World within world: Intestinal bacteria combining physiological parameters to investigate the response of Metaphire guillelmi to tetracycline stress

Are earthworms the victim, facilitator or antidote of antibiotics and antibiotic resistance at the soil-animal-human interface? A One-Health perspective

The transfer of antibiotics and antibiotic resistance (AR) to the soil systems poses ecological hazards to various organisms, including earthworms. Understanding the complex interactions between earthworms, antibiotics, and AR in the soil system requires a comprehensive assessment. Hence, the present review investigates the behaviour, fate, impacts, and mechanisms involved in the interaction of earthworms with antibiotics and AR. The antibiotics and AR detected in earthworms and their associated media, such as vermicompost, are presented, but several other antibiotics and AR widely detected in soils remain understudied. As receptors and bioassay organisms, earthworms are adversely affected by antibiotics and AR causing (1) acute and chronic toxicity, and (2) emergence of AR in previously susceptible earthworm gut microbiota, respectively. The paper also highlights that, apart from this toxicity, earthworms can also mitigate against antibiotics, antibiotic-resistant bacteria and antibiotic-resistance genes by reducing bacterial diversity and abundance. The behaviour and fate processes, including biodegradation pathways, biomarkers of antibiotics and AR in earthworms, are discussed. In addition, the factors controlling the behaviour and fate of antibiotics and AR and their interactions with earthworms are discussed. Overall, earthworms mitigate antibiotics and AR via various proximal and distal mechanisms, while dual but contradictory functions (i.e., mitigatory and facilitatory) were reported for AR. We recommend that future research based on the One-World-One-Health approach should address the following gaps: (1) under-studied antibiotics and AR, (2) degradation mechanisms and pathways of antibiotics, (3) effects of environmentally relevant mixtures of antibiotics, (4) bio-augmentation in earthworm-based bioremediation of antibiotics, (5) long-term fate of antibiotics and their metabolites, (6) bio-transfers of antibiotics and AR by earthworms, (7) development of earthworm biomarkers for antibiotics and AR, (8) application of earthworm-based bioremediation of antibiotics and AR, (9) cascading ecological impacts of antibiotics and AR on earthworms, and (10) pilot-scale field applications of earthworm-based bioremediation systems.

Alterations of the bile microbiome is associated with progression-free survival in pancreatic ductal adenocarcinoma patients

BACKGROUND

Patients with pancreatic ductal adenocarcinoma (PDAC) display an altered oral, gastrointestinal, and intra-pancreatic microbiome compared to healthy individuals. However, knowledge regarding the bile microbiome and its potential impact on progression-free survival in PDACs remains limited.

METHODS

Patients with PDAC (n = 45), including 20 matched pairs before and after surgery, and benign controls (n = 16) were included prospectively. The characteristics of the microbiomes of the total 81 bile were revealed by 16  S-rRNA gene sequencing. PDAC patients were divided into distinct groups based on tumor marker levels, disease staging, before and after surgery, as well as progression free survival (PFS) for further analysis. Disease diagnostic model was formulated utilizing the random forest algorithm.

RESULTS

PDAC patients harbor a unique and diverse bile microbiome (PCoA, weighted Unifrac, p = 0.038), and the increasing microbial diversity is correlated with dysbiosis according to key microbes and microbial functions. Aliihoeflea emerged as the genus displaying the most significant alteration among two groups (p < 0.01). Significant differences were found in beta diversity of the bile microbiome between long-term PFS and short-term PFS groups (PCoA, weighted Unifrac, p = 0.005). Bacillota and Actinomycetota were identified as altered phylum between two groups associated with progression-free survival in all PDAC patients. Additionally, we identified three biomarkers as the most suitable set for the random forest model, which indicated a significantly elevated likelihood of disease occurrence in the PDAC group (p < 0.0001). The area under the receiver operating characteristic (ROC) curve reached 80.8% with a 95% confidence interval ranging from 55.0 to 100%. Due to the scarcity of bile samples, we were unable to conduct further external verification.

