Mobile Incubator for Iron(III) Reduction in the Gut of the Soil-Feeding Earthworm Pheretima guillelmi and Interaction with Denitrification

Integrated assessment of the chemical, microbiological and ecotoxicological effects of a bio-packaging end-of-life in compost

The present study aimed to i) assess the disintegration of a novel bio-packaging during aerobic composting (2 and 6 % tested concentrations) and evaluate the resulting compost ii) analyse the ecotoxicity of bioplastics residues on earthworms; iii) study the microbial communities during composting and in 'earthworms' gut after their exposure to bioplastic residues; iv) correlate gut microbiota with ecotoxicity analyses; v) evaluate the chemico-physical characterisation of bio-packaging after composting and earthworms' exposure. Both tested concentrations showed disintegration of bio-packaging close to 90 % from the first sampling time, and compost chemical analyses identified its maturity and stability at the end of the process. Ecotoxicological assessments were then conducted on Eisenia fetida regarding fertility, growth, genotoxic damage, and impacts on the gut microbiome. The bioplastic residues did not influence the earthworms' fertility, but DNA damages were measured at the highest bioplastic dose tested. Furthermore bioplastic residues did not significantly affect the bacterial community during composting, but compost treated with 2 % bio-packaging exhibited greater variability in the fungal communities, including Mortierella, Mucor, and Alternaria genera, which can use bioplastics as a carbon source. Moreover, bioplastic residues influenced gut bacterial communities, with Paenibacillus, Bacillus, Rhizobium, Legionella, and Saccharimonadales genera being particularly abundant at 2 % bioplastic concentration. Higher concentrations affected microbial composition by favouring different genera such as Pseudomonas, Ureibacillus, and Streptococcus. For fungal communities, Pestalotiopsis sp. was found predominantly in earthworms exposed to 2 % bioplastic residues and is potentially linked to its role as a microplastics degrader. After composting, Attenuated Total Reflection analysis on bioplastic residues displayed evidence of ageing with the formation of hydroxyl groups and amidic groups after earthworm exposure.

Long-term Application of Agricultural Amendments Regulate Hydroxyl Radicals Production during Oxygenation of Paddy Soils

Hydroxyl radicals (•OH) play a significant role in contaminant transformation and element cycling during redox fluctuations in paddy soil. However, these important processes might be affected by widely used agricultural amendments, such as urea, pig manure, and biochar, which have rarely been explored, especially regarding their impact on soil aggregates and associated biogeochemical processes. Herein, based on five years of fertilization experiments in the field, we found that agricultural amendments, especially coapplication of fertilizers and biochar, significantly increased soil organic carbon contents and the abundances of iron (Fe)-reducing bacteria. They also substantially altered the fraction of soil aggregates, which consequently enhanced the electron-donating capacity and the formation of active Fe(II) species (i.e., 0.5 M HCl-Fe(II)) in soil aggregates (0-2 mm), especially in small aggregates (0-3 μm). The highest contents of active Fe(II) species in small aggregates were mainly responsible for the highest •OH production (increased by 1.7-2.4-fold) and naphthalene attenuation in paddy soil with coapplication of fertilizers and biochar. Overall, this study offers new insights into the effects of agricultural amendments on regulating •OH formation in paddy soil and proposes feasible strategies for soil remediation in agricultural fields, especially in soils with frequent occurrences of redox fluctuations.

Amorphous Fe substrate enhances nitrogen and phosphorus removal in sulfur autotrophic process

The autotrophic denitrification of coupled sulfur and natural iron ore can remove nitrogen and phosphorus from wastewater with low C/N ratios. However, the low solubility of crystalline Fe limits its bioavailability and P absorption capacity. This study investigated the effects of amorphous Fe in drinking water treatment residue (DWTR) and crystalline Fe in red mud (RM) on nitrogen and phosphorus removal during sulfur autotrophic processes. Two types of S-Fe cross-linked filler particles with three-dimensional mesh structures were obtained by combining sulfur with the DWTR/RM using the hydrogel encapsulation method. Two fixed-bed reactors, sulfur-DWTR autotrophic denitrification (SDAD) and sulfur-RM autotrophic denitrification (SRAD), were constructed and stably operated for 236 d Under a 5-8-h hydraulic retention time, the average NO3--N, TN, and phosphate removal rates of SDAD and SRAD were 99.04 %, 96.29 %, 94.03 % (SDAD) and 97.33 %, 69.97 %, 82.26 % (SRAD), respectively. It is important to note that fermentative iron-reducing bacteria, specifically Clostridium_sensu_stricto_1, were present in SDAD at an abundance of 58.17 %, but were absent from SRAD. The presence of these bacteria facilitated the reduction of Fe (III) to Fe (II), which led to the complete denitrification of the S-Fe (II) co-electron donor to produce Fe (III), completing the iron cycle in the system. This study proposes an enhancement method for sulfur autotrophic denitrification using an amorphous Fe substrate, providing a new option for the efficient treatment of low-C/N wastewater.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Molecular mechanisms of nano-sized polystyrene plastics induced cytotoxicity and immunotoxicity in Eisenia fetida

