A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

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High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

10.21203/rs.3.rs-34433/v1 ◽

2020 ◽

Author(s):

Wu Qu ◽

Boliang Gao ◽

Jie Wu ◽

Min Jin ◽

Jianxin Wang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Fungal Community ◽

Amplicon Sequencing ◽

Biotic Factors ◽

Community Structures ◽

Mangrove Sediments ◽

Element Cycling ◽

Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.02676-16 ◽

2016 ◽

Vol 83 (4) ◽

Cited By ~ 18

Author(s):

Nastassia V. Patin ◽

Michelle Schorn ◽

Kristen Aguinaldo ◽

Tommie Lincecum ◽

Bradley S. Moore ◽

...

Keyword(s):

Microbial Community ◽

Secondary Metabolites ◽

Microbial Communities ◽

Community Composition ◽

Marine Sediments ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Next Generation ◽

Content Type ◽

Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

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Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

10.21203/rs.3.rs-33130/v1 ◽

2020 ◽

Author(s):

Oskar Modin ◽

Raquel Liebana ◽

Soroush Saheb-Alam ◽

Britt-Marie Wilén ◽

Carolina Suarez ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Null Model ◽

Amplicon Sequencing ◽

Null Models ◽

Marker Genes ◽

Experimental Systems ◽

Microbial Community Assembly ◽

The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

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Spatiotemporal Correlations Between Water Quality And Microbial Community of Typical Inflow River Into Taihu Lake, China

10.21203/rs.3.rs-1000115/v1 ◽

2021 ◽

Author(s):

Yajie Zhang ◽

Ye Zhang ◽

Lecheng Wei ◽

Mengyan Li ◽

Weitang Zhu ◽

...

Keyword(s):

Water Quality ◽

Microbial Community ◽

Microbial Communities ◽

Taihu Lake ◽

Wastewater Treatment Plants ◽

Ammonia Nitrogen ◽

Pollution Sources ◽

Storm Water ◽

Urban Wastewater Treatment ◽

The Impact

Abstract Changxing River, which is a typical inflow river into the Taihu Lake and occurs severe algae invasion, is selected to study the effect of different pollution sources on the water quality and ecological system. Four types of pollution sources, including the estuary of Taihu Lake, discharge outlets of urban wastewater treatment plants, storm water outlets, and non-point source agricultural drainage areas are chosen, and next-generation sequencing and multi-variate statistical analyses are used to characterize the microbial communities and reveal their relationship with water physicochemical properties. Results showed that ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) are the main pollutant in Changxing River, especially at storm water outlets. At the same time, the diversity of microbial communities was the highest in the summer, and dominant phyla included Proteobacteria (40.9%), Bacteroidetes (21.0%) and Euryarchaeota (6.1%) under the condition of algal bloom. Water temperature (T), air pressure (P), concentrations of TP and CODMn were the important variables for the succession of microbial community. From the perspective of different pollution types, relative abundances of Microcystis and Nostocaceae at the estuary of Taihu Lake were correlated positively with dissolved oxygen (DO) and pH, and Pseudomonas and Arcobacter were correlated positively with concentrations of TN and nitrate nitrogen (NO3--N) at storm water outlets. The results provide a reference for the impact of pollution types on river microbial ecosystem under complex hydrological condition and a guidance for the selection of restoration techniques for polluted rivers entering an important lake.

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Heavy Metal Tolerance Genes Associated With Contaminated Sediments From an E-Waste Recycling River in Southern China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.665090 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shengqiao Long ◽

Hui Tong ◽

Xuxiang Zhang ◽

Shuyu Jia ◽

Manjia Chen ◽

...

