Biomass acid pretreatment impacts on metabolic routes and bacterial composition of dark fermentation process

Complex organic matter represents a suitable substrate to produce hydrogen through dark fermentation (DF) process. To increase H2 yields, pretreatment technology is often required. The main objective of the present work was to investigate thermo-acid pretreatment impact on sugar solubilization and biotic parameters of DF of sorghum or organic fraction of municipal solid waste (OFMSW). Biochemical hydrogen potential tests were carried out without inoculum using raw or thermo-acid pretreated substrates. Results showed an improvement in sugar solubilization after thermo-acid pretreatments. Pretreatments led to similar DF performances (H2 and total metabolite production) compared to raw biomasses. Nevertheless, they were responsible for bacterial shifts from Enterobacteriales towards Clostridiales and Bacillales as well as metabolic changes from acetate towards butyrate or ethanol. The metabolic changes were attributed to the biomass pretreatment impact on indigenous bacteria as no change in the metabolic profile was observed after performing thermo-acid pretreatments on irradiated OFMSW (inactivated indigenous bacteria and inoculum addition). Consequently, acid pretreatments were inefficient to improve DF performances but led to metabolic and bacterial community changes due to their impact on indigenous bacteria.

Deciphering the removal of antibiotics and the antibiotic resistome from typical hospital wastewater treatment systems

Hospital wastewater treatment systems (HWTSs) are a significant source and reservoir of antibiotic resistance genes (ARGs) and a crucial hub for transmitting ARGs from clinical to natural environments. However, there is a lack of research on the antibiotic resistome of clinical wastewater in HWTSs. In this study, we used metagenomics to analyze the prevalence and abundance of ARGs in five typical HWTSs. A total of 17 antibiotics from six categories were detected in the five HWTSs; β-lactam antibiotics were found at the highest concentrations, with up to 4074.08 ng·L-1. We further found a total of 21 ARG types and 1106 subtypes of ARGs with the highest percentage of multi-drug resistance genes (evgS, msbA, arlS, and baeS). The most abundant last-resort ARGs were mcr, which were detected in 100 % of the samples. HWTSs effluent is a major pathway for the transmission of last-resort ARGs into urban wastewater networks. The removal of antibiotics, antibiotic-resistant bacteria, and ARGs from HWTSs was mainly achieved by tertiary treatment, i.e., chlorine disinfection, but antibiotics and ARGs were still present in the HWTSs effluent or even increased after treatment. Moreover, antibiotics and heavy metals (especially mercury) in hospital effluents can exert selective pressure for antibiotic resistance, even at low concentrations. Qualitative analyses based on metagenome-assembled genome analysis revealed that the putative hosts of the identified ARGs are widely distributed among Pseudomonas, Acidovorax, Flavobacterium, Polaromonas, and Arcobacter. Moreover, we further assessed the clinical availability of ARGs and found that multidrug ARGs had the highest clinical relevance values. This study provides new impulses for monitoring and removing antibiotics and ARGs in the hospital sewage treatment process.

Geographic distribution of bacterial communities of inland waters in China

Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.

Bacterial microbiota shifts in vacuum-packed beef during storage at different temperatures: Impacts on blown pack spoilage

We aimed to evaluate the bacterial growth and diversity in vacuum-packed beef bags stored at different temperatures and to monitor blown-pack spoilage. We used culture-based methods and high-throughput sequencing to study the development of the main bacterial groups naturally present in beef stored at 4 and 15 °C for 28 days. The growth of sulfite-reducing clostridium (SRC) was impaired in beef bags stored at 4 °C; significant differences among SRC counts were observed in beef bags stored at 4 and 15 °C on days 14, 21, and 28 (P = 0.001). Blown pack was observed in most beef bags stored at 15 °C, from day 14 to day 28, but not in beef bags stored at 4 °C. A storage temperature of 4 °C was able to maintain a stable bacterial microbiota (most prevalent: Photobacterium, Hafnia-Obesumbacterium, and Lactococcus). Remarkable changes in microbial abundance occurred at 15 °C from day 14 to day 28, with a predominance of strict anaerobes (Bacteroides) and the presence of Clostridium spp. The relative frequencies of strict anaerobes and Clostridium were statistically higher in the beef bags stored at 15 °C (P < 0.001 and P = 0.004, respectively). The temperature influenced the microbial counts and relative abundance of spoilage bacteria, leading to blown pack spoilage.

The biocontrol potentials of rhizospheric bacterium Bacillus velezensis K0T24 against mulberry bacterial wilt disease

Mulberry bacterial wilt disease, caused by Ralstonia pseudosolanacearum, is a devastating soil-borne disease in the silk-mulberry-related industry. In this study, through high-throughput sequencing, we compared the rhizosphere bacterial composition of the mulberry-resistant cultivar (K10) and susceptible cultivar (G12), confirming Bacillus as a genus-level biomarker for K10. Next, twelve Bacillus spp. isolates, derived from the rhizosphere of K10, were screened for their antagonistic activity against R. pseudosolanacearum. The isolate showing strong antagonism was identified as B. velezensis K0T24 and selected for further analysis. The fermentation supernatant of B. velezensis K0T24 significantly inhibited the growth of R. pseudosolanacearum (82.47%) and the expression of its pathogenic genes. Using B. velezensis K0T24 in mulberry seedlings also increased defense enzyme activities and achieved a control efficacy of up to 55.17% against mulberry bacterial wilt disease. Collectively, our findings demonstrate the potential of B. velezensis K0T24 in suppressing mulberry bacterial wilt disease.

Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil

Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.

Antibiotics and antibiotic resistance change bacterial community compositions in marine sediments

Emerging contaminants, including antibiotics, antibiotic-resistant bacteria (ARB), and extracellular antibiotic resistance genes (eARGs), have been detected in large numbers in the aquatic environment. The effects of emerging contaminants on bacterial communities in marine sediments are not well studied. In this study, the effects of emerging contaminants (antibiotics, ARB, and eARGs) on the variations of bacterial populations in marine sediments of the Bohai Sea, Yellow Sea, East China Sea, and South China Sea were investigated. The results showed that the abundance of the host bacterial phylum Probacteria in the marine sediments of the Bohai Sea was the lowest among the four seas after exposure to different antibiotics, ARB, and eARGs. The inputs of exogenous antibiotics and resistance genes significantly affected the community function, resulting in significant differences in community abundance at the genus level. The abundance of Halomonas, Sulfitobacter, and Alcanivorax in the four sea areas displayed noteworthy differences in response to the addition of exogenous antibiotics and eARGs. These findings contribute to a more comprehensive understanding of the intricate interplay between emerging contaminants and the dynamics of bacterial communities in natural ecosystems.

Temporal dynamics of bacterial colonization on five types of microplastics in a freshwater lake

Microplastics (MPs), as a new substrate, provide a unique niche for microbial colonization in the freshwater ecosystems; however, the impacts of long-term MP exposure on colonized bacteria are still unclear. In this study, five MP types were exposed in a freshwater lake for approximately one year, and the MP particles, together with the surrounding water, were collected on days 60, 150, 250 and 330 during the in situ field experiment. Bacteria on the MP surface, as well as free-living bacteria in the surrounding water, were analyzed to evaluate the temporal dynamics of these bacterial communities. Results show that all five MP types exhibited signs of degradation during the exposure process. Additionally, the alpha diversity, community structure and composition of MP-attached bacteria significantly differed from that of the free-living bacteria in the surrounding water, indicating that the five MP types could provide a preferable niche for bacterial colonization in a freshwater environment. Proteobacteria, Chloroflexi, Verrucomicrobiota, Actinobacteriota and Firmicutes were the top five dominant phyla. Some plastic-degrading bacteria included in these phyla were detected, verifying that MP-attached biofilms had a certain degree of MP degradation potential. Some potentially pathogenic bacteria were also detected, suggesting an ecological threat for spreading disease in the aquatic ecosystem. Furthermore, the bacterial community and some metabolic pathways were significantly affected by the MP type (P < 0.01) and exposure time (P < 0.01), indicating that the presence of MPs not only alters the bacterial community structure and composition, but also influences their potential functional properties in freshwater ecosystems. Multiple factors, including the physicochemical properties related to MPs and the environmental parameters of the surrounding water, affect the community composition and the function of MP-attached bacteria to different degrees. Our findings indicate that the presence of MPs has a potential ecological impact on freshwater ecosystems.