Nanoplastics (NPs) are currently everywhere and environmental pollution by NPs is a pressing global problem. Nevertheless, until now, few studies have concentrated on the mechanisms and pathways of cytotoxic effects and immune dysfunction of NPs on soil organisms employing a multidimensional strategy. Hence, earthworm immune cells and immunity protein lysozyme (LZM) were selected as specific receptors to uncover the underlying mechanisms of cytotoxicity, genotoxicity, and immunotoxicity resulting from exposure to polystyrene nanoplastics (PS-NPs), and the binding mechanisms of PS-NPs-LZM interaction. Results on cells indicated that when earthworm immune cells were exposed to high-dose PS-NPs, it caused a notable rise in the release of reactive oxygen species (ROS), resulting in oxidative stress. PS-NPs exposure significantly decreased the cell viability of earthworm immune cells, inducing cytotoxicity through ROS-mediated oxidative stress pathway, and oxidative injury effects, including reduced antioxidant defenses, lipid peroxidation, DNA damage, and protein oxidation. Moreover, PS-NPs stress inhibited the intracellular LZM activity in immune cells, resulting in impaired immune function and immunotoxicity by activating the oxidative stress pathway mediated by ROS. The results from molecular studies revealed that PS-NPs binding destroyed the LZM structure and conformation, including secondary structure changes, protein skeleton unfolding/loosening, fluorescence sensitization, microenvironment changes, and particle size changes. Molecular docking suggested that PS-NPs combined with active center of LZM easier and inhibited the protein function more, and formed a hydrophobic interaction with TRP 62, a crucial amino acid residue closely associated with the function and conformation of LZM. This is also responsible for LZM conformational changes and functional inhibition /inactivation. These results of this research offer a fresh outlook on evaluating the detriment of NPs to the immune function of soil organisms using cellular and molecular strategies.

Exploring the toxicity of biodegradable microplastics and imidacloprid to earthworms (Eisenia fetida) from morphological and gut microbial perspectives

Biodegradable microplastics (BMPs) pose serious environmental problems to soil organisms, and their adsorption capacity might make pesticides more dangerous for soil organisms. Therefore, in this study, polylactic acid (PLA) BMPs and imidacloprid (IMI) were used as a representative of BMPs and pesticides, respectively. Eisenia fetida was used as a test animal to investigate the effects of environmentally relevant concentrations of single and compound contaminated PLA BMPs and IMI on mortality, growth, number of offspring, tissue damage, and gut microorganisms of E.fetida. Exposure to PLA BMPs treatment and PLA BMPs + IMI treatment resulted in a sustained increase in E.fetida mortality, reaching 16.7% and 26.7%, respectively. The growth inhibition rate of single treatments was significantly increased. The compound contamination had the greatest effect on E.fetida offspring compared to the control. PLA BMPs and IMI cause histological damage to E.fetida, with the compound treatment causing the most severe damage. Based on the results of 16S sequencing, the bacterial communities in E.fetida gut and soil treated to PLA BMPs and IMI were significantly different. PLA BMPs + IMI treatment suppresses the abundance and diversity of E.fetida gut microorganisms, disrupting the homeostasis of bacterial communities and causing immune and metabolic dysfunction. These findings highlight the more severe damage of combined PLA BMPs and IMI pollution to E.fetida, and help to assess the risk of earthworm exposure to environmentally relevant concentrations of PLA BMPs and IMI.

Phages in vermicomposts enrich functional gene content and facilitate pesticide degradation in soil

Organic fertilizer microbiomes play substantial roles in soil ecological functions, including improving soil structure, crop yield, and pollutant dissipation. However, limited information is available about the ecological functions of phages and phage-encoded auxiliary metabolic genes (AMGs) in orga9nic fertilizers. Here we used a combination of metagenomics and phage transplantation trials to investigate the phage profiles and their potential roles in pesticide degradation in four organic fertilizers from different sources. Phage annotation results indicate that the two vermicomposts made from swine (PV) and cattle (CV) dung had more similar phage community structures than the swine (P) and cattle (C) manures. After vermicomposting, the organic fertilizers (PV and CV) exhibited enriched phage-host pairings and phage AMG diversity in relative to the two organic fertilizers (P and C) without composting. In addition, the number of broad-host-range phages in the vermicomposts (182) was higher than that in swine (153) and cattle (103) manures. Notably, phage AMGs associated with metabolism and pesticide biodegradation were detected across the four organic fertilizers. The phage transplantation demonstrated that vermicompost phages were most effective at facilitating the degradation of pesticide precursor p-nitrochlorobenzene (p-NCB) in soil, as compared to swine and cattle manures (P < 0.05). Taken together, our findings highlight the significance of phages in vermicompost for biogeochemical cycling and biodegradation of pesticide-associated chemicals in contaminated soils.

Earthworms synergize with indigenous soil functional microorganisms to accelerate the preferential degradation of the highly toxic S-enantiomer of the fungicide imazalil in soil

The roles of soil and earthworm gut microorganisms in the degradation of the chiral fungicide imazalil (IMA) enantiomers were systemically studied in soil-earthworm systems. S-IMA degraded slower than R-IMA in soil without earthworms. After the addition of earthworms, S-IMA degraded faster than R-IMA. Methylibium was the potential degradative bacterium likely related to the preferential degradation of R-IMA in soil. However, the addition of earthworms significantly decreased the relative abundance of Methylibium, especially in R-IMA-treated soil. Meanwhile, a new potential degradative bacterium Aeromonas first appeared in soil-earthworm systems. Compared with enantiomer-treated soil, the relative abundance of indigenous soil bacterium Kaistobacter significantly boomed in enantiomer-treated soil with earthworms. Interestingly, Kaistobacter in the earthworm gut also obviously increased after exposure to enantiomers, particularly in S-IMA-treated soil, which was associated with the significant increase in Kaistobacter in soil. More importantly, the relative abundances of Aeromonas and Kaistobacter in S-IMA-treated soil were obviously higher than those in R-IMA-treated soil after the addition of earthworms. Moreover, these two potential degradative bacteria were also potential bacterial hosts of the biodegradation genes p450 and bph. Collectively, gut microorganisms are important helpers in soil pollution remediation by participating in the preferential degradation of S-IMA mediated by indigenous soil microorganisms.