CONCLUSION

PDAC is characterized by an altered microbiome of bile ducts. Biliary dysbiosis is linked with progression-free survival in all PDACs. This study revealed the alteration of the bile microbiome in PDACs and successfully developed a diagnostic model for PDAC.

Pig manure-derived fulvic acid more strongly drives the fate of arsenic and antibiotic resistance genes in paddy soil

Antibiotic resistance genes (ARGs) can threaten the clean production of rice owing to continuous selective pressure in heavy metal-antibiotic co-contaminated paddy soils. As an important soil carbon reservoir, the role of humic substances from different types of manure in the regulation of soil ARGs remains unclear. In this study, fulvic acid (FA) and humic acid (HA) were extracted from pig manure (PM), cow dung (CD), and chicken manure (CM). The influence of their characteristics and doses on the fate of ARGs was investigated in arsenic (As)-antibiotic co-contaminated paddy soils. The release of As and degradation of antibiotics were promoted in 1% PM-FA treatment, with increases of 4.8%-5.6% and 8.3%-8.8% compared with CM-FA and CD-FA treatments, respectively. The coexistence of FA/HA, Fe, As, and antibiotics in soil pore water affected the environmental behavior of ARGs, with FA showing a more positive effect. Species including Bacillus, Geobacter, Desulfitobacterium, and Christensenellaceae_R-7_group were considered potential hosts of ARGs, and their resistance to co-contamination increased after the addition of FA. Membrane transport is a potential strategy for host bacteria of ARGs to cope with As-antibiotic complex pressure. These results demonstrate the coupling mechanisms of As, antibiotics, and ARGs regulated by different humic substances in co-contaminated paddy soils, which could support the clean production of rice in agricultural practice.

Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg^-1) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg^-1) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.

Soil indigenous microorganisms alleviate soluble vanadium release from industrial dusts

Vanadium-bearing dusts from industrial processes release abundant toxic vanadium, posing imminent ecological and human health concerns. Although the precipitation of these dusts has been recognized as the main source of soil vanadium pollution, little is known regarding the interrelationships between industrial dusts and soil inherent compositions. In this study, the interactions between dusts from vanadium smelting and soil indigenous microorganisms were investigated. Soluble vanadium (V) [V(V)] released from industrial dusts was reduced by 41.5 ± 0.39% with soil addition, compared to water leaching. Reducible fraction accounted for the highest proportion (55.1 ± 1.73%) of vanadium speciation in the resultant soils, while residual vanadium fraction increased to 83.7 ± 3.22% in the leached dusts. Functional genera (e.g., Aliihoeflea, Actinotalea) that transformed V(V) to insoluble vanadium (IV) alleviated dissolved vanadium release. Nitrate/nitrite reduction and glutathione metabolisms contributed to V(V) immobilization primarily. Structural equation model analysis indicated that V(V) reducers had significant negative impacts on soluble V(V) in the leachate. This first-attempt study highlights the importance of soil microorganisms in immobilizing vanadium from industrial dusts, which is helpful to develop novel strategies to reduce their environmental risks associated to vanadium smelting process.

Analyses of locomotion, wing morphology, and microbiome in Drosophila nigrosparsa after recovery from antibiotics

Antibiotics, such as tetracycline, have been frequently used to cure arthropods of Wolbachia endosymbionts. After the symbionts have been removed, the hosts must recover for some generations from the side effects of the antibiotics. However, most studies do not assess the direct and indirect longer‐term effects of antibiotics used to remove Wolbachia, which may question the exact contribution of this endosymbiont to the effects observed. Here, we used the fly Drosophila nigrosparsa treated or not with tetracycline for three generations followed by two generations of recovery to investigate the effects of this antibiotic on the fly locomotion, wing morphology, and the gut microbiome. We found that antibiotic treatment did not affect fly locomotion two generations after being treated with the antibiotic. In addition, gut‐microbiome restoration was tested as a more efficient solution to reduce the potential side effects of tetracycline on the microbiome. There was no significant difference in alpha diversity between gut restoration and other treatments, but the abundance of some bacterial taxa differed significantly between the gut‐restoration treatment and the control. We conclude that in D. nigrosparsa the recovery period of two generations after being treated with the antibiotic is sufficient for locomotion, and suggest a general assessment of direct and indirect effects of antibiotics after a particular recovery time.