Insight into bacterial role attribution in dissolved organic matter humification during rice straw composting with microbial inoculation

This study aims to investigate the effect of microbial role distribution in microbial carbon pumps on dissolved organic matter (DOM) humification during rice straw composting with microbial inoculation. Three composting groups were designed, named CK (control), B4 (with Bacillus subtilis, OR058594) and Z1 (with Aspergillus fumigatus, AF202956.1). As a result of inoculation, the composition of microbial communities was changed, so that the microorganisms that promoted DOM humification were concentrated in the responders in the microbial carbon pump. DOM was divided into three components in three composting treatments: C1, C2 and C3. After inoculation with Bacillus subtilis, the C2 component was significantly affected, while after inoculation with Aspergillus fumigatus, the C3 component was significantly affected. The results of physicochemical factors affecting the transformation of DOM fluorescence components indicated that C1, C2 and C3 were related to the abundance of the cellulose-degrading enzyme-encoding gene GH7 in CK and B4 composting. However, the C2 was susceptible to organic matter in Z1 composting. This study explored the distribution of microbial communities from a new perspective, which provided new information for analyzing DOM humification and treating agricultural straws to achieve clean conditions for environmental friendliness.

Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters

Rivers are at risk from a variety of pollution sources. Faecal pollution is of particular concern since it disperses pathogenic microorganisms in the aquatic environment. Currently, faecal pollution levels in rivers is monitored using faecal indicator bacteria (FIB) that do not offer information about pollution sources and associated risks. This study used a combined molecular approach, along with measurements of water quality, to gain information on pollution sources, and risk levels, in a newly designated recreational bathing site in the River Wharfe (UK). Physico-chemical parameters were monitored in situ, with water quality multiparameter monitoring sondes installed during the 2021 bathing season. The molecular approach was based on quantitative PCR (qPCR)-aided Microbial Source Tracking (MST) and 16S rRNA gene metabarcoding to obtain a fingerprint of bacterial communities and identify potential bioindicators. The analysis from the water quality sondes showed that ammonium was the main parameter determining the distribution of FIB values. Lower faecal pollution levels were detected in the main river when compared to tributaries, except for samples in the river located downstream of a wastewater treatment plant. The faecal pollution type (anthropogenic vs. zoogenic) changed the diversity and the structure of bacterial communities, giving a distinctive fingerprint that can be used to inform source. DNA-based methods showed that the presence of human-derived bacteria was associated with Escherichia coli spikes, coinciding with higher bacterial diversity and the presence of potential pathogenic bacteria mainly of the genus Mycobacterium, Aeromonas and Clostridium. Samples collected after a heavy rainfall event were associated with an increase in Bacteroidales, which are markers of faecal pollution, including Bacteroides graminisolvens, a ruminant marker associated with surface run-off from agricultural sources. The combined use of qPCR and 16S rRNA sequencing was able to identify pollution sources, and novel bacterial indicators, thereby aiding decision-making and management strategies in recreational bathing rivers.

Influence of rapid vertical mixing on bacterial community assembly in stratified water columns

Water column mixing homogenizes thermal and chemical gradients which are known to define distribution of microbial communities and influence the prevailing biogeochemical processes. Little is however known about the effects of rapid water column mixing on the vertical distribution of microbial communities in stratified reservoirs. To address this knowledge gap, physicochemical properties and microbial community composition from 16 S rRNA amplicon sequencing were analyzed before and after mixing of vertically stratified water-column bioreactors. Our results showed that α-diversity of bacterial communities decreased from bottom to surface during periods of thermal stratification. After an experimental mixing event, bacterial community diversity experienced a significant decrease throughout the water column and network connectivity was disrupted, followed by slow recovery. Significant differences in composition were seen for both total (DNA) and active (RNA) bacterial communities when comparing surface and bottom layer during periods of stratification, and when comparing samples collected before mixing and after re-stratification. The dominant predicted community assembly processes for stratified conditions were deterministic while such processes were less important during recovery from episodic mixing. Water quality characteristics of stratified water were significantly correlated with bacterial community diversity and structure. Furthermore, structural equation modeling analyses showed that changes in sulfur may have the greatest direct effect on bacterial community composition. Our results imply that rapid vertical mixing caused by episodic weather extremes and hydrological operations may have a long-term effect on microbial communities and biogeochemical processes.

Comparative analysis of hydrogen production and bacterial communities in mesophilic and thermophilic consortia using multiple inoculum sources

This study investigates the hydrogen (H2) production performance and bacterial communities in mesophilic (37 °C) and thermophilic (50 °C) H2-producing consortia derived from different inoculum sources and utilizing food waste as a substrate. This study found notable variations in H2 production characteristics among these consortia. Among the mesophilic consortia (MC), the W-MC obtained with wetland (W) as the inoculum source exhibited the highest hydrogen production (3900 mL·L-1 and 117 mL·L-1·h-1), while among the thermophilic consortia (TC), the FP-TC obtained with forest puddle sediment (FP) as the inoculum source showed the highest performance (2112 mL·L-1 and 127 mL·L-1·h-1). This study reveals that the choice of inoculum source plays a crucial role in determining hydrogen production efficiency. Furthermore, the bacterial community analysis demonstrated varying microbial diversity and richness in different inoculum sources. Clostridium, a well-known H2-producing bacterium, was found in both mesophilic and thermophilic consortia and showed a positive correlation with H2 production. Other bacteria, such as Sporanaerobacter, Caproiciproducens, and Caldibacillus, also exhibited significant correlations with H2 production, suggesting their potential roles in the process. The study highlights the complex interactions between bacterial communities and hydrogen production performance, shedding light on the critical factors influencing this renewable energy source. Overall, this study contributes to our understanding of the microbial ecology and the factors affecting hydrogen production in different temperature conditions, which can have practical implications for optimizing biohydrogen production processes using organic waste substrates.

