carbon isotope values predominantly reflect oxygenic photosynthesis from surface waters.

Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland.

Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.

Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River.

As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6')-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.

Metagenome-assembled genomes from particle-associated microbial communities in the mesopelagic zone of the Pacific Ocean.

We report 10 particle-associated metagenome-assembled genomes (MAGs) from the mesopelagic zone of Pacific Ocean seawaters. MAGs comprise members of Flavobacteria Halomonas, Blastomonas, Brevundimonas, Alteromonas, Shingomonas, Sphingopyxis, Tabrizicola, Proteobacteria, and Gammaproteobacteria. Functional annotation suggests that these bacteria are involved in central particulate organic carbon conversion, nitrogen cycling, and phosphorus cycling.

Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard).

Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3+) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.

Service-lines as major contributor to water quality deterioration at customer ends.

Biofilm detachment contributes to water quality deterioration. However, the contributions of biofilm detachment from different pipes have not been quantified or compared. Following the introduction of partial reverse osmosis (RO) in drinking water production, this study analyzed particles at customers' ends and tracked their origins to water distribution mains and service lines. For doing so, filter bags were installed in front of water meters to capture upstream detached particles, while biofilm from water main and service line were sampled by cutting pipe specimens. The results showed that elemental concentrations of the biofilm in mains were higher than those of service lines (54.3-268.5 vs. 27.1-44.4 µg/cm2), both dominated by Ca. Differently, filter bags were dominated by Fe/Mn (77.5-98.1%). After introducing RO, Ca significantly decreased in biofilms of mains but not service lines, but the released Fe/Mn rather than Ca arrived at customers' ends. The ATP concentrations of service lines were higher than mains, which decreased on mains but increased in service lines after introducing RO. For the core ASVs, 13/24 were shared by service lines (17), mains (21), and filter bags (17), which were assigned mainly to Nitrospira spp., Methylomagnum spp., Methylocytis spp., and IheB2-23 spp. According to source tracking results, service lines contributed more than mains to the particulate material collected by filter bags (57.6 ± 13.2% vs. 13.0 ± 11.6%). To the best of our knowledge, the present study provides the first evidence of service lines' direct and quantitative contributions to potential water quality deterioration at customers' ends. This highlights the need for the appropriate management of long-neglected service line pipes, e.g., regarding material selection, length optimization, and proper regulation.

Monitoring bacterial composition and assemblage in the Gulf of Corcovado, southern Chile: Bacteria associated with harmful algae.

Harmful Algal Blooms (HABs) have caused damage to the marine environment in Isla San Pedro in the Gulf of Corcovado, Chile. While rising water temperature and artificial eutrophication are the most discussed topics as a cause, marine bacteria is a recent attractive parameter as an algal bloom driver. This study monitored algal and bacterial compositions in the water of Isla San Pedro for one year using microscopy and 16S rRNA metabarcoding analysis, along with physicochemical parameters. The collected data were analyzed with various statistical tools to understand how the particle-associated bacteria (PA) and the free-living (FL) bacteria were possibly involved in algal blooms. Both FL and PA fractions maintained a stable bacterial composition: the FL fraction was dominated by Proteobacteria (α-Proteobacteria and γ-Proteobacteria), and Cyanobacteria dominated the PA fraction. The two fractions contained equivalent bacterial taxonomic richness (c.a. 8,000 Operational Taxonomic Units) and shared more than 50% of OTU; however, roughly 20% was exclusive to each fraction. The four most abundant algal genera in the Isla San Pedro water were Thalassiosira, Skeletonema, Chaetoceros, and Pseudo-nitzchia. Statistical analysis identified that the bacterial species Polycyclovorans algicola was correlated with Pseudo-nitzschia spp., and our monitoring data recorded a sudden increase of particle-associated Polycyclovorans algicola shortly after the increase of Pseudo-nitzschia, suggesting that P. algicola may have regression effect on Pseudo-nitzschia spp. The study also investigated the physicochemical parameter effect on algal-bacterial interactions. Oxygen concentration and chlorophyll-a showed a strong correlation with both FL and PA bacteria despite their assemblage differences, suggesting that the two groups had different mechanisms for interacting with algal species.

Fine-Scale Structuring of Planktonic Vibrio spp. in the Chinese Marginal Seas.