Contrasted effects of Metaphire guillelmi on tetracycline diffusion and dissipation in soil

Earthworms are important in soil bioremediation because of their capability of pollutant degradation. However, the trade-off between pollutant dissemination and degradation arising from earthworm activities remains unclear, as well as the potential biodegradation mechanism. Herein, an earthworm avoidance experiment was established to investigate Metaphire guillelmi-mediated tetracycline (TC) diffusion and degradation. The results showed that above 1600 mg kg^-1 TC pollution in soil induced avoidance behaviour of earthworms (p < 0.05), below which the random worm behaviour accelerated TC diffusion by 8.2% at most (p < 0.05), resulting in elevated levels of antibiotic-resistant bacteria and genes in the soil. Nevertheless, earthworms enhanced TC degradation regardless of whether their avoidance behaviour occurred (14.6-25.8%, p < 0.05). Compared with in soil, metabolic pathways affiliated with xenobiotic degradation and metabolism in the intestines were enriched (LDA >3). Given the abundant glutathione S-transferases in the intestines and their close relationship with Δ degradation, they may play a key role in intestinal TC biodegradation. In general, earthworms had good tolerance to soil TC contamination and their impact on promoting TC degradation outweighed that accelerating TC diffusion. This work provides a comprehensive view of earthworms as a potential remediation method for TC-contaminated soil.

Quantitative relationship between earthworms' sensitivity to organic pollutants and the contaminants' degradation in soil: A meta-analysis

Using earthworms to remove soil organic pollutants is a common bioremediation method. However, it remains challenging to evaluate and predict their effect on removing soil organic pollutants based on earthworm toxicology and pollutant degradation rates. Peer-reviewed journal articles on ecotoxicology and bioremediation from the years 1974-2020 (cutoff date September 2020) were selected for meta-analysis to quantify the effect size of earthworms on organic pollutant degradation. The meta-analysis shows that the average effect size of earthworms on organic pollutant degradation is 128.5% (p < 0.05). Soils with high soil organic matter or clay textures are more conducive to earthworm-mediated removal of organic pollutants. Structural equation modeling reveals that earthworms' sensitivity to contaminant exposure may be a greater limiting factor on pollutant degradation than environmental factors. In addition, the quantitative relationship existed between LC50 and the pollutants' degradation that an elevated LC50 threshold resulted in at least 1.5 times increase in the pollutants' degradation size. This correlation was dually confirmed via meta-analysis and the validation trial. The results of this study contribute to a more profound understanding of the potential to use earthworms to mitigate organic pollution in soils and develop earthworm-based soil remediation techniques on a global scale.

Toxicity assessment and microbial response to soil antibiotic exposure: differences between individual and mixed antibiotics

Increasing amounts of antibiotics are introduced into soils, raising great concerns on their ecotoxicological impacts on the soil environment. This work investigated the individual and joint toxicity of three antibiotics, tetracycline (TC), sulfonamide (SD) and erythromycin (EM) via a whole-cell bioreporter assay. TC, SD and EM in aqueous solution demonstrated cytotoxicity, whilst soil exposure showed genotoxicity, indicating that soil particles possibly affected the bioavailability of antibiotics. Toxicity of soils exposed to TC, SD and EM changed over time, demonstrating cytotoxic effects within 14-d exposure and genotoxic effects after 30 days. Joint toxicity of TC, SD and EM in soils instead showed cytotoxicity, suggesting a synergetic effect. High-throughput sequencing suggested that the soil microbial response to individual antibiotics and their mixtures showed a different pattern. Soil microbial community composition was more sensitive to TC, in which the abundance of Pseudomonas, Pirellula, Subdivision3_genera_incertae_sedis and Gemmata varied significantly. Microbial community functions were significantly shifted by EM amendments, including signal transduction mechanisms, cytoskeleton, cell wall/membrane/envelope biogenesis, transcription, chromatin structure and dynamics, and carbohydrate transport and metabolism. This work contributes to a better understanding of the ecological effects and potential risks of individual and joint antibiotics on the soil environment.