Structures and diversities of bacterial communities in oil-contaminated soil at shale gas well site assessed by high-throughput sequencing

Currently, there is limited understanding of the structures and variabilities of bacterial communities in oil-contaminated soil within shale gas development. The Changning shale gas well site in Sichuan province was focused, and high-throughput sequencing was used to investigate the structures of bacterial communities and functions of bacteria in soil with different degrees of oil pollution. Furthermore, the influences of the environmental factors including pH, moisture content, organic matter, total nitrogen, total phosphorus, oil, and the biological toxicity of the soil on the structures of bacterial communities were analyzed. The results revealed that Proteobacteria and Firmicutes predominated in the oil-contaminated soil. α-Proteobacteria and γ-Proteobacteria were the main classes under the Proteobacteria phylum. Bacilli was the main class in the Firmicutes phylum. Notably, more bacteria were only found in CN-5 which was the soil near the storage pond for abandoned drilling mud, including Marinobacter, Balneola, Novispirillum, Castellaniella, and Alishewanella. These bacteria exhibited resilience to higher toxicity and demonstrated proficiency in oil degradation. The functions including carbohydrate transport and metabolism, energy metabolism, replication, recombination and repair replication, signal transduction mechanisms, and amino acid transport and metabolism responded differently to varying concentrations of oil. The disparities in bacterial genus composition across samples stemmed from a complex play of pH, moisture content, organic matter, total nitrogen, total phosphorus, oil concentration, and biological toxicity. Notably, bacterial richness correlated positively with moisture content, while bacterial diversity showed a significant positive correlation with pH. Acidobacteria exhibited a significant positive correlation with moisture content. Litorivivens and Luteimonas displayed a significant negative correlation with pH, while Rhizobium exhibited a significant negative correlation with moisture content. Pseudomonas, Proteiniphilum, and Halomonas exhibited positive correlations not only with organic matter but also with oil concentration. Total nitrogen exhibited a significant positive correlation with Taonella and Sideroxydans. On the other hand, total phosphorus showed a significant negative correlation with Sphingomonas. Furthermore, Sphingomonas, Gp6, and Ramlibacter displayed significant negative correlations with biological toxicity. The differential functions exhibited no significant correlation with environmental factors but displayed a significant positive correlation with the Proteobacteria phylum. Aridibacter demonstrated a significant positive correlation with cell motility and cellular processes and signaling. Conversely, Pseudomonas, Proteiniphilum, and Halomonas were negatively correlated with differential functions, particularly in amino acid metabolism, carbohydrate metabolism, and membrane transport. Compared with previous research, more factors were considered in this research when studying structural changes in bacterial communities, such as physicochemical properties and biological toxicity of soil. In addition, the correlations of differential functions of communities with environmental factors, bacterial phyla, and genera were investigated.

Dynamics of the benthic and planktic microbiomes in a Planktothrix-dominated toxic cyanobacterial bloom in Australia

Cyanobacterial blooms are a concerning issue that threaten ecosystems, ecology and animal health. Bloom frequency has increased tremendously in recent times due to pollution, eutrophication of waterways, climate change, and changes in microbial community dynamics within the aquatic environment. Information about the spatiotemporal variation in microbial communities that drive a cyanobacterial bloom is very limited. Here, we analysed the spatiotemporal diversity and composition of bacterial communities, with a focus on cyanobacteria, during the bloom phase in a natural reservoir in Eastern Australia using high throughput amplicon sequencing. Sampling points and season had no influence on the richness and evenness of microbial communities during the bloom period, however some compositional differences were apparent across the seasons. Cyanobacteria were highly abundant during summer and autumn compared to winter and spring. The dominant cyanobacterial taxa were Planktothrix, Cyanobium and Microcystis and were found to be significantly abundant during summer and autumn. While cyanobacterial abundance soared in summer (25.4 %), dominated by Planktothrix (12.2 %) and Cyanobium (8.0 %), the diversity was highest in autumn (24.9 %) and consisted of Planktothrix (7.8 %), Nodularia (5.3 %), Planktothricoides (4.6 %), Microcystis (3.5 %), and Cyanobium (2.3 %). The strongly correlated non-photosynthetic Gastranaerophilales found in the sediment and water, suggested vertical transmission from the animal gut through faeces. To our knowledge, this is the first report of Planktothrix-driven toxic cyanobacterial bloom in Australia. Our study expands current understanding of the spatiotemporal variation in bacterial communities during a cyanobacterial bloom and sheds light on setting future management strategies for its control.

Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing

Bacterial transcription is not monolithic. Microbes exist in a wide variety of cell states that help them adapt to their environment, acquire and produce essential nutrients, and engage in both competition and cooperation with their neighbors. While we typically think of bacterial adaptation as a group behavior, where all cells respond in unison, there is often a mixture of phenotypic responses within a bacterial population, where distinct cell types arise. A primary phenomenon driving these distinct cell states is transcriptional heterogeneity. Given that bacterial mRNA transcripts are extremely short-lived compared to eukaryotes, their transcriptional state is closely associated with their physiology, and thus the transcriptome of a bacterial cell acts as a snapshot of the behavior of that bacterium. Therefore, the application of single-cell transcriptomics to microbial populations will provide novel insight into cellular differentiation and bacterial ecology. In this review, we provide an overview of transcriptional heterogeneity in microbial systems, discuss the findings already provided by single-cell approaches, and plot new avenues of inquiry in transcriptional regulation, cellular biology, and mechanisms of heterogeneity that are made possible when microbial communities are analyzed at single-cell resolution.

Marine sediments are identified as an environmental reservoir for Escherichia coli: comparing signature-based and novel amplicon sequencing approaches for microbial source tracking

Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.

Biostimulation of indigenous microbes for uranium bioremediation in former U mine water: multidisciplinary approach assessment

Characterizing uranium (U) mine water is necessary to understand and design an effective bioremediation strategy. In this study, water samples from two former U-mines in East Germany were analysed. The U and sulphate (SO42-) concentrations of Schlema-Alberoda mine water (U: 1 mg/L; SO42-: 335 mg/L) were 2 and 3 order of magnitude higher than those of the Pöhla sample (U: 0.01 mg/L; SO42-: 0.5 mg/L). U and SO42- seemed to influence the microbial diversity of the two water samples. Microbial diversity analysis identified U(VI)-reducing bacteria (e.g. Desulfurivibrio) and wood-degrading fungi (e.g. Cadophora) providing as electron donors for the growth of U-reducers. U-bioreduction experiments were performed to screen electron donors (glycerol, vanillic acid, and gluconic acid) for Schlema-Alberoda U-mine water bioremediation purpose. Thermodynamic speciation calculations show that under experimental conditions, U(VI) is not coordinated to the amended electron donors. Glycerol was the best-studied electron donor as it effectively removed 99% of soluble U, 95% of Fe, and 58% of SO42- from the mine water, probably by biostimulation of indigenous microbes. Vanillic acid removed 90% of U, and no U removal occurred using gluconic acid.

Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland

Many factors, including microbiome structure and activity in the drinking water distribution system (DWDS), affect the colonization potential of opportunistic pathogens. The present study aims to describe the dynamics of active bacterial communities in DWDS and identify the factors that shape the community structures and activity in the selected DWDSs. Large-volume drinking water and hot water, biofilm, and water meter deposit samples were collected from five DWDSs. Total nucleic acids were extracted, and RNA was further purified and transcribed into its cDNA from a total of 181 water and biofilm samples originating from the DWDS of two surface water supplies (disinfected with UV and chlorine), two artificially recharged groundwater supplies (non-disinfected), and a groundwater supply (disinfected with UV and chlorine). In chlorinated DWDSs, concentrations of <0.02-0.97 mg/l free chlorine were measured. Bacterial communities in the RNA and DNA fractions were analysed using Illumina MiSeq sequencing with primer pair 341F-785R targeted to the 16S rRNA gene. The sequence libraries were analysed using QIIME pipeline, Program R, and MicrobiomeAnalyst. Not all bacterial cells were active based on their 16S rRNA content, and species richness was lower in the RNA fraction (Chao1 mean value 490) than in the DNA fraction (710). Species richness was higher in the two DWDSs distributing non-disinfected artificial groundwater (Chao1 mean values of 990 and 1 000) as compared to the two disinfected DWDSs using surface water (Chao1 mean values 190 and 460) and disinfected DWDS using ground water as source water (170). The difference in community structures between non-disinfected and disinfected water was clear in the beta-diversity analysis. Distance from the waterworks also affected the beta diversity of community structures, especially in disinfected distribution systems. The two most abundant bacteria in the active part of the community (RNA) and total bacterial community (DNA) belonged to the classes Alphaproteobacteria (RNA 28 %, DNA 44 %) and Gammaproteobacteria (RNA 32 %, DNA 30 %). The third most abundant and active bacteria class was Vampirovibrionia (RNA 15 %), whereas in the total community it was Paceibacteria (DNA 11 %). Class Nitrospiria was more abundant and active in both cold and hot water in DWDS that used chloramine disinfection compared to non-chlorinated or chlorine-using DWDSs. Thirty-eight operational taxonomic units (OTU) of Legionella, 30 of Mycobacterium, and 10 of Pseudomonas were detected among the sequences. The (RT)-qPCR confirmed the presence of opportunistic pathogens in the DWDSs studied as Legionella spp. was detected in 85 % (mean value 4.5 × 104 gene copies/100 ml), Mycobacterium spp. in 95 % (mean value 8.3 × 106 gene copies/100 ml), and Pseudomonas spp. in 78 % (mean value 1.6 × 105 gene copies/100 ml) of the water and biofilm samples. Sampling point inside the system (distance from the waterworks and cold/hot system) affected the active bacterial community composition. Chloramine as a chlorination method resulted in a recognizable community composition, with high abundance of bacteria that benefit from the excess presence of nitrogen. The results presented here confirm that each DWDS is unique and that opportunistic pathogens are present even in conditions when water quality is considered excellent.