Keyword(s):

Heavy Metal ◽

Microbial Community ◽

Microbial Communities ◽

Southern China ◽

Risk Index ◽

River Sediments ◽

Microbial Community Composition ◽

Heavy Metal Tolerance ◽

Waste Recycling ◽

The Impact

Heavy metal pollution that results from electronic waste (e-waste) recycling activities has severe ecological environmental toxicity impacts on recycling areas. The distribution of heavy metals and the impact on the bacteria in these areas have received much attention. However, the diversity and composition of the microbial communities and the characteristics of heavy metal resistance genes (HMRGs) in the river sediments after long-term e-waste contamination still remain unclear. In this study, eight river sediment samples along a river in a recycling area were studied for the heavy metal concentration and the microbial community composition. The microbial community consisted of 13 phyla including Firmicutes (ranging from 10.45 to 36.63%), Proteobacteria (11.76 to 32.59%), Actinobacteria (14.81 to 27.45%), and unclassified bacteria. The abundance of Firmicutes increased along with the level of contaminants, while Actinobacteria decreased. A canonical correspondence analysis (CCA) showed that the concentration of mercury was significantly correlated with the microbial community and species distribution, which agreed with an analysis of the potential ecological risk index. Moreover, manually curated HMRGs were established, and the HMRG analysis results according to Illumina high-throughput sequencing showed that the abundance of HMRGs was positively related to the level of contamination, demonstrating a variety of resistance mechanisms to adapt, accommodate, and live under heavy metal-contaminated conditions. These findings increase the understanding of the changes in microbial communities in e-waste recycling areas and extend our knowledge of the HMRGs involved in the recovery of the ecological environment.

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Unique physiological and genetic features of ofloxacin-resistant Streptomyces mutants

Applied and Environmental Microbiology ◽

10.1128/aem.02327-21 ◽

2021 ◽

Author(s):

Kanata Hoshino ◽

Ryoko Hamauzu ◽

Hiroyuki Nakagawa ◽

Shinya Kodani ◽

Takeshi Hosaka

Keyword(s):

Drug Resistance ◽

Secondary Metabolites ◽

Secondary Metabolite ◽

Antimicrobial Agents ◽

Gene Clusters ◽

Resistant Bacteria ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Resistance Selection ◽

Resistant Mutants

New antimicrobial agents are urgently needed to combat the emergence and spread of multidrug-resistant bacteria. Activating the cryptic biosynthetic gene clusters for actinomycete secondary metabolites can provide essential clues for research into new antimicrobial agents. An effective method for this purpose is based on drug resistance selection. This report describes interesting results for drug resistance selection using antibiotics that target DNA replication can effectively potentiate secondary metabolite production by actinomycetes. Ofloxacin-resistant mutants were isolated from five different streptomycetes. Ofloxacin is an antibiotic that binds to DNA complexes and type II topoisomerase, causing double-stranded breaks in bacterial chromosomes. Physiological and genetic characterization of the mutants revealed that the development of ofloxacin resistance in streptomycetes leads to the emergence of various types of secondary metabolite-overproducing strains. In Streptomyces coelicolor A3(2), ofloxacin-resistant mutants that overproduced actinorhodin, undecylprodigiosin, or carotenoid were identified. Also, an ofloxacin-resistant mutant that overproduces methylenomycin A, whose biosynthetic gene cluster is located on the endogenous plasmid, SCP1, was isolated. These observations indicate that ofloxacin resistance might activate biosynthetic genes on both chromosomes and on endogenous plasmids. We also identified the mutations that are probably involved in the phenotype of ofloxacin resistance and secondary metabolite overproduction in S. coelicolor A3(2). Furthermore, we observed an interesting phenomenon in which several ofloxacin-resistant mutants overproduced antibiotics in the presence of ofloxacin. Based on these results, we present the unique physiological and genetic characteristics of ofloxacin-resistant Streptomyces mutants and discuss the importance and potential development of the new findings. IMPORTANCE The abuse or overuse of antibacterial agents for therapy and animal husbandry has caused an increased population of antimicrobial-resistant bacteria in the environment. Consequently, there are now fewer effective antimicrobials available. Due to the depleted antibiotic pipeline, pandemic outbreaks caused by antimicrobial-resistant bacteria are deeply concerned, and the development of new antibiotics is now an urgent issue. Promising sources of antimicrobial agents include cryptic biosynthetic gene clusters for secondary metabolites in streptomycetes and rare actinomycetes. This study’s significance is an unprecedented activation method to accelerate drug discovery research on a global scale. The technique developed in this study could allow for simultaneous drug discovery in different countries, maximizing the world’s microbial resources.