Evolution of the earthworm (Eisenia fetida) microbial community in vitro and in vivo under tetracycline stress

Bioremediation of contaminated soil has received increasing attention, and the effects of antibiotic residues on the soil ecological environment are a current research hotspot. Earthworms are the first choice of soil organisms to indicate the degree of soil pollution, and their detoxification mechanism after antibiotic stress must be further explored. Taking Eisenia fetida as the research object, an antibiotic (tetracycline) stress test was carried out in sterile artificial soil. The stress concentrations were set at 0, 0.3, 3, 30, 300 and 600 mg/kg. The ECO method was used to cultivate microbes in earthworms and soil. The carbon source utilization intensity algorithm developed by our team was used for data statistics, and a factor analysis model was constructed to explore the succession process of microbes of earthworms in vivo and in vitro under tetracycline stress. The results showed that there were four processes in the evolution of microbes under short-term tetracycline stress: at 1-3 days, the microbes in worms played a leading role; at 4-5 days, the microbes in the worms and the soil microbes jointly resisted TET stress; after 6-8 days of stress, the microbes in worms still played the main role, but their role was weakened; and after 9-10 days, soil microbes played a leading role, and tolerant microbes appeared. Under long-term stress, the microbes of earthworms in vivo and in vitro were obvious different, and there may be no regulatory relationship. And the factor analysis model is suitable for the analyse of the changes in microbial communities in vivo and in vitro under TET stress. The research results provide a reference method and model basis for the bioremediation of antibiotic-contaminated soil and the study of earthworm detoxification mechanisms, and help agricultural development.

Construction of perylene diimide/CuS supramolecular heterojunction for the highly efficient visible light-driven environmental remediation

Developing photocatalysts that are inexpensive and efficient in degrading pollutants are essential for environmental remediation. Herein, a novel system of perylene diimide (PDI)/CuS p-n heterojunction was synthesized by a two-step self-assembly strategy for removal of tetracycline in waste water. Results showed that PDI/CuS-10% exhibited highest photocatalytic behavior. The apparent rate constants for tetracycline (TC) degradation for the blend were 5.27 and 2.68 times higher than that of CuS or PDI, respectively. The enhancement of photocatalytic activity was mainly attributed to the π-π stacking and p-n junction, which can accelerate the separation of the photo-generated h⁺-e^- pairs. Besides, the light absorption of PDI/CuS from 800 to 200 nm was significantly enhanced and the absorption edge even reached the near-infrared region, which also played an important role in providing desired photocatalytic properties. Surprisingly, PDI/CuS could maintain high catalytic activity even after 5 cycles under simulated conditions, indicating that the composite had high potential for practical applications. Owing to high efficiency, low cost and wide application range, the PDI/CuS nanocomposites are promising candidates for environmental remediation.

Keystone taxa shared between earthworm gut and soil indigenous microbial communities collaboratively resist chlordane stress