Physiological tolerance of black locust (Robinia pseudoacacia L.) and changes of rhizospheric bacterial communities in response to Cd and Pb in the contaminated soil

Woody plants possess great potential for phytoremediation of heavy metal-contaminated soil. A pot trial was conducted to study growth, physiological response, and Cd and Pb uptake and distribution in black locust (Robinia pseudoacacia L.), as well as the rhizosphere bacterial communities in Cd and Pb co-contaminated soil. The results showed that R. pseudoacacia L. had strong physiological regulation ability in response to Cd and Pb stress in contaminated soil. The total chlorophyll, malondialdehyde (MDA), soluble protein, and sulfhydryl contents, as well as antioxidant enzymes (superoxide dismutase, peroxidase, catalase) activities in R. pseudoacacia L. leaves under the 40 mg·kg-1 Cd and 1000 mg·kg-1 Pb co-contaminated soil were slightly altered. Cd uptake in R. pseudoacacia L. roots and stems increased, while the Pb content in the shoots of R. pseudoacacia L. under the combined Cd and Pb treatments decreased in relative to that in the single Pb treatments. The bacterial α-diversity indices (e.g., Sobs, Shannon, Simpson, Ace, and Chao) of R. pseudoacacia L. rhizosphere soil under Cd and Pb stress were changed slightly relative to the CK treatment. However, Cd and Pb stress could significantly (p < 0.05) alter the rhizosphere soil microbial communities. According to heat map and LEfSe (Linear discriminant analysis Effect Size) analysis, Bacillus, Sphingomonas, Terrabacter, Roseiflexaceae, Paenibacillus, and Myxococcaceae at the genus level were notably (p < 0.05) accumulated in the Cd- and/or Pb-contaminated soil. Furthermore, the MDA content was notably (p < 0.05) negatively correlated with the relative abundances of Isosphaeraceae, Gaiellales, and Gemmatimonas. The total biomass of R. pseudoacacia L. was positively (p < 0.05) correlated with the relative abundances of Xanthobacteraceae and Vicinamibacreraceae. Network analysis showed that Cd and Pb combined stress might enhance the modularization of bacterial networks in the R. pseudoacacia L. rhizosphere soil. Thus, the assembly of the soil bacterial communities in R. pseudoacacia L. rhizosphere may improve the tolerance of plants in response to Cd and/or Pb stress.

Diversity, composition and ecological networks of bacterial communities in response to a full cultivation cycle of the seaweed, Gracilariopsis lemaneiformis

Cultivation of the seaweed, Gracilariopsis lemaneiformis, supports environmental bioremediation and the aquaculture economy in coastal ecosystems, and microorganisms play important roles during the cultivation process. In this study, we aimed to understand the response of bacterial communities through a full cultivation cycle of G. lemaneiformis. We analyzed the bacterial communities using 16S rRNA gene amplicon sequencing and defined the environmental factors of 144 water samples from the Nan'ao Island, South China Sea. Community diversity, keystone species and ecological networks of bacterial communities shifted markedly in the cultivation zone largely due to changes in the environmental factors, seaweed biomass and cultivation stages. The bacterial communities at the seaweed zone have lower species richness, more seaweed-associated taxa and simpler but more stable co-occurrence networks compared to the control zone. Persistent microbial groups such as Aquimarina, Formosa, Glaciecola and Marinobacter exhibited a strong association with seaweed during the growth and maturity stages. We describe a conceptual model to summarize the changes in the bacterial community composition, its diversity and the ecological networks in seaweed cultivation zone. Overall, this study provides new perspectives on the dynamic interaction of seaweed cultivation, bacterial communities and environment factors and their potential ecosystem services as observed in the example of the G. lemaneiformis cultivation ecosystem.

Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens

BACKGROUND

Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022.

RESULTS

Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites.

CONCLUSIONS

Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.

Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness

BACKGROUND

Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.

RESULTS

The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.

CONCLUSION

Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.

Characterizing dissolved organic matter and bacterial community interactions in a river network under anthropogenic landcover

Anthropogenic landcover could rise nutrient concentrations and impact the characteristics and bioavailability of dissolved organic matter (DOM) in a river network. Exploring the interactions between DOM and microbials might be conducive to revealing biogeochemistry behaviors of organic matter. In this study, synchronous fluorescence spectra (SFS) with Gaussian band fitting and two-dimensional correlation spectroscopy (2D-COS) were employed to identify DOM fractions and reveal their interactions with bacterial communities. DOM was extracted from a river network under eco-agricultural rural (RUR), eco-residential urban (URB), eco-economical town (TOW), and eco-industrial park (IND) regions in Jiashan Plain of eastern China. The overlapping peaks observed in the SFS were successfully separated into four fractions using Gaussian band fitting, i.e., tyrosine-like fluorescence (TYLF), tryptophan-like fluorescence (TRLF), microbial humic-like fluorescence (MHLF), and fulvic-like fluorescence (FLF) materials. Across all four regions, TRLF (44.79% ± 7.74%) and TYLF (48.09% ± 8.85%) were the dominant components. Based on 2D-COS, variations of TYLF and TRLF were extremely larger than those of FLF in RUR-TOW. However, in URB-IND, the former exhibited lower variations compared to the latter. These suggested that FLF be likely derived continuously from lignin and other residue of terrestrial plant origin along the river network, and TYLF and TRLF be originated discontinuously from domestic wastewater in RUR-TOW. By high-throughput sequenced OTUs, the number of organisms in RUR-TOW could be higher than those in URB-IND, while genes associated with carbohydrate metabolism were lower in former than those in the latter. According to co-occurrence networks, microbes could promote the production of TYLF and TRLF in RUR-TOW. In contrast, microbial communities in URB-IND might contribute to decompose FLF. The obtained results could not only reveal interactions between DOM fractions and bacterial communities in the river network, but this methodology may be applied to other water bodies from different landscapes.