Role of microbial iron reduction in arsenic metabolism from soil particle size fractions in simulated human gastrointestinal tract

Gut microbiota provides protection against arsenic (As) induced toxicity, and As metabolism is considered an important part of risk assessment associated with soil As exposures. However, little is known about microbial iron(III) reduction and its role in metabolism of soil-bound As in the human gut. Here, we determined the dissolution and transformation of As and Fe from incidental ingestion of contaminated soils as a function of particle size (<250 μm, 100-250 μm, 50-100 μm and < 50 μm). Colon incubation with human gut microbiota yielded a high degree of As reduction and methylation of up to 53.4 and 0.074 μg/(log CFU/mL)/hr, respectively; methylation percentage increased with increasing soil organic matter and decreasing soil pore size. We also found significant microbial Fe(III) reduction and high levels of Fe(II) (48 %-100 % of total soluble Fe) may promote the capacity of As methylation. Although no statistical change in Fe phases was observed with low Fe dissolution and high molar Fe/As ratios, higher As bioaccessibility of colon phase (avg. 29.4 %) was mainly contributed from reductive dissolution of As(V)-bearing Fe(III) (oxy)hydroxides. Our results suggest that As mobility and biotransformation by human gut microbiota (carrying arrA and arsC genes) are strongly controlled by microbial Fe(III) reduction coupled with soil particle size. This will expand our knowledge on oral bioavailability of soil As and health risks from exposure to contaminated soils.

Iron scraps packing rapidly enhances nitrogen removal in an aerobic sludge system and the mechanism

Simultaneous nitrification and denitrification (SND) has the advantage of energy saving and carbon demand reduction. Here, readily available low-cost iron scraps packing was added to an aerobic sludge system. This successfully enhanced the efficiency of total nitrogen removal from 37.7 ± 13.2 % to 62.7 ± 7.9 % over 2 days. While electrons from iron biocorrosion did not contribute to nitrate reduction, iron promoted heterotrophic denitrification. The iron scraps changed the spatial distribution of the microbial community, where more denitrification bacteria accumulated around the packing and higher denitrification capacity was noted. Metagenomic analysis of the sludge cultured in the presence of iron scraps for 2 days revealed that, with the exception of the enriched amoA/B/C gene expression, the abundance of other key nitrogen removal genes showed little variation. Furthermore, the structure of the microbial community was unchanged probably due to the relatively short culturing period. However, metatranscriptomic analysis indicated that iron increased the abundance of nitrifying bacteria (i.e. unclassified Nitrosomonas, Nitrosomonas sp. Is79A3 and Nitrospira defluvii) and promoted higher expression of nitrification genes. Notably, iron scraps packing decreased the abundance of the key denitrification bacteria Thauera sp. MZ1T from 52.92 to 7.58 %. The expression of napA/B also decreased, while expression of narG/H/I increased by 9 to 23 fold and a 2 to 3 fold over expression was noted for nirS, norB/C and nosZ in the presence of iron scraps. This suggested that aerobic denitrification was inhibited and anaerobic denitrification was promoted. This study has provided in-depth understanding of the influence of iron on SND to improve the application of iron-supported biological processes.

The synergistic effect between biofertility properties and biological activities in vermicomposting: A comparable study of pig manure

Vermicomposting is a resource technology for managing animal excreta, whereas the internal relationships of the process are vital for its wide applications. The present study examined how macronutrient and micronutrient concentrations, microbial communities, and enzymatic activity of pig manure (PM) changed during the composting and vermicomposting processes and their internal interactions. The vermicomposting process increased macronutrients more significantly than composting (32.40% of total available nitrogen, 21.70% of total available phosphorous, and 12.70% of total available potassium). The vermicomposting reduced total organic carbon (7.91%), C/N ratio (61.35%), and humification index (56.47%) more than composting due to the quick decomposition of PM. After continual fertility optimization, the total microbial population, with the exception of total fungi, rose significantly to accelerate organics mineralization and improve macronutrients in vermicomposting compared to composting. Moreover, earthworm addition favored the stabilization of the PM containing higher concentrations of micronutrients after being catalyzed by the enhanced catalase activity and reduced sucrase activity after 90 days of vermicomposting. Principal component analysis and chord plots found that the generated vermicomposting products had higher fertility properties and biological activities induced by the synergistic effect of microorganisms and earthworms. These findings highlight vermicomposting is an eco-friendly management technology for processing PM and can be scaled up for agricultural applications.