Vibrio is ubiquitous in marine environments with high metabolism flexibility and genome plasticity. Studies have investigated the ecological distribution of Vibrio spp. in several narrow zones, but a broad scale pattern of distribution and community assembly is still lacking. Here, we elucidated the distribution of Vibrio spp. in seawater along the Chinese marginal seas with a high spatial range. Comparison of Vibrio abundance between 3- and 0.2-µm-pore-size membranes showed distinction in preferential lifestyle. Vibrio spp. in the Yellow Sea (YS) was low in abundance and adopted a particle-associated lifestyle, whereas that in the East China Sea (ECS) and South China Sea (SCS) was more abundant and was likely in a temporary free-living state as a strategy to cope with nutrient limitation. Vibrio community compositions were also separated by sampling area, with different dominant groups in YS (Vibrio chagasii and Vibrio harveyi), ECS and SCS (Vibrio japonicus and V. chagasii). The community niche breadth was significantly wider in ECS and SCS than that of YS. Among species, V. chagasii and V. harveyi had the largest niche breadths likely reflecting strong competitive positions. Stochastic processes played important roles in shaping the geographical pattern of the vibrionic community. Environmental selection (e.g., temperature, salinity, and dissolved oxygen) had a much greater impact on the community in surface than in bottom water. The large proportions of unexplained variations (78.9%) imply complex mechanisms in their community assembly. Our study provides insights into the spatial distribution patterns and underlying assembly mechanisms of Vibrio at a broad spatial scale. IMPORTANCE Vibrio spp. may exert large impacts on biogeochemical cycling in coastal habitats, and their ecological importance has drawn increasing attention. Here, we investigated the spatial distribution pattern and community assembly of Vibrio populations along the Chinese marginal seas, spanning a wide spatial scale. Our results showed that the abundances of the Vibrio population increased with decreasing latitude and their preferential lifestyle differed among adjacent coastal areas. The compositions of Vibrio spp. were also separated by geographical location, which was mainly attributable to stochastic processes. Overall, this work contributes to the understanding of the ecological distribution patterns and the community assembly mechanisms of marine vibrios at a high spatial range. The large proportion of unexplained variations indicates the existence of complex mechanisms in the assembly of vibrionic community which should be considered comprehensively in future.

Stochastic processes shape the aggregation of free-living and particle-attached bacterial communities in the Yangtze River Estuary, China.

An estuary plays an important role in material and energy exchange between the land and sea, where complex physical, chemical, and biological processes occur. Here, we investigated the assembly processes of free-living (FL) and particle-associated (PA) bacterial communities in two seawater layers at five stations in the Yangtze River Estuary (YRE) by using 16S rRNA sequencing methods. The results indicated that Proteobacteria was the most abundant phylum in the YRE. The α-diversity of PA community was significantly higher than FL community, and analysis of similarity showed significantly different (Global R = 0.2809, p < 0.005). RDA revealed that phosphate (PO4 3- ) was significantly correlated with PA bacterial community abundance (p < 0.05). An ecological null model showed that both PA and FL bacterial communities were mainly influenced by stochastic processes (PA: 100%, FL: 70%), which PA attached to nutrient particles and are less affected by environmental filtration. Dispersal limitation (50%) was the main assembly process of the PA community, while homogeneous selection (30%) and drift (30%) were important processes in the FL community assembly. The available substrate for colonization limits the transformation from FL to PA bacteria. This study would improve our understanding of FL and PA bacterial community structure and factors affecting assembly process in estuarine environments.

Salinity and seasonality shaping free-living and particle-associated bacterioplankton community assembly in lakeshores of the northeastern Qinghai-Tibet Plateau.

Microorganisms in lakeshore zones are essential for pollution interception and biodiversity maintenance. However, the biogeographic patterns of bacterioplankton communities in lakeshore zones and the mechanisms that driving them are poorly understood. We analyzed the 16 S rRNA gene sequences of particle-associated (PA) and free-living (FL) bacterioplankton communities in the lakeshore zones of 14 alpine lakes in two seasons on Qinghai-Tibet Plateau to investigate the bacterial diversity, composition and assembly processes. Our results revealed that PA and FL bacterioplankton communities were driven by both seasonality and salinity in the lakeshores on Qinghai-Tibet Plateau. Compared to FL bacterioplankton, PA bacterioplankton communities were more susceptible to seasonality than spatial salinity. FL bacterioplankton communities were more salinity constrained than the PA counterpart. Besides, the Stegen null model analyses have validated a quantitative bias on stochastic processes at different spatial scales. At a regional scale, stochasticity was the predominant assembly process in both PA and FL bacterioplankton. While at a subregional scale, dispersal limitation was the main contributor of stochastic processes for PA bacterioplankton in summer and heterogeneous selection was the dominant deterministic processes in winter, whereas the community assembly of FL bacterioplankton was more stochastic processes (i.e., dispersal limitation) dominated in the freshwater type but deterministic process (i.e., heterogeneous selection) increased with increasing salinity. Our study provides new insights into both significant spatiotemporal patterns and distinct assembly processes of PA and FL bacterioplankton in alpine lakeshores on the northeastern Qinghai-Tibet Plateau.