Maize straw application reduced cadmium and increased arsenic uptake in wheat and enhanced the rhizospheric bacterial communities in alkaline-contaminated soil

Many fields where wheat is grown in northern China are co-polluted by arsenic (As) and cadmium (Cd). Thus, remediation of As and Cd-contaminated alkaline soils is crucial for safe wheat production. In this study, a pot experiment was carried out to investigate the impact of 1% and 2% maize straw (MS) incorporation on As and Cd bioavailability, binding forms, uptake by winter wheat (Triticum aestivum L.), and bacterial communities in smelter (SS) and irrigation (IS) alkaline contaminated soils. The results indicated that 2% MS incorporation significantly (p < 0.05) increased bioavailable-As by 37% (SS) and 39% (IS) with no significant change in the bioavailable-Cd in SS2% (31.95%) from 31.95% (SSCK) and IS2% (33.33%) from 32.82% (ISCK). Incorporation of 2% MS increased the grain As concentration from 0.22 mg kg-1 (SSCK) to 0.51 mg kg-1 (SS2%) and from 0.59 mg kg-1 (ISCK) to 0.84 mg kg-1 (IS2%) which is above the acceptable standard of 0.5 mg kg-1 (GB2726-2017). In contrast, the Cd content in grains was maintained at 0.09 (SS1%), 0.04 (SS2%) and 0.03 (IS1%), 0.02 (IS2%) below the acceptable standard of 0.10 mg kg-1 (GB2762-2017). The amendment through dissolved organic carbon mediated As desorption enhanced As transfer to wheat grain, decreasing DTPA-Cd in the soils and its consequent translocation to wheat leaves and grain. The 2% MS incorporation increased the active As fractions, reduced mobile Cd into immobile fractions, and promoted the abundance of Actinobacteria, Bacteroidetes, and Firmicutes in the two soils. These attributes of MS in decreasing the accumulation of Cd in wheat leaves and grains signified its potential as a suitable ingredient for Cd sequestration and food safety in Cd-contaminated soils.

Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil

The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs' abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.

Role of traveling microplastics as bacterial carriers based on spatial and temporal dynamics of bacterial communities

Microplastics (MPs) are considered as distinct substrates for bacterial colonization, they can carry bacterial communities to travel around environments. The bacterial communities on traveling MPs prefer to be gradually consistent with those on local MPs that were always in the same environment, and this process of change in the bacterial communities on traveling MPs was called 'localization'. However, the dynamics of localization process and their influencing factors are still unclear. Therefore, we simulated the MPs migration process along the water flow direction in the estuary. We used quantitative analysis to study the dynamics of bacterial communities on the migrated MPs. We found the localization characteristics depended on the differences between the former and latter environments, as well as the preexisting bacteria. The localization degree was higher when the former and latter environments were similar. In most cases, compared with the first cultivation of pristine MPs, the time for localization was shorter. Moreover, although the entire bacterial communities tended to be localized, the preexisting bacteria on the migrated MPs had selective effects on subsequent bacterial colonization. Furthermore, the preexisting bacteria on MPs could set up the connections with the bacteria that existed at the latter site, and the stability of the entire bacterial communities on the migrated MPs increased with time. Overall, our findings indicated that the localization characteristics of bacterial communities on traveling MPs were related to the precultured time and environmental differences, which were helpful to understand the colonized bacteria transportation and MPs ecological effects.

Spatial distribution of sediment bacterial communities from São Francisco River headwaters is influenced by human land-use activities and seasonal climate shifts

Riverbed sediments are dynamic freshwater environments colonized by a great diversity of microorganisms which play important roles in supporting freshwater ecosystem by performing a vast array of metabolic functions. Recent evidence generated by HTS approaches has revealed that the structure of sediment microbial communities is influenced by natural seasonal variations in water such as temperature or streamflow as well by disturbances caused by local human activities. Here, a spatiotemporal analysis of sediment microbial distribution from São Francisco River headwaters section was conducted using Illumina 16S rRNA-V4 region amplicon sequencing in order to accomplish three major goals: (i) to investigate whether the diversity and composition of bacterial communities accessed in riverbed sediments vary in response to distinct land-use activities; (ii) to estimate whether the diversity patterns vary between the dry and wet seasons; and (iii) to evaluate whether the diversity of bacterial metabolic functions, predicted by PICRUSt2 approach, varies similarly to the estimated taxonomic diversity. Our findings revealed that bacterial communities in the sediment show differences in diversity and taxonomic composition according to the anthropic activities performed in the local environment. However, the patterns in which this taxonomic diversity is spatially structured show differences between the dry and wet seasons. On the other hand, the most changes in predicted bacterial metabolic functions were verified between sediment samples accessed in portions of the river located in protected and unprotected areas. Our findings contributed with new evidence about the impact of typical land-use practices conducted in countryside landscapes from developing countries on riverbed bacterial communities, both in their taxonomic and functional structure.

Exploring the nitrogen fixing strategy of bacterial communities in nitrogen cycling by adding calcium superphosphate at various periods during composting

Chicken manure, as an organic solid waste with a high nitrogen content, generates large amounts of ammonia during composting, which leads to pollution of the surrounding environment, and causes a reduction in the quality of the compost product. Nitrogen is transformed through the nitrogen cycle and bacterial communities are the main contributors to the transformation of the nitrogen cycle. The microbial composition changes dramatically at different stages during composting. Therefore, calcium superphosphate (SSP) was added to compost as a nitrogen-fixing agent to elucidate the strategy and function of the bacterial community involved in the nitrogen cycle. The results showed that the addition of SSP at the initial, high temperature and cooling stages increased the inorganic nitrogen (NH4+-N, NO3--N) content by 51.99 %, 202.72 % and 173.37 % compared to CK, respectively. In addition, nitrogen cycle functional genes (gdh, nifH, pmoA-amoA, hao, nxrA, nirK, napA, nosZ, narG) abundance were determined by real-time qPCR. The nitrogen cycle genetic results showed that SSP addition at high temperature phase resulted in a 62.43 % down-regulation of ammonification genes, while nitrogen fixation and nitrification genes were enhanced. Random forests revealed a shift in the participation strategy of bacterial communities (e.g., Mycobacterium, Izemoplasmatales, Paracoccus, Ruminococcus) within the nitrogen cycle, leading to altered importance rankings despite involvement in different nitrogen cycle pathways. Moreover, Regression analysis and structural equation modelling revealed that SSP addition at high temperature stage stimulated the bacterial community engaged in nitrogen fixation and nitrification, resulting in increased nitrogen accumulation as NO3--N during composting. This paper offers the potential to yield novel scientific insights into the impact of microbially mediated nitrogen transformation processes and reduce gaseous pollution.

Effects of regular zooplankton supplement on the bacterial communities and process performance of biofilm for wastewater treatment

Biofilm processing technologies were widely used for wastewater treatment due to its advantages of low cost and easy management. However, the aging biofilms inevitably decrease the purification efficiency and increase the sludge production, which limited the widely application of biofilms technologies in rural area. In this study, we proposed a novel strategy by introducing high-trophic organisms to prey on low-trophic organisms, and reduce the aged biofilms and enhance treatment efficiencies in rural wastewater treatment. The effect of three typical zooplankton (Paramecium, Daphnia, and Rotifer) supplement on the purification efficiency and biofilm properties in the contact oxidation process were investigated, and the reaction conditions were optimized by an orthogonal experiment. Under optimal conditions, the biofilms weight decreased 67.6%, the oxygen consumption rate of biofilms increased 9.4%, and wastewater treatment efficiency was obviously increased after zooplankton supplement. Microbial sequencing results demonstrated that the zooplankton optimize the contact oxidation process by altering the bacterial genera mainly Diaphorobacter, Thermomonas, Alicycliphilus and Comamonas. This research provides insight into mechanism of the zooplankton supplement in biological contact oxidation process and provides a feasible strategy for improving the rural sewage treatment technology.