Bacterial Keystone Taxa Regulate Carbon Metabolism in the Earthworm Gut

As important ecosystem engineers in soils, earthworms strongly influence carbon cycling through their burrowing and feeding activities. Earthworms do not perform these roles in isolation, because their intestines create a special habitat favorable for complex bacterial communities. However, how the ecological functioning of these earthworm-microbe interactions regulates carbon cycling remains largely unknown. To fill this knowledge gap, we investigated the bacterial community structure and carbon metabolic activities in the intestinal contents of earthworms and compared them to those of the adjacent soils in a long-term fertilization experiment. We discovered that earthworms harbored distinct bacterial communities compared to the surrounding soil under different fertilization conditions. The bacterial diversity was significantly larger in the adjacent soils than that in the earthworm gut. Three statistically identified keystone taxa in the bacterial networks, namely, Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans, were shared across the earthworm gut and adjacent soil. Environmental factors (pH and organic matter) and keystone taxa were important determinants of the bacterial community composition in the earthworm gut. Both PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) and FAPROTAX (Functional Annotation of Prokaryotic Taxa) predicted that carbon metabolism was significantly higher in adjacent soil than in the earthworm gut, which was consistent with the average well color development obtained by the Biolog assay. Structural equation modeling combined with correlation analysis suggested that pH, organic matter, and potential keystone taxa exhibited significant relationships with carbon metabolism. This study deepens our understanding of the mechanisms underlying keystone taxa regulating carbon cycling in the earthworm gut. IMPORTANCE The intestinal microbiome of earthworms is a crucial component of the soil microbial community and nutrient cycling processes. If we could elucidate the role of this microbiome in regulating soil carbon metabolism, we would make a crucial contribution to understanding the ecological role of these gut bacterial taxa and to promoting sustainable agricultural development. However, the ecological functioning of these earthworm-microbe interactions in regulating carbon cycling has so far not been fully investigated. In this study, we revealed, first, that the bacterial groups of Solirubrobacterales, Ktedonobacteraceae, and Jatrophihabitans were core keystone taxa across the earthworm gut and adjacent soil and, second, that the environmental factors (pH and organic carbon) and keystone taxa strongly affected the bacterial community composition and exhibited close correlations with microbial carbon metabolism. Our results provide new insights into the community assembly of the earthworm gut microbiome and the ecological importance of potential keystone taxa in regulating carbon cycling dynamics.

Comparative Study on Bacterial Population Dynamics of Foregut, Midgut, and Hindgut Content of Perionyx excavatus (Perrier) Isolated from Eco-friendly, Non-hazardous Vermicompost

The ideal condition of earthworm gut promotes growth and multiplication of beneficial soil microorganisms eliminating pathogens and converts organic wastes into nutrients rich compost. The present study has been carried out to determine the population dynamics of earthworm gut bacteria and to find out relative abundance of different functional bacterial groups in the foregut, midgut, and hindgut of earthworm Perionyx excavatus. To assess bacterial diversity, a viable plate count method was adopted. In the different gut region of earthworm, aerobic heterotrophic, amylolytic, Bacillus, Gram-negative, proteolytic, fat hydrolyzing, nitrate-reducing, nitrifying, asymbiotic nitrogen-fixing, Azotobacter, and phosphate solubilizing bacterial populations ranged from 22.2 to 241.6 × 10⁶, 8.0 to 171.60 × 10⁶, 1.83 to 2.79 × 10⁶, 10.68 to 23.04 × 10⁴, 3.70 to 5.52 × 10⁴, 59.60 to 208.40 × 10⁴, 1.86 to 7.34 × 10⁴, 10.94 to 19.78 × 10⁴, 0.80 to 3.42 × 10⁴, 7.83 to 13.70 × 10⁴, 1.31 to 2.67 × 10⁴ cfu/ml gut suspension, respectively. The results of the one-way ANOVA revealed that the bacterial load of most of the bacterial groups was significantly higher (p < 0.05) in the hindgut region, followed by midgut and foregut. Only the density of the proteolytic group was significantly higher (p < 0.05) in the midgut region followed by foregut and hindgut. Starch hydrolyzing bacteria constitute the largest group of bacteria in the gut content. From principal component analysis, two components were extracted with the eigenvalues of 8.485 and 1.132. Agglomerative hierarchical cluster analysis revealed that the bacterial populations were clustered into four different groups. Quantitative variation among bacterial groups in earthworm's gut seems to determine the soil health and composting efficiency; from this point of view, the present study will provide a better understanding about different functional bacterial groups of earthworm's guts and might be helpful in sustainable agriculture and waste management.

Effects of diisononyl phthalate exposure on the oxidative stress and gut microorganisms in earthworms (Eisenia fetida)

Phthalate esters (PAEs) are widely used as plasticizers and can be ubiquitously detected in environment. However, the toxic effects and mechanisms of diisononyl phthalate (DINP) on earthworms are still poorly understood. In this study, earthworms (Eisenia fetida) were exposed to DINP at various doses (0, 300, 600, 1200, and 2400 mg/kg) to investigate their subchronic toxicity. The results demonstrated that the reactive oxygen species (ROS) levels displayed an "increase-decrease" trend with the increasing DINP doses after DINP exposure on days 7, 14, 21, and 28. The malondialdehyde (MDA) content increased with increasing DINP doses on days 7, 14, and then decreased on days 21, 28. The values of superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST) showed similar variation patterns and reached a maximum level on 21 d. Moreover, on day 28, the SOD and CAT gene expression levels were upregulated, while the GST gene expression levels were downregulated. Meanwhile, 16S rRNA genes of E. fetida gut bacteria and surrounding soil bacteria were measured after 28 days of exposure to DINP. The Chao index of E. fetida gut bacteria decreased when the treatment with the highest concentration (2400 mg/kg) was applied. At the phylum level, the abundance of Chloroflexi was significantly lower in the gut of E. fetida. In addition, the abundance of Proteobacteria at the phylum level and Ottowia at the genus level significantly increased in the surrounding soil. Overall, our results shed light on the toxic mechanism of DINP at biochemical, molecular, and omics levels, and contributed to a better understanding of the ecotoxicity of DINP.