Chlordane is an organochlorine pesticide that is applied extensively. Residual concentrations that remain in soils after application are highly toxic to soil organisms, particularly affecting the earthworm gut and indigenous soil microorganisms. However, response mechanisms of the earthworm gut and indigenous soil microorganism communities to chlordane exposure are not well known. In this study, earthworms (Metaphire guillelmi) were exposed to chlordane-contaminated soils to investigate their response mechanisms over a gradient of chlordane toxicity. Results from high-throughput sequencing and network analysis showed that the bacterial composition in the earthworm gut varied more significantly than that in indigenous soil microbial communities under different concentrations of chlordane stress (2.3-60.8 mg kg^-1; p < 0.05). However, keystone species of Flavobacterium, Candidatus Nitrososphaera, and Acinetobacter remained stable in both the earthworm gut and bacterial communities despite varying degrees of chlordane exposure, and their relative abundance was slightly higher in the low-concentration treatment group (T1, T2) than in the high-concentration treatment group (T3, T4). Additionally, network analysis demonstrated that the average value of the mean degree of centrality, closeness centrality, and eigenvector centrality of all keystone species screened by four methods (MetagenomeSeq, LEfSe, OPLS-DA, Random Forest) were 161.3, 0.5, and 0.63, respectively, and that these were significantly higher (p < 0.05) than values for non-keystone species (84.9, 0.4, and 0.2, respectively). Keystone species had greater network connectivity and a stronger capacity to degrade pesticides and transform carbon and nitrogen than non-keystone species. The keystone species, which were closely related to the microbial community in soil indigenous flora and earthworm intestinal flora, could resist chlordane stress and undertake pesticide degradation. These results have increased understanding of the role of the earthworm gut and indigenous soil bacteria in resisting chlordane stress and sustaining microbial equilibrium in soil.

Metagenomic sequencing reveals detoxifying and tolerant functional genes in predominant bacteria assist Metaphire guillelmi adapt to soil vanadium exposure

Due to extensive vanadium (V) mining and processing, an increasing amount of V has accumulated in soil, which poses a threat to public health. Consequently, we used earthworm (Metaphire guillelmi) incubation trials in V-contaminated soil (0-300 mg kg^-1) to explore the response of soil indigenous bacteria and earthworm intestinal bacteria to V stress. Metagenomic analysis revealed that V exposure changed the bacterial composition in the soil and the worm gut. However, although the core species varied between soil and worm gut, the two systems shared the predominant bacteria, including Staphylococcus, Nocardioides, Streptococcus, and Nitrosopumilales. Two functional genotypes were detected in the shared core species, i.e., reductive genes and resistant genes. The reductive genes mainly consisted of those involved in glutathione, cysteine, methionine, sulfur, and nitrogen metabolisms. The resistant genes included those encoding the oxidation damage repair system, the outer membrane protein, the antioxidant enzyme system, the metal-binding, and the heavy-metal efflux. Therefore, the shared core species exert a comprehensive strategy to survive V stress involving the alliance of heavy metal detoxifying and tolerant genes. This study provides novel information about the detoxification mechanisms of bacterial populations in soil and worm gut to survive V stress.

Metagenomics reveals functional profiling of microbial communities in OCP contaminated sites with rapeseed oil and tartaric acid biostimulation

Organochlorine pesticides (OCPs) contaminated sites pose great threats to both human health and environmental safety. Targeted bioremediation in these regions largely depends on microbial diversity and activity. This study applied metagenomics to characterize the microbial communities and functional groups composition features during independent or simultaneous rapeseed oil and tartaric acid applications, as well as the degradation kinetics of OCPs. Results showed that: the degradation rates of α-chlordane, β-chlordane and mirex were better when (0.50% w/w) rapeseed oil and (0.05 mol L^-1) tartaric acid were applied simultaneously than singular use, yielding removal rates of 56.4%, 53.9%, and 49.4%, respectively. Meanwhile, bio-stimulation facilitated microbial enzyme (catalase/superoxide dismutase/peroxidase) activity in soils significantly, promoting the growth of dominant bacterial communities. Classification at phylum level showed that the relative abundance of Proteobacteria was significantly increased (p < 0.05). Network analysis showed that bio-stimulation substantially increased the dominant bacterial community's proportion, especially Proteobacteria. The functional gene results illustrated that bio-stimulation facilitated total relative abundance of degradation genes, phosphorus, carbon, nitrogen, sulfur metabolic genes, and iron transporting genes (p < 0.05). In metabolic pathways, functional genes related to methanogenesis and ammonia generation were markedly upregulated, indicating that bio-stimulation promoted the transformation of metabolic genes, such as carbon and nitrogen. This research is conducive to exploring the microbiological response mechanisms of bio-stimulation in indigenous flora, which may provide technical support for assessing the microbial ecological remediation outcomes of bio-stimulation in OCP contaminated sites.