The impact of maize straw incorporation on arsenic and cadmium availability, transformation and microbial communities in alkaline-contaminated soils

Increasing evidence of the uncertainty of crop straw returning in heavy metal-contaminated soil is a significant concern. The present study investigated the influence of 1 and 2% maize straws (MS) amendment on As and Cd bioavailability in two different alkaline soils (A-industrial and B-irrigation) after 56 days of ageing. Adding MS to the two soils decreased the pH by 1.28 (A soil) and 1.13 (B soil) and increased the concentration of dissolved organic carbon (DOC) by 54.40 mg/kg (A soil) and 100.00 mg/kg (B soil) during the study period. After 56 days of ageing, the overall NaHCO3-As and DTPA-Cd increased by 40% and 33% (A) and 39% and 41% (B) soils, respectively. The MS additions increased the alteration of As and Cd exchangeable and residual fractions, whereas advanced solid-state 13C nuclear magnetic resonance (NMR) revealed that alkyl C and alkyl O-C-O in A soil and alkyl C, Methoxy C/N-alkyl, and alkyl O-C-O in B soil significantly contributed to the As and Cd mobilisation. Collectively, 16 S rRNA analyses revealed Acidobacteria, Firmicutes, Chloroflexi, Actinobacteria and Bacillus promoted the As and Cd mobilisation following the MS addition, while principle component analysis (PCA) demonstrated that bacterial proliferation significantly influenced MS decomposition, resulting in As and Cd mobilisation in the two soils. Overall, the study highlights the implications of applying MS to As- and Cd-contaminated alkaline soil and offers the framework for conditions to be considered during As- and Cd-remediation efforts, especially when MS is the sole remediation component.

Effect of inoculating thermophilic bacterial consortia on compost efficiency and quality

The objective of this study was to investigate the potential effects of thermophilic bacterial consortia on compost efficiency and quality. The application of bacterial consortia resulted in an earlier onset of the thermophilic period (THP), an increased upper temperature limit, and an extended duration of the THP by 3-5 days compared to the control group (CK). Microbial inoculation significantly improved the efficiency of organic matter degradation, as well as the content of water-soluble nitrogen (WSN) and humic acid-carbon (HAC). In the case of consortium Ⅱ inoculation (T2), the activities of cellobiohydrolase, β-glucosidase, and protease were increased by 81.81 %, 70.13 %, and 74.09 % at the THP respectively compared to CK. During the maturation stage, T2 also exhibited the highest PV, n/PIII, n value (1.33) and HAC content (39.53 mg·g-1), indicating that inoculation of consortium Ⅱ effectively promoted substrate maturity and product quality. Moreover, this inoculation effectively optimized the bacterial communities, particularly the growth of Planococcus, Chelatococcus, and Chelativorans during the composting, which were involved in carbon and nitrogen conversion or HAC synthesis. Carbohydrate and amino acid metabolism, and membrane transport were predominant in the consortia-inoculated samples, with an increased gene abundance, suggesting that inoculation contributed to promoting the biodegradation of lignocellulose and the exchange of favorable factors. In conclusion, this study demonstrates that inoculating thermophilic bacterial consortia has a positive impact on enhancing the resource utilization efficiency of agricultural waste and improving the quality of compost products.

Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile

Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.

Exploring the bacterial diversity and composition with special emphasis on pathogens in ship ballast water and sediments using full-length 16S rRNA gene sequencing

Accurate detecting bacterial communities in ballast water and sediments supports risk management. This study uses full-length 16S rRNA gene sequencing to investigate the bacterial communities in ballast water and sediments, focusing on detecting pathogens. The results indicate that full-length sequencing more accurately reveals the species diversity. There is a significant difference (P < 0.05) in bacterial communities between ballast water and sediments, despite both being dominated by the Proteobacteria phylum. Thirty human and fish pathogens were identified by full-length sequencing, yet only five pathogens were detected from V3-V4 sequencing. Notably, emerging pathogens such as Citrobacter freundii and Nocardia nova are detected in samples, which are harmful to aquaculture and human health. Several opportunistic pathogens were also identified. In summary, this study provides important insights into the bacterial communities in ballast water and sediments, highlighting the need for strict management.

Bacterial community succession and the enrichment of antibiotic resistance genes on microplastics in an oyster farm

Microplastics can be colonized by microorganisms and form plastisphere. However, knowledge of bacterial community succession and the enrichment of antibiotic resistance genes (ARGs) and pathogens on microplastics in aquaculture environments is limited. Here, we conducted a 30-day continuous exposure experiment at an oyster farm. Results showed that the alpha-diversity of communities on most microplastics continuously increased and was higher than in planktonic communities after 14 days. Microplastics could selectively enrich certain bacteria from water which can live a sessile lifestyle and promote colonization by other bacteria. The composition and function of plastisphere communities were distinct from those in the surrounding water and influenced by polymer type and exposure time. Microplastics can enrich ARGs (sul1, qnrS and blaTEM) and harbor potential pathogens (e.g., Pseudomonas aeruginosa). Therefore, microplastic pollution may pose a critical threat to aquaculture ecosystems and human health. Our study provides further insight into the ecological risks of microplastics.

Effect of sodium alginate-gelatin-polyvinyl pyrrolidone microspheres on cucumber plants, soil, and microbial communities under lead stress

Lead is highly persistent and toxic in soil, hindering plant growth. Microspheres are a novel, functional, and slow-release preparation commonly used for controlled release of agricultural chemicals. However, their application in the remediation of Pb-contaminated soil has not been studied; furthermore, the remediation mechanism involved has not been systematically assessed. Herein, we evaluated the Pb stress mitigation ability of sodium alginate-gelatin-polyvinyl pyrrolidone composite microspheres. Microspheres effectively attenuated the Pb toxic effect on cucumber seedlings. Furthermore, they boosted cucumber growth, increased peroxidase activity, and chlorophyll content, while reducing malondialdehyde content in leaves. Microspheres promoted Pb enrichment in cucumber, especially in roots (about 4.5 times). They also improved soil physicochemical properties, promoted enzyme activity, and increased soil available Pb concentration in the short term. In addition, microspheres selectively enriched functional (heavy metal-tolerating and plant growth promoting) bacteria to adapt to and resist Pb stress by improving soil properties and nutrients. These results indicated that even a small amount (0.025-0.3 %) of microspheres can significantly reduce the adverse effects of Pb on plants, soil, and bacterial communities. Composite microspheres have shown great value in Pb remediation, and their application potential in phytoremediation is also worth evaluating to expand the application.

Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies

Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them.

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

BACKGROUND

The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment.

RESULTS

As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench.

CONCLUSIONS

This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.

Assessing the promoting effect of compound microbial agents on flax dew retting: Based on the relationship between metabolites and core genera

In this study, 16S rRNA sequencing and GC-MS (gas chromatography-mass spectrometry) techniques were employed to examine the relationship between bacterial succession and metabolite alterations during the dew retting process of flax. The results indicated that the addition of compound microbial agents may affect the production and transformation of metabolites by re-establishing bacterial communities and promoting the degradation of pectic substances and the release of metabolites, and the best retting effect was achieved under the combined addition (BA). In addition, Chryseobacterium, Bacillus, and Pseudoonas were closely associated with the production of fatty acids and alcohols; the addition of compound microbial agents increased the content of critical metabolites while decreasing the environmental pollutant bis(2-ethylhexyl) phthalate. In summary, the addition of compound microbial agents can positively regulate the retting process of flax, shorten the retting cycle, improve the quality of flax fibre, and reduce the pollution of the environment.