Medicinal Earthworm: Speciation and Bioaccessibility of Arsenic and Its Potential Health Risks

Arsenic in environmental health has caused public concerns all over the world. However, high levels of arsenic residues in medicinal animals have not received enough attention. Medicinal earthworms are consumed widely in China, but its arsenic potential health risks to humans are unknown. This work investigated the total concentration, bioaccessibility, and speciation of arsenic in earthworms by ICP-MS and HPLC-ICP-MS to evaluate its potential health risks to humans. Arsenic was found in all earthworms at concentrations ranging from 0.4 to 53.6 mg kg⁻¹. The bioaccessibility of arsenic (bAs) varied significantly and ranged from 12.1 to 69.1%, with inorganic arsenic (iAs, including As(III) and As(V)) as the predominant species. Furthermore, a small amount of arsenobetaine (AB) was found. The estimated daily intake dose (EDI), hazard quotient (HQ), and carcinogenic risk (CR) of arsenic in most of the samples exceeded the safe threshold level. Results from this study indicated that the potential health risks by the consumption of earthworms may not be negligible. Herein, recommendations for the use of earthworms and regulatory recommendations for arsenic limit standards were proposed. This study reminds us that more control and monitoring of arsenic in medicinal animals should be carried out.

Host age increased conjugal plasmid transfer in gut microbiota of the soil invertebrate Caenorhabditis elegans

Plasmid conjugation contributes greatly to the spread of antibiotic resistance genes (ARGs) in soils. However, the spread potential in the gut of soil fauna remains poorly studied, and little was known about the impact of host age on ARGs dissemination in the gut microbiota of soil animals. Here, the typical nematode-Caenorhabditis elegans was employed as the model soil animal, aiming to investigate transfer of broad-host-range IncP-1ɛ from Escherichia coli MG1655 to gut microbiota within 6 days under varied temperature gradients (15, 20 and 25 °C) using qPCR combined with plate screening. Results showed that conjugation rates increased with incubation time and rising temperature in the gut of C. elegans, sharing a similar trend with abundances of plasmid conjugation relevant genes such as trbBp (mating pair formation) and trfAp (plasmid replication). Incubation time and temperature significantly shaped the gut microbial community of C. elegans. Core microbiota in the gut of C. elegans, including Enterobacteriaceae, Lactobacillaceae and Leuconostocaceae, constituted a large part of transconjugal pool for plasmid IncP-1ɛ. Our results highlight an important sink of gut microbiota for ARGs dissemination and upregulation of ARGs transfer in the gut microbiota with host age, further potentially stimulating evolution of ARGs in terrestrial environments.

Incubation trial indicated the earthworm intestinal bacteria as promising biodigestor for mitigating tetracycline resistance risk in anthropogenic disturbed forest soil

The continuous input of antibiotics due to frequent anthropogenic activities have increased the dissemination risk of antibiotic resistance genes (ARGs) in forest soil. As soil engineers, it remains unclear whether earthworm intestinal microbial communities might play a role in controlling the ARG proliferation in forest soil. This study collected forest soil in the Yangtze River Delta, China, and its resident Metaphire guillelmi to investigate the interaction between tetracycline (50 μg kg^-1) and the bacteria in worm gut and soil. Metagenome sequencing analysis indicated that the abundance of the total ARGs in both the soil (S2) and the worm gut (E2) was 1.3 (p < 0.001) and 1.2 (p < 0.001) times higher than the soil (S1) and (E1) without tetracycline exposure; and under tetracycline stress, the relative abundance of 36 and 20 bacterial genera in forest soil and worm gut were significantly increased respectively. However, the ARGs/ARB abundance decreased in the soil with the worm addition than that without, which may be related to the fact that earthworm intestinal bacteria harbored more tetracycline-degrading genes, i.e. dehydrogenase genes adh, ETFDH, and gpr, etc. Structural equation model analysis indicated that bacteria in worm intestinal has stronger ability to degrade tetracycline than in soil, and the main dissipate way was dehydrogenation. Together, the results contributed to understanding the promising role of worm intestinal bacteria in controlling the ARG risk caused by antibiotic disturbed forest soil.

Combined pollution of arsenic and Polymyxin B enhanced arsenic toxicity and enriched ARG abundance in soil and earthworm gut microbiotas

Polymyxin B (PMB) is considered as the last line of antibiotic defense available to humans. The environmental effects of the combined pollution with PMB and heavy metals and their interaction mechanisms are unclear. We explored the effects of the combined pollution with PMB and arsenic (As) on the microbial composition of the soil and in the earthworm gut, as well as the spread and transmission of antibiotic resistance genes (ARGs). The results showed that, compared with As alone, the combined addition of PMB and As could significantly increase the bioaccumulation factor and toxicity of As in earthworm tissues by 12.1% and 16.0%, respectively. PMB treatment could significantly increase the abundance of Actinobacteria in the earthworm gut (from 35.6% to 45.2%), and As stress could significantly increase the abundance of Proteobacteria (from 19.8% to 56.9%). PMB and As stress both could significantly increase the abundance of ARGs and mobile genetic elements (MGEs), which were positively correlated, indicating that ARGs might be horizontally transferred. The inactivation of antibiotics was the main resistance mechanism that microbes use to resist PMB and As stress. Network analysis showed that PMB and As might have antagonistic effects through competition with multi-drug resistant ARGs. The combined pollution by PMB and As significantly promoted the relative abundance of microbes carrying multi-drug resistant ARGs and MGEs, thereby increasing the risk of transmission of ARGs. This research advances the understanding of the interaction mechanism between antibiotics and heavy metals and provides new theoretical guidance for the environmental risk assessment and combined pollution management.