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Phytoremediation of landfill leachate in constructed wetland

Linnaeus Eco-Tech ◽

10.15626/eco-tech.2005.046 ◽

2019 ◽

pp. 441-446

Author(s):

Jaak Truu ◽

Jaanis Juhanson ◽

Mait Kriipsalu ◽

Marit Seene

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Plant Species ◽

Landfill Leachate ◽

Water Samples ◽

Free Water ◽

Vegetation Period ◽

Quality Of Water ◽

Remediation Plan ◽

The Impact

The integrated remediation plan of the Laguja landfill, Estonia, includes creation of aconstructed wetland for treatment of landfill leachate. A mesocosm experiment wasconducted in order to estimate the impact of different plant species on purification efficiencyof wetland. The quality of water in mesocosms was monitored during vegetation period. Allplant treatments enhanced reduction of organic matter (BOD: 87-96%, COD: ca 30%, TOC:ca 50%) as well as ammonia and total nitrogen in water compared to unplanted control.Presence of plants enhanced biodegradative bacterial abundance and activity as well asmetabolic diversity of microbial community in water. Water samples from all plant treatmentswere characterized by distinct microbial communities as revealed by molecular fingerprintingtechniques. Most different from the rest of microbial communities were water samples frommesocosm with plants on floating mats. Our results show that in free-water constructedwetlands with vegetation the purification efficiency is not dependent on plant species, whilestructure of water microbial community differs due to plant species.

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Supercritical Fluid Extraction Enhances Discovery of Secondary Metabolites from Myxobacteria

10.26434/chemrxiv.12640073.v1 ◽

2020 ◽

Author(s):

Chantal Bader ◽

Markus Neuber ◽

Fabian Panter ◽

Daniel Krug ◽

Rolf Müller

Keyword(s):

Natural Products ◽

Secondary Metabolites ◽

Supercritical Fluid Extraction ◽

Secondary Metabolite ◽

Supercritical Fluid ◽

Extraction Efficiency ◽

Antimicrobial Activities ◽

Fluid Extraction ◽

Microbial Natural Products ◽

The Impact

Supercritical fluid extraction (SFE) is widely used for the isolation of natural products from plants, but its application in efforts to identify structurally and physicochemically often dissimilar microbial natural products is limited to date. In this study we evaluated the impact of SFE on the extractability of myxobacterial secondary metabolites aiming to improve the prospects of discovering novel natural products. We investigated the influence of different co-solvents on the extraction efficiency of secondary metabolites from three myxobacterial strains as well as the antimicrobial activity profiles of the corresponding extracts. For each known secondary metabolite we found extraction conditions using SFE leading to superior yields in the extracts compared to conventional solvent extraction. Compounds with a logP higher than 3 showed best extraction efficiency using 20% EtOAc as a co-solvent, whereas compounds with logP values lower than 3 were better extractable using more polar co-solvents like MeOH. Extracts generated with SFE showed increased antimicrobial activities including the presence of activities not explained by known myxobacterial secondary metabolites, highlighting the advantage of SFE for bioactivity-guided isolation. Moreover, non-targeted metabolomics analysis revealed a group of chlorinated metabolites produced by the well-studied model myxobacterium Myxococcus xanthus DK1622 which were not accessible previously due to their low concentration in conventional extracts. The enriched SF extracts were used for isolation and subsequent structure elucidation of chloroxanthic acid A as founding member of a novel secondary metabolite family. Our findings encourage the increased utilization of SFE as part of future microbial natural products screening workflows.

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The Effect of Rhizophagus irregularis, Bacillus subtilis and Water Regime on the Plant–Microbial Soil System: The Case of Lactuca sativa

Agronomy ◽

10.3390/agronomy11112183 ◽

2021 ◽

Vol 11 (11) ◽

pp. 2183

Author(s):

Charitini Nikolaidou ◽

Nikolaos Monokrousos ◽

Pantelitsa D. Kapagianni ◽

Michael Orfanoudakis ◽

Triantafyllia Dermitzoglou ◽

...