Comparison of the basic processes of aerobic, anaerobic, and aerobic-anaerobic coupling composting of Chinese medicinal herbal residues

Chinese medicinal herbal residues (CMHRs) are waste generated after extracting Chinese medicinal materials, and they can be used as a renewable bioresource. This study aimed to evaluate the potential of aerobic composting (AC), anaerobic digestion (AD), and aerobic-anaerobic coupling composting (AACC) for the treatment of CMHRs. CMHRs were mixed with sheep manure and biochar, and composted separately under AC, AD, and AACC conditions for 42 days. Physicochemical indices, enzyme activities, and bacterial communities were monitored during composting. Results showed that AACC- and AC-treated CMHRs were well-rotted, with the latter exhibiting the lowest C/N ratio and maximal germination index (GI) values. Higher phosphatase and peroxidase activities were detected during the AACC and AC treatments. Better humification was observed under AACC based on the higher catalase activities and lower E4/E6. AC treatment was effective in reducing compost toxicity. This study provides new insights into biomass resource utilisation.

Mechanistic insights into dissolved organic matter-driven protistan and bacterial community dynamics influenced by vegetation restoration

Vegetation restoration projects can not only improve water quality by absorbing and transferring pollutants and nutrients from non-vegetation sources, but also protect biodiversity by providing habitat for biological growth. However, the mechanism of the protistan and bacterial assembly processes in the vegetation restoration project were rarely explored. To address this, based on 18 S rRNA and 16 S rRNA high-throughput sequencing, we investigated the mechanism of protistan and bacterial community assembly processes, environmental conditions, and microbial interactions in the rivers with (out) vegetation restoration. The results indicated that the deterministic process dominated the protistan and bacterial community assembly (94.29% and 92.38%), influenced by biotic and abiotic factors. For biotic factors, microbial network connectivity was higher in the vegetation zone (average degree = 20.34) than in the bare zone (average degree = 11.00). For abiotic factors, the concentration of dissolved organic carbon ([DOC]) was the most important environmental factor affecting the microbial community composition. [DOC] was lower significantly in vegetation zone (18.65 ± 6.34 mg/L) than in the bare zone (28.22 ± 4.82 mg/L). In overlying water, vegetation restoration upregulated the protein-like fluorescence components (C1 and C2) by 1.26 and 1.01-folds and downregulated the terrestrial humic-like fluorescence components (C3 and C4) by 0.54 and 0.55-folds, respectively. The different DOM components guided bacteria and protists to select different interactive relationships. The protein-like DOM components led to bacterial competition, whereas the humus-like DOM components resulted in protistan competition. Finally, the structural equation model was established to explain that DOM components can affect protistan and bacterial diversity by providing substrates, facilitating microbial interactions, and promoting nutrient input. In general, our study provides insights into the responses of vegetation restored ecosystems to the dynamics and interactives in the anthropogenically influenced river and evaluates the ecological restoration performance of vegetation restoration from a molecular biology perspective.

Characterization of bacterial communities in ticks parasitizing cattle in a touristic location in southwestern China

The purpose of this study was to investigate tick species around Mount Fanjing and analyze bacterial communities in two species - Rhipicephalus microplus and Haemaphysalis longicornis - parasitizing cattle in Tongren, Guizhou province, Southwest China, using high-throughput sequencing methods. In April 2019, ticks were collected from five sites in Jiangkou County, Yinjiang County, and Songtao County. In total, 296 ticks were collected, comprising two genera and three species: H. longicornis, Haemaphysalis flava, and R. microplus. Rhipicephalus microplus was the most representative species (57.4%) within the collected group, being the dominant species in Tongren City, followed by H. longicornis (39.5%) and H. flava (3.0%). Beta-diversity analysis revealed differences in bacterial community composition among the tick species. The bacterial community structure of R. microplus collected in the three counties was highly similar. Chlorella and Bacillus were highly abundant in H. longicornis. Rickettsia was detected at high relative abundance in R. microplus but in low relative abundance in H. longicornis, suggesting that Rickettsia is more associated with R. microplus than with H. longicornis. More in-depth investigations are needed to determine the pathogenic risk of Rickettsia and its relationship with the host. This is the first survey on tick-borne bacterial communities in this area, which is of great significance for the prevention and control of tick-borne diseases locally.

Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems

Mangrove receives aquaculture wastewater and urban sewage, and thus is a potential reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of a comprehensive profile of ARGs in mangrove ecosystems. We used metagenomic techniques to uncover the occurrence, host range, and potential mobility of ARGs in six mangrove ecosystems in southeastern China. Based on deep sequencing data, a total of 348 ARG subtypes were identified. The abundant ARGs were associated with acriflavine, bacitracin, beta-lactam, fluoroquinolone, macrolide-lincosamide-streptogramin, and polymyxin. Resistance genes tetR, aac(6')-Iae, aac(3)-IXa, vanRA, vanRG, and aac(3)-Ig were proposed as ARG indicators in mangrove ecosystems that can be used to evaluate the abundance of 100 other co-occurring ARGs quantitatively. Remarkably, 250 of 348 identified ARG subtypes were annotated as mobile genetic elements-associated ARGs, indicating a high potential risk of propagation of ARGs in mangrove ecosystems. By surveying the distribution of ARGs in 6281 draft genomes, more than 42 bacterial phyla were identified as the putative hosts of the ARGs. Among them, 21.97% were potentially multidrug-resistant hosts, including human and animal opportunistic pathogens. This research adds to our understanding of the distribution and spread of antibiotic resistomes in mangrove ecosystems, helping improve ARG risk assessment and management worldwide.

Soil drying legacy does not affect phenanthrene fate in soil but modifies bacterial community response

Alteration of the structure of soil microbial communities following the elimination of hydrophobic organic pollutants (e.g., polycyclic aromatic hydrocarbons, PAHs) is generally assessed using DNA-based techniques, and soil is often required to dry prior to pollutant addition, to facilitate a better mix when establishing microcosms. However, the drying practice may have a legacy effect on soil microbial community structure, which would in turn influence the biodegradation process. Here, we used ¹⁴C-labeled phenanthrene to examine the potential side effects of precedent short-term drought events. The results indicate that the drying practice had legacy effects on soil microbial community structure, illustrated by irreversible shifts in the communities. The legacy effects had no significant impact on phenanthrene mineralization and non-extractable residue formation. However, they altered the response of bacterial communities to PAH degradation, leading to a decrease in the abundance of potential PAH degradation genes plausibly attributed to moderately abundant taxa. Based on a comparison of the varied effects of different drying intensity levels, an accurate description of microbial responses to phenanthrene degradation strongly relies on the establishment of stable microbial communities before PAH amendment. Concurrent alterations in the communities resulting from environmental perturbation could greatly mask minor alterations from the degradation of recalcitrant hydrophobic PAH. In practice, to minimize the legacy effects, a soil equilibration step with a reduced drying intensity is indispensable.

Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau

In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.

Variance of soil bacterial community and metabolic profile in the rhizosphere vs. non-rhizosphere of native plant Rumex acetosa L. from a Sb/As co-contaminated area in China

Heavy metals (HMs) contamination poses a serious threat to soil health. However, the rhizosphere effect of native pioneer plants on the soil ecosystem remains unclear. Herein, how the rhizosphere (Rumex acetosa L.) influenced the process of HMs threatening soil micro-ecology was investigated by coupling various fractions of HMs, soil microorganisms and soil metabolism. The rhizosphere effect alleviated the HMs' stress by absorbing and reducing HMs' direct bioavailability, and the accumulation of ammonium nitrogen increased in the rhizosphere soil. Meanwhile, severe HMs contamination covered the rhizosphere effect on the richness, diversity, structure and predicted function pathways of soil bacterial community, but the relative abundance of Gemmatimonadota decreased and Verrucomicrobiota increased. The content of total HMs and physicochemical properties played a more important role than rhizosphere effect in shaping soil bacterial community. Furthermore, As was observed to have a more significant impact compared to Sb. Moreover, plant roots improved the stability of bacterial co-occurrence network, and significantly changed the critical genera. The process influenced bacterial life activity and nutrient cycling in soil, and the conclusion was further supported by the significant difference in metabolic profiles. This study illustrated that in Sb/As co-contaminated area, rhizosphere effect significantly changed soil HMs content and fraction, soil properties, and microbial community and metabolic profiles.