Evaluating the interaction of soil microorganisms and gut of soil fauna on the fate and spread of antibiotic resistance genes in digested sludge-amended soil ecosystem

Earthworms have shown their effectiveness in reducing the abundances of antibiotic resistance genes (ARGs) from solid waste. However, the mechanisms of the reduced ARGs by earthworm and whether the solid waste would affect the ARGs profile in earthworm gut were poorly understood. Herein, the patterns of ARGs and microbial communities in digested sludge-amended soil and earthworm gut after 80-day cultivation were investigated. Results show that the enrichment of ARGs (e.g., tetA, tetQ, and sulII) in soil caused by digested sludge-amendment was temporary and would recover to their original levels before amendment. In addition, earthworms could contribute to the further reduction of ARG abundances, which was mainly attributed to their gut digestion via shifting the microbial community (e.g., attenuating the anaerobes). However, the amended soil could significantly increase ARGs abundance in the earthworm gut, which may enhance the potential risk of ARGs spread via the food chain. These findings may provide a new sight on the control of ARGs occurrence and dissemination in sludge-amended soil ecosystem with consideration of earthworms.

Anammox Bacteria Are Potentially Involved in Anaerobic Ammonium Oxidation Coupled to Iron(III) Reduction in the Wastewater Treatment System

Anaerobic ammonium oxidation coupled to nitrite reduction (termed as Anammox) was demonstrated as an efficient pathway to remove nitrogen from a wastewater treatment system. Recently, anaerobic ammonium oxidation was also identified to be linked to iron(III) reduction (termed Feammox) with dinitrogen, nitrite, or nitrate as end-product, reporting to enhance nitrogen removal from the wastewater treatment system. However, little is known about the role of Anammox bacteria in the Feammox process. Here, slurry from wastewater reactor amended with ferrihydrite was employed to investigate activity of Anammox bacteria in the Feammox process using the ¹⁵N isotopic tracing technique combined with 16S rRNA gene amplicon sequencing. A significantly positive relationship between rates of ¹⁵N₂ production and iron(III) reduction indicated the occurrence of Feammox during incubation. Relative abundances of Anammox bacteria including Brocadia, Kuenenia, Jettenia, and unclassified Brocadiaceae were detected with low relative abundances, whereas Geobacteraceae dominated in the treatment throughout the incubation. ¹⁵N₂ production rates significantly positively correlated with relative abundances of Geobacter, unclassified Geobacteraceae, and Anammox bacteria, revealing their contribution to nitrogen generation via Feammox. Overall, these findings suggested Anammox bacteria or cooperation between Anammox bacteria and iron(III) reducers serves a potential role in Feammox process.

Variations in bacterial taxonomic profiles and potential functions in response to the gut transit of earthworms (Eisenia fetida) feeding on cow manure

Earthworms play an important role in the organic matter decomposition in terrestrial ecosystems. Earthworms interact directly with the microorganisms to affect the organic matter decomposition via gut transit, i.e., the digestion and assimilation of organic matter in the foregut and midgut and its excretion by the hindgut. However, how the microbial community ingested by earthworms respond to the transit processes in different gut segments of earthworms is not clear. We used composted cow manure to feed earthworms and sampled vermicompost and the contents of foregut, midgut and hindgut for bacterial 16S rRNA gene sequencing analysis. We observed that earthworm gut transit decreased the abundances of the dominant phyla Proteobacteria and Bacteroidetes but increased Actinobacteria, Chloroflexi and Acidobacteria. The alpha diversity of bacterial community in midgut was the lowest of the different gut segments, and the bacterial community structure of the foregut was significantly different from the midgut and hindgut. The enrichment analysis results revealed different selective stimulatory and inhibitory effects on the ingested bacterial community in the different gut segments, which extended to vermicompost. The FAPROTAX data indicated that C and N metabolic microbes were enriched in the earthworm gut. Microbes involved in fermentation and methanogenesis were enriched in the hindgut, and denitrification microbes were enriched in the foregut. The N metabolism microbes in vermicompost were significantly enriched after the stimulation of earthworm gut transit (P < 0.05), and the pathogenic microbes of animals and plants were inhibited. Combined with the results of subsequent correlation and biochemical analyses, earthworm gut transit significantly altered the structure and function of the bacterial community to accelerate the degradation and mineralization of organic matter and the enrichment of phosphorus and potassium. Our study suggests that the gut transit process of earthworms plays an important role in regulating organic matter dynamics in terrestrial ecosystems.

Active iron species driven hydroxyl radicals formation in oxygenation of different paddy soils: Implications to polycyclic aromatic hydrocarbons degradation

The frequently occurring redox fluctuations in paddy soil are critical to the cycling of redox-sensitive elements (e.g., iron (Fe) and carbon) due to the driving of microbial processes. However, the associated abiotic process, such as hydroxyl radical (^•OH) formation, was rarely investigated. Hence, we examined the under-appreciated role of ^•OH formation in driving polycyclic aromatic hydrocarbons (PAHs) degradation upon oxygenation of anoxic paddy slurries. Results showed that ^•OH production largely differed in different paddy slurries, in the range of 271.5-581.2 μmol kg^-1 soil after 12 h reaction. The ^•OH production was highly hinged on the contents of active Fe species, i.e., exchangeable, surface-bound Fe and Fe in low-crystalline phases rather than Fe in high-crystalline minerals or silicates. Besides, ^•OH production significantly decreased with increasing soil depth due to the declined active Fe species and abundance of functional microbes. Oxygenation also induced the transformation of these active Fe species into the low- and high-crystalline phases, which might affect the following redox process. The produced ^•OH can efficiently degrade PAHs with degradation extents depending on their physiochemical properties. Our findings highlight the key roles of active Fe species in driving ^•OH formation and organic contaminants degradation during redox fluctuations of paddy soils.

Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms

Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.

Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems

Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.

Fates of Antibiotic Resistance Genes in the Gut Microbiome from Different Soil Fauna under Long-Term Fertilization

Applying organic fertilizers has been well documented to facilitate the dissemination of antibiotic resistance genes (ARGs) in soil ecosystems. However, the role of soil fauna in this process has been seldom addressed, which hampers our ability to predict the fate of and to manage the spread of ARGs. Here, using high-throughput quantitative polymerase chain reaction (HT-qPCR), we examined the effect of long-term (5-, 8-, and 10-year) fertilization treatments (control, inorganic fertilizers, and mixed fertilizers) on the transfer of ARGs between soil, nematodes, and earthworms. We found distinct fates for ARGs in the nematodes and earthworms, with the former having higher enriched levels of ARGs than the latter. Fertilization impacted the number and abundance of ARGs in soil, and fertilization duration altered the composition of ARGs. Shared ARGs among soil, nematodes, and earthworm guts supported by a fast expectation-maximization microbial source tracking analysis demonstrated the trophic transfer potential of ARGs through this short soil food chain. The transfer of ARGs was reduced by fertilization duration, which was mainly ascribed to the reduction of ARGs in the earthworm gut microbiota. This study identified the transfer of ARGs in the soil-nematode-earthworm food chain as a potential mechanism for a wider dissemination of ARGs in the soil ecosystem.

Effescts of acute diclofenac exposure on intestinal histology, antioxidant defense, and microbiota in freshwater crayfish (Procambarus clarkii)

In the present study, we exposed Procambarus clarkii to different doses (0, 1, and 10 mg/L) of diclofenac (DCF). Meanwhile, we investigated the effects of exposure to DCF on intestinal histology, antioxidant defense, and microbial communities in P. clarkii. The results showed DCF caused histological changes in the intestines. Additionally, DCF induced significant changes in the expression of antioxidant genes including Mn-sod, cat, gst, and gpx. High-throughput sequencing of 16 S rRNA gene revealed DCF changed the diversity, richness, and composition of intestinal microbial communities. The relative abundances of the predominant phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria showed significant changes at the phylum level after treatment with DCF. At the genus level, the most predominant genera with marked differences in abundance were Lucibacterium, Shewanella, Bacteroides, Anaerorhabdus, Aeromonas, Acinetobacter, Clostridium XlVb, Arcobacter, Bosea, and so on. To conclude, treatment with DCF could cause intestinal histological damage, induce significant changes of the expression of intestinal antioxidant genes, and impact the composition of intestinal microbiota in P. clarkii. This research will provide novel insights into the toxic effects of DCF on aquatic crustaceans.

Ecological role of earthworm intestinal bacteria in terrestrial environments: A review

Increasing evidence demonstrated the critical role the earthworm gut played in sustaining earthworm's metabolism and transformation of nutrients and pollutants in the environment. Being rich in nutrients, the earthworm gut is favorable for the colonization of (facultative) anaerobic bacteria, which bridge the host earthworm gut with adjacent terrestrial environment. Therefore, the status quo of earthworm gut research was primarily reviewed in this work. It was found that most studies focused on the bacterial composition and diversity of the earthworm gut, and their potential application in nutrient element and pollutant transformation, such as nitrification, methanogens, heavy metal detoxification, etc. Yet limited information was available about the specific mechanism of intestinal bacteria in nutrient and pollutant transformation. Therefore, in this work we highlighted the current problems and concluded the future prospect of worm's intestinal bacteria research. On one hand, high throughput sequencing and bioinformatics tools are critical to break the bottleneck in the intestinal bacteria research via clarifying the molecular mechanism involved in the transformation processes described above. In addition, a global dataset concerning worm gut bacteria will be needed to provide comprehensive information about intestinal bacteria pool, and act as a communication platform to further encourage the progress of worm gut research.

Silver Sulfide Nanoparticles Reduce Nitrous Oxide Emissions by Inhibiting Denitrification in the Earthworm Gut

The accumulation of Ag₂S in agricultural soil via application of Ag-containing sludge potentially affects the functioning of soil microorganisms and earthworms (EWs) due to the strong antimicrobial properties of Ag. This study examined the effects of Ag₂S nanoparticles (Ag₂S-NPs) on the EW-mediated (Eisenia fetida and Pontoscolex corethrurus) soil N cycle. We used 16S rRNA gene-based sequencing and quantitative polymerase chain reaction to examine the bacterial community and nitrification/denitrification-related gene abundance. The presence of either EWs or Ag significantly increased denitrification and N₂O emissions. However, the addition of Ag₂S to EW-inhabited soil reduced N₂O emissions by 14-33%. Furthermore, Ag₂S caused a low-dose stimulation but a high-dose inhibition to N₂O flux from the EW gut itself. Accordingly, an increase in Ag in the EW gut caused a decrease in the relative abundance of denitrifiers in both the soil and the gut, especially for the dominant genus Bacillus. Ag₂S also decreased the copy numbers of nitrification gene (nxrB) and denitrification genes (napA, nirS, and nosZ) in EW gut, leading to the observed decrease in N₂O emissions. Collectively, applying Ag₂S-containing sludge disturbs the denitrification function of the EW gut microbiota and the cycling of N in soil-based systems.