Capturing and tracing the spatiotemporal variations of planktonic and particle-associated bacteria in an unchlorinated drinking water distribution system.

The aperiodic changes in the quantity and community of planktonic and particle-associated bacteria have hampered the understanding and management of microbiological water quality in drinking water distribution systems. In this study, online sampling was combined with the microbial fingerprint-based SourceTracker2 to capture and trace the spatiotemporal variations in planktonic and particle-associated bacteria in an unchlorinated distribution system. The results showed that spatially, the particle load significantly increased, while in contrast, the quantity of particle-associated bacteria decreased sharply from the treatment plant to the distribution network. Similar to the trend of particle-associated bacterial diversity, the number of observed OTUs first slightly decreased from the treatment plant to the transportation network and then sharply increased from the transportation network to the distribution network. The SourceTracker2 results revealed that the contribution of particle-associated bacteria from the treatment plant decreased along the distribution distance. The spatial results indicate the dominant role of sedimentation of particles from the treatment plant, while the observed increases in particles and the associated bacteria mainly originated from the distribution network, which were confirmed directly by the increased contributions of loose deposits and biofilm. Temporally, the daily peaks of particle-associated bacterial quantity, observed OTU number, and contributions of loose deposits and biofilms were captured during water demand peaks (e.g., 18-21 h). The temporal results reveal clear linkages between the distribution system harboring bacteria (e.g., within loose deposits and biofilms) and the planktonic and particle-associated bacteria flowing through the distribution system, which are dynamically connected and interact. This study highlights that the spatiotemporal variations in planktonic and particle-associated bacteria are valuable and unneglectable for the widely on-going sampling campaigns required by water quality regulations and/or drinking water microbiological studies.

Flow cytometric assessment of the chlorine/chloramine efficacy of particle-associated bacteria in drinking water.

Chlorine and chloramine are widely used to maintain the microbial safety after drinking water treatment plants. Particles existing in the treated water may react with these chemical disinfectants, and impact the efficacy of disinfection. However, the protective effects of particles without-disinfectant demand on bacteria in the chlorination/chloramination are not well known. In this study, two laboratory-derived bacteria (Staphylococcus aureus and Escherichia coli) and two no-disinfectant demand particles (Fe2O3 and kaolin) in drinking water were selected to build particle-associated bacteria (PAB) systems, and their resistance to chlorine/chloramine was further assessed. Flow cytometry (FCM) was employed to image PAB systems and assess the removal rate of bacteria. The results were that particles showed protective effects on bacteria in half of chlorine experiments and 90% of chloramination. The protection was related to the combination form of particles and bacteria tied to neither particle species nor size, and there was no positive relationship between the protection effect and water turbidity. S. aureus attached to Fe2O3 had stronger resistance than kaolin, and kaolin protected E. coli better than Fe2O3. The same trend was observed in both chemical disinfectants, and more significant resistance had been shown in chloramination than chlorination. FCM images which gave a qualitative description on the combination states of different PAB systems may be a clue to explain the strength of the resistance. Environmental bacterial strains and particles are recommended in the future to explore practical applications.

Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea.

Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities' driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.

Spatially resolved assembly, connectivity and structure of particle-associated and free-living bacterial communities in a high Arctic fjord.

The assembly processes that underlie the composition and connectivity of free-living (FL) and particle-associated (PA) bacterial communities from surface to deep waters remain little understood. Here, using phylogenetic null modeling, we quantify the relative influence of selective and stochastic mechanisms that assemble FL and PA bacterial communities throughout the water column in a high Arctic fjord. We demonstrate that assembly processes acting on FL and PA bacterial communities are similar in surface waters, but become increasingly distinct in deep waters. As depth increases, the relative influence of homogeneous selection increases for FL but decreases for PA communities. In addition, dispersal limitation and variable selection increase with depth for PA, but not for FL communities, indicating increased residence time of taxa on particles and less frequent decolonization. As a consequence, beta diversity of PA communities is greater in bottom than in surface waters. The limited connectivity between these communities with increasing depth leads to highly distinct FL and PA bacterial communities in bottom waters. Finally, depth-related trends for FL and PA beta diversity and connectivity in this study are consistent with previous observations in the open ocean, suggesting that assembly processes for FL and PA bacterial communities may also be distinct in other aquatic environments.

Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria.