Improvement of cadmium immobilization in contaminated paddy soil by using ureolytic bacteria and rice straw

Cadmium (Cd) in paddy soil can be immobilized via microbially induced carbonate precipitation (MICP), but it poses a risk to the properties and eco-function of the soil. In this study, rice straw coupled with Sporosarcina pasteurii (S. pasteurii) was used to treat Cd-contaminated paddy soil with minimizing the detrimental effects of MICP. Results showed that the application of rice straw coupled with S. pasteurii reduced Cd bioavailability. The X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) confirmed that Cd immobilization efficiency was increased in the rice straw coupled with S. pasteurii treatment via co-precipitating with CaCO₃. Moreover, rice straw coupled with S. pasteurii enhanced soil fertility and ecological functions as reflected by the high amount of alkaline hydrolysis nitrogen (AN) (14.9 %), available phosphorus (AP) (13.6 %), available potassium (AK) (60.0 %), catalase (9.95 %), dehydrogenase (736 %), and phosphatase (214 %). Further, the relative abundance of dominant phyla such as Proteobacteria and Firmicutes significantly increased when applying both rice straw coupled with S. pasteurii. The most significant environmental factors that affected the composition of the bacterial community were AP (41.2 %), phosphatase (34.2 %), and AK (8.60 %). In conclusion, using rice straw mixed with S. pasteurii is a promising application to treat Cd-contaminated paddy soil due to its positive effects on treating soil Cd as well as its ability to reduce the detrimental effects of the MICP process.

Urbanization influenced the interactions between dissolved organic matter and bacterial communities in rivers

Increased urbanization and anthropogenic activities can alter dissolved organic matter (DOM) and complicate its interaction with bacteria in rivers' ecosystems, however, there is limited information about how bacterial communities respond to DOM components in rivers with different urbanization levels. Here, we combined spectroscopy-based DOM analysis and 16S rRNA gene amplicon sequencing to investigate the associations of bacterial taxa and DOM properties as well as the impacts of DOM on bacterial niche breadth in North River (NR) and West River (WR) of Jiulong River watershed, southern China, which had low and high urbanization levels, respectively. Spectroscopy analysis showed that hydrophilic DOM was predominant in both rivers whereas chromophoric DOM was higher in WR. Network analysis indicated that only seven bacterial genera (i.e., hg clade, chthoniobacter, Geobacter, Acidibacter, Alphal Cluster, Fluviicola, and Lacunisphaera) showed strong associations with DOM optical variables in both rivers, whereas more than 85% of DOM-bacterial genera associations were different between rivers. These results suggest that the relationship between DOM and bacterial communities had different responses in rivers with different urbanization levels. The partial least square path model indicated that the total standardized effect of physico-chemicals on bacterial niche breadth was higher in NR (0.62) than in WR (0.35), whereas humic substances showed an opposite pattern (NR: -0.42; WR: 1.67). The distinct effects of physico-chemicals and DOM on bacterial niche breadths between rivers could be due to the different effects of urbanization and human activities on the environmental conditions of riverine ecosystems. Our findings revealed a huge dissimilarity in the bacteria-DOM co-occurrence networks between rivers with different urbanization levels and provide a novel insight that urbanization may enhance DOM's importance to bacterial niche breadths.

Temporal variations, distribution, and dissemination of antibiotic resistance genes and changes of bacterial communities in a biofloc-based zero-water-exchange mariculture system

Antibiotic resistance genes (ARGs) have obtained an increasing number of global concerns for the severe risks they pose to food safety and public health. Studies have investigated the concentrations and distribution of ARGs in the environment. However, the distribution and dissemination of ARGs, the bacterial communities, and the key influencing factors during the entire rearing period in the biofloc-based zero-water-exchange mariculture system (BBZWEMS) remain unclear. The current study investigated the concentrations, temporal variations, distribution, and dissemination of ARGs, the changes in the bacterial communities, as well as the key influencing factors during the rearing period in the BBZWEMS. Sul1 and sul2 were dominant ARGs. Total concentrations of ARGs followed a trend of decrease in pond water, while they followed a trend of increase in source water, biofloc, and shrimp gut. Total concentrations of targeted ARGs in the water source were higher than those in the pond water and biofloc samples for each corresponding rearing stage by 2.25-122.97-fold (p < 0.05). The bacterial communities in biofloc and pond water did not change much, while they changed considerably in the shrimp gut samples during the rearing period. Pearson correlation, redundancy analysis, and multivariable linear regression analysis showed that suspended substances and Planctomycetes were positively correlated with the concentrations of ARGs (p < 0.05). The current study indicates that the water source may be a critical source of ARGs, and that suspended substances is a key factor influencing the distribution and dissemination of ARGs in the BBZWEMS. Early intervention measures on ARGs in water sources should be implemented to aid in the prevention and control of resistance genes in aquaculture industry, and reduce the potential risks of ARGs to public health and food safety.

Biodegradable mulch films significantly affected rhizosphere microbial communities and increased peanut yield

Biodegradable mulch films are widely used to replace conventional plastic films in agricultural fields. However, their ecological effects on different microbial communities that naturally inhabit agricultural fields are scarcely explored. Herein, differences in bacterial communities recovered from biofilms, bulk soil, and rhizosphere soil were comparatively assessed for polyethylene film (PE) and biodegradable mulch film (BDM) application in peanut planted fields. The results showed that the plastic film type significantly influenced the bacterial community in different ecological niches of agricultural fields (P < 0.001). Specifically, BDMs significantly increased the diversity and abundance of bacteria in the rhizosphere soil. The bacterial communities in each ecological niche were distinguishable from each other; bacterial communities in the rhizosphere soil showed the most pronounced response among different treatments. Acidobacteria and Pseudomonas were significantly enriched in the rhizosphere soil when BDMs were used. BDMs also increased the rhizosphere soil bacterial network complexity and stability. The enrichment of beneficial bacteria in the rhizosphere soil under BDMs may also have implications for the observed increase in peanut yield. Deepening analyses indicated that Pseudoxanthomonas and Glutamicibacter are biomarkers in biofilms of PE and BDMs respectively. Our study provides new insights into the consequences of the application of different types of plastic films on microbial communities in different ecological niches of agricultural fields.

Hydrogen peroxide treatment mitigates antibiotic resistance gene and mobile genetic element propagation in mariculture sediment

Mariculture sediments have been exchange and propagation sources of antibiotic resistance genes (ARGs). However, no efficient methods have been generated to remove ARGs from sediments. Here, we explored the impact of hydrogen peroxide (H₂O₂) and aeration on the efficient removal of ARGs and mobile genetic elements (MGEs) in mariculture sediments. When compared with the aeration group, the ARG abundance was 3.8-32.3% lower in the H₂O₂ group during the first 14 days. ARG and MGE abundances were also significantly associated with reduced total bacterial population and diversity (P < 0.05). Based on partial squares path modeling, reduction of MGEs had important roles in ARG removal from H₂O₂ treatments, while in the aeration group, ARG reductions were mainly determined by changes in bacterial community composition. These results suggested that H₂O₂ treatment represent a promising method for controlling ARG abundance after dosing feed stuff and limit the spread of ARGs in aquaculture environments.