Biological removal of cadmium from biogas residues during vermicomposting, and the effect of earthworm hydrolysates on Trichoderma guizhouense sporulation

The removal efficiency of Cd from biogas residues (BR) by earthworms (Eisenia fetida) during vermicomposting and the optimum addition of earthworm hydrolysates for production of Trichoderma guizhouense NJAU 4742 spores were determined. The results showed that vermicomposting could effectively remove Cd (up to 18.9%) from the BR. Synchrotron radiation based FTIR spectromicroscopy demonstrated a weakened correlation between functional groups after vermicomposting, suggesting that the activity of earthworms affects the binding sites and bioavailability of heavy metals. Under optimum conditions, the hydrolysis rate of earthworms was ~97% and the removal efficiency of Cd was up to 93%. Furthermore, addition of 20% of earthworm hydrolysate promoted the largest production of Trichoderma sporulation (~2.95 × 10⁸ cfu/g straw), indicating the possibility of earthworm hydrolysates promoting the growth of Trichoderma guizhouense is a suitable way to recycle earthworms after vermicomposting.

Does reduced usage of antibiotics in livestock production mitigate the spread of antibiotic resistance in soil, earthworm guts, and the phyllosphere?

The overuse of antibiotics in animal husbandry is widespread and believed to significantly contribute to the selection of antibiotic resistance genes (ARGs) in animals. Thus, there is a global drive to reduce antibiotic use in the agricultural sector. However, it has not been established whether a reduction in the use of antibiotics in livestock production would be effective in reducing the spread of ARGs. A microcosm approach was used to determine how the addition of manure with either reduced antibiotic levels or with typical antibiotic levels could affect the spread of antibiotic resistance genes between soil, earthworms and the phyllosphere. When compared to the control soil, earthworm and phyllosphere samples had the greater increase in ARG abundance in conventional manure treatments (P < 0.05). Reduced antibiotic manure also enriched the abundance of ARGs in the phyllosphere and soil but not earthworm guts when compared to the control (P < 0.05). In both soil and earthworm guts, the enrichment of ARGs was lower in reduced antibiotic manure than in conventional manure. This study has identified bacterial transfer through the soil-earthworm-phyllosphere system as a potential means to spread ARGs between habitats after fertilization with livestock derived manures.

Effects of cadmium on intestinal histology and microbiota in freshwater crayfish (Procambarus clarkii)

In this study, Procambarus clarkii (P. clarkii) were exposed to different concentrations (0, 2, 5 and 10 mg/L) of cadmium (Cd). We studied the effects of Cd exposure on intestinal histology and microbiota in P. clarkii. The results demonstrated that exposure to Cd caused histological alterations in the intestines of P. clarkii. Meanwhile, high-throughput sequencing analysis revealed that Cd exposure could alter the richness, diversity, and composition of intestinal microbiota in P. clarkii. At the phylum level, the relative abundances of the prevalent phyla Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria changed significantly after exposure to Cd. At the genus level, the most prevalent genera with significant difference in relative abundance were Bacteroides, Clostridium XlVb, Hafnia, Buttiauxella, Shewanella, Anaerorhabdus, Alistipes, Arcobacter, Azoarcus, Chryseobacterium, and so on. Furthermore, functional prediction analysis of intestinal microbial communities showed that Cd exposure could significantly alter the pathways related to metabolism, diseases, cellular processes, and so on. Taken together, exposure to Cd could induce intestinal histological damage and affect intestinal microbiota composition and functions of P. clarkii. Our study can be an important step toward a better understanding of the toxic effects of Cd on aquatic crustaceans.

Metabolic Inactivity and Re-awakening of a Nitrate Reduction Dependent Iron(II)-Oxidizing Bacterium Bacillus ferrooxidans

Microorganisms capable of anaerobic nitrate-dependent Fe(II) (ferrous iron) oxidation (ANDFO) contribute significantly to iron and nitrogen cycling in various environments. However, lab efforts in continuous cultivation of ANDFO strains suffer from loss of activity when ferrous iron is used as sole electron donor. Here, we used a novel strain of nitrate-dependent Fe(II)-oxidizing bacterium Bacillus ferroxidians as a model and focused on the physiological activity of cells during ANDFO. It was shown that B. ferrooxidans entered a metabolically inactive state during ANDFO. B. ferrooxidans exhibited nitrate reduction coupled with Fe(II) oxidation, and the activity gradually declined and was hardly detected after 48-h incubation. Propidium monoazide (PMA) assisted 16S rRNA gene real-time PCR suggested that a large number of B. ferrooxidans cells were alive during incubation. However, ²H(D)-isotope based Raman analysis indicated that the cells were metabolically inactive after 120-h of ANDFO. These inactive cells re-awakened in R2A medium and were capable of growth and reproduction, which was consistent with results in Raman analysis. Scanning electron microscopy (SEM) observation and x-ray diffraction (XRD) revealed the formation of Fe minerals in close proximity of cells in the Fe(II)-oxidizing medium after Fe(II) oxidation. Overall, our results demonstrated that continued ANDFO can induce a metabolically inactive state in B. ferrooxidans, which was responsible for the loss of activity during ANDFO. This study provides an insight into the ANDFO process and its contribution to iron and nitrogen cycling in the environments.