Keyword(s):

Bacillus Subtilis ◽

Acid Phosphatase ◽

Microbial Community ◽

Microbial Communities ◽

Lactuca Sativa ◽

Water Regime ◽

Rhizophagus Irregularis ◽

Fungal Colonization ◽

The Impact ◽

Rhizosphere Microbial Community

Inoculation with beneficial microbes represents a promising solution for sustainable agricultural production; however, knowledge on the effects of inoculants on the indigenous microbial communities remains limited. Here, we evaluated the impact of the arbuscular mycorrhizal fungus Rhizophagus irregularis and the promoting rhizobacterium Bacillus subtilis on the growth of Lactuca sativa. The biomass, the composition, and the enzyme activity (urease, acid phosphatase, and β-glycosidase) of the rhizosphere microbial community at two soil moisture levels (5 and 10% soil water content) were evaluated. Fungal colonization was lower in co-inoculated plants than those only inoculated with R. irregularis. Plant growth was enhanced in co-inoculated and B. subtilis inoculated soils. Bacterial biomass and the composition of the microbial communities responded to the joint effect of inoculant type × water regime while the biomass of the other microbial groups (fungi, actinomycetes, microeukaryotes) was only affected by inoculant type. Co-inoculation enhanced the activity of acid phosphatase, indicating a synergistic effect of the two inoculants. Co-inoculation positively impacted the index reflecting plant–microbial soil functions under both water regimes. We concluded that the interactions between the two inocula as well as between them and the resident rhizosphere microbial community were mainly negative. However, the negative interactions between R. irregularis and B. subtilis were not reflected in plant biomass. The knowledge of the plant and rhizosphere microbial responses to single and co-inoculation and their dependency on abiotic conditions is valuable for the construction of synthetic microbial communities that could be used as efficient inocula.

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Did Application of Digested Sewage Sludge as Soil Amendment Alter the Abundances of Antibiotic Resistance Genes and Microbial Communities in Soil and Earthworm Gut?

10.21203/rs.3.rs-44156/v1 ◽

2020 ◽

Author(s):

Zheng-Hao Li ◽

Li Yuan ◽

Wei Shao ◽

Guo-Ping Sheng

Keyword(s):

Microbial Community ◽

Sewage Sludge ◽

Microbial Communities ◽

Soil Amendment ◽

Antibiotic Resistance Genes ◽

Digested Sludge ◽

Earthworm Gut ◽

The Impact ◽

Digested Sewage Sludge ◽

Amended Soil

Abstract Background Digested sewage sludge has been widely applied as soil amendment for enhanced crop production. However, given that digested sludge is abundant with antibiotic resistance genes (ARGs) and antibiotic resistant bacteria, the impact of digested sludge amendment on the abundances of ARGs and microbial communities in soil and soil fauna (e.g., earthworms) remains largely unknown. In this study, the patterns of ARGs and microbial communities in soil and gut of earthworms after 80-days cultivation with digested sewage sludge amendment were investigated to gain insights into this impact. Results The results show that the digested sludge amendment increased the initial abundances of ARGs (e.g., tetA, tetQ, and sulII) in soil. However, after 80-days cultivation, the absolute abundances of target ARGs decreased by 62.3–95.4%. The reduction in ARGs absolute abundances was further enhanced by 31.4–84.7% in the presence of earthworms. In contrast, the relative abundances of some ARGs (e.g., tetA, sulI, and blaTEM−1) in the gut of earthworms increased by 41–130 folds. The microbial community structure of soil was greatly altered because of the introduction of digested sewage sludge at initial, but it recovered to its original pattern after 80-days cultivation. This could be attributed to the gradual attenuation of anaerobic microorganisms under aerobic conditions in soil. In particular, the presence of earthworms further enhanced this phenomenon. The reduction of ARGs in the amended soils was likely attributed to microbial community shift based on redundancy analysis. Several bacterial families (e.g., Saprospiraceae, Chitinophagaceae, and Rhodanobacteraceae) were significantly correlated with the target ARGs. Conclusions Our results reveal that the enrichment of ARGs in soil caused by digested sludge-amendment would recover to their original levels before amendment, highlighting the contribution of earthworms to reducing the ARG abundances in amended soil via shifting the microbial community. However, we also found that the amended soil could increase ARGs abundance in the earthworm gut, which may enhance the potential risk of ARGs spread via food chain. These results may provide a new sight on the control of ARGs occurrence and dissemination in sludge-amended soil ecosystem with consideration of the impact of earthworms.

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