Marine heterotrophic microorganisms remineralize about half of the annual primary production, with the microbiomes on and around algae and particles having a major contribution. These microbiomes specifically include free-living chemotactic and particle-attached bacteria, which are often difficult to analyze individually, as the standard method of size-selective filtration only gives access to particle-attached bacteria. In this study, we demonstrated that particle collection in Imhoff sedimentation cones enriches microbiomes that included free-living chemotactic bacteria and were distinct from particle microbiomes obtained by filtration or centrifugation. Coastal seawater was collected during North Sea phytoplankton spring blooms, and the microbiomes were investigated using 16S rRNA amplicon sequencing and fluorescence microscopy. Enrichment factors of individual operational taxonomic units (OTUs) were calculated for comparison of fractionated communities after separation with unfractionated seawater communities. Filtration resulted in a loss of cells and yielded particle fractions including bacterial aggregates, filaments, and large cells. Centrifugation had the lowest separation capacity. Particles with a sinking rate of >2.4 m day-1 were collected in sedimentation cones as a bottom fraction and enriched in free-living chemotactic bacteria, i.e., Sulfitobacter, Pseudoalteromonas, and Vibrio. Subfractions of these bottom fractions, obtained by centrifugation, showed enrichment of either free-living or particle-attached bacteria. We identified five distinct enrichment patterns across all separation techniques: mechano-sensitive and mechano-stable free-living bacteria and three groups of particle-attached bacteria. Simultaneous enrichment of particle-attached and chemotactic free-living bacteria in Imhoff sedimentation cones is a novel experimental access to these groups providing more insights into the diversity, structure, and function of particle-associated microbiomes, including members of the phycosphere.

Potential of coagulation to remove particle-associated and free-living antibiotic resistome from wastewater.

Coagulation has been accepted as a cost-effective and environmental-friendly method to remove pollutants. In our recent work, two coagulants of polyaluminum chloride (PAC) and polyaluminum ferric chloride (PAFC) with dosage gradients, and one coagulant aid of anionic polyacrylamide (PAM) were used to investigate their potential to remove particle-associated (PA) and free-living (FL) ARGs and MGEs detected by high throughput qPCR (HT-qPCR) method. The results indicated that the maximum removal efficiencies of PA- and FL-ARGs (4.67- and 3.18-logs) were obtained at the PAFC dosage of 50.0 mg/L. Excessive PAFC dosage can hamper the removal of size-fractionated ARGs. As PAC aid, anionic PAM (1.0 mg/L) had limited effects to promote the removal of PA-ARG, while FL-ARG removal was enhanced by 0.34 log at the PAC dosage of 50.0 mg/L. The fitted curves suggested that the optimal chemical dosages of PAC, PAFC and PAC coupled with PAM in the removal of total ARGs and MGEs were 40.5, 64.7 and 50.0 mg/L, respectively. In addition, we found that much more coagulants were needed to remove FL-ARGs compared to that of PA-ARGs. The removal efficiencies of size-fractionated ARGs by flocculation can be affected by coagulant type, dosage, coagulant aid, Zeta potential and microorganism lifestyle (PA or FL).

Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants.

Serious concerns have been raised regarding antibiotic resistance genes (ARGs) with respect to their potential threat to human health. Wastewater treatment plants (WWTPs) have been considered to be hotspots for ARGs. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) was used to profile size-dependent ARGs and mobile genetic elements (MGEs) divided by particle-associated (PA) assemblages (>3.0-µm), free-living (FL) bacteria (0.2 - 3.0-µm) and cell-free (CF) DNA (< 0.2-µm) in two full-scale WWTPs (plants A and B) and a receiving stream. The results revealed that FL-ARGs were predominant in WWTPs and the receiving stream, especially in the final effluent of both plants. More than 40 types of CF-ARGs and CF-MGEs were detected with absolute abundances ranging from 6.0 ± 0.7 × 105 to 1.0 ± 0.2 × 108 copies/mL in wastewater, and relatively high abundances were also detected in the final effluent of the two plants, suggesting that CF-ARGs were important sources spreading from the WWTPs to the receiving environment. Plant A exhibited higher log-removal of size-fractionated ARGs and MGEs than was observed for plant B, which was attributed to the enhanced settleability of PA assemblages and FL bacteria by additional macrophytes and chemical coagulants. Ultraviolet disinfection had limited effects on ARGs and MGEs of the PA and FL fractions, which was probably ascribed to the protective matrices of the particles and cell walls. The bacterial communities of the two plants were significantly different among the size fractions (p < 0.01). The variation partitioning analysis (VPA) indicated that the microbial community structures and MGEs contributed a variation of 68.2% in total to the relative abundance changes of size-fractionated ARGs. Procrustes analyses and Mantel tests showed that the relative abundances of ARGs were significantly correlated with bacterial community structures. These results suggested that the bacterial community structures and MGEs might have been the main drivers of the size-fractionated ARG disseminations. This study provides novel insights into size-fractionated ARGs and MGEs in full-scale WWTPs and may lead to the identification of key targets to control the spread of ARGs.