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

Roxarsone reduces earthworm-mediated nutrient cycling by suppressing aggregate formation and enzymic activity in soil with manure application

The application of manure and earthworms are frequently used in fertilization practices to improve C, N, and P cycling in soil, which may be adversely affected by roxarsone (ROX), as an organoarsenical pollutant. To effectively address this issue, in this work, the interactive impacts of ROX and earthworm Eisenia foetida on the aggregate formation, input of organic carbon (OC), and changes in the available N and P following 56-day cultivation were systematically investigated. Compared to the control, earthworms increased the mean weight diameter (MWD) of the soil aggregates from 0.6 to 1.1 mm. Thereby, they activated soil enzymes including catalase (CAT), sucrase (SC), urease (UE), and neutral phosphatase (NP), with the soil's pH decreased to 7.1. Consequently, the values of OC, soluble nitrite (NO3-N), and Olsen-P content were respectively increased by 0.78-, 1.69-, and 0.87- folds in the E treatment (14.3 vs. 25.5 g/kg, 12.8 vs. 33.3 mg/kg, and 7.8 vs. 14.6 mg/kg). Although the changes in the R treatment were slight, ROX reduced the earthworm-mediated improvements of soil fertility during the application of the RE treatment compared to the E treatment, i.e., the values of MWD, OC, NO3-N, and Olsen-P were reduced to 0.9 mm, 20.4 g/kg, 25.4 mg/kg, and 11.6 mg/kg, respectively. From the well-fitted structural equation models, it was demonstrated that earthworms enhanced the aggregate formation and nutrient cycling of OC, NO3-N, and Olsen-P, which were inhibited by ROX. Overall, these adverse effects can be offset by earthworm addition, which can play the dual role of monitor and driver for the soil properties. Our work provides insightful strategies for ROX-bearing manure management.

Comparative Analysis of Bacterial Community Structures in Earthworm Skin, Gut, and Habitat Soil across Typical Temperate Forests

Earthworms are essential components in temperate forest ecosystems, yet the patterns of change in earthworm-associated microbial communities across different temperate forests remain unclear. This study employed high-throughput sequencing technology to compare bacterial community composition and structure in three earthworm-associated microhabitats (skin, gut, and habitat soil) across three typical temperate forests in China, and investigated the influence of environmental factors on these differential patterns. The results indicate that: (1) From warm temperate forests to cold temperate forests, the soil pH of the habitat decreased significantly. In contrast, the physicochemical properties of earthworm skin mucus exhibited different trends compared to those of the habitat soil. (2) Alpha diversity analysis revealed a declining trend in Shannon indices across all three microhabitats. (3) Beta diversity analysis revealed that the transition from warm temperate deciduous broad-leaved forest to cold temperate coniferous forest exerted the most significant impact on the gut bacterial communities of earthworms, while its influence on the skin bacterial communities was comparatively less pronounced. (4) Actinobacteria and Proteobacteria were the predominant phyla in earthworm skin, gut, and habitat soil, but the trends in bacterial community composition differed among the three microhabitats. (5) Mantel tests revealed significant correlations between bacterial community structures and climatic factors, physicochemical properties of earthworm habitat soil, and physicochemical properties of earthworm skin mucus. The findings of this study offer novel perspectives on the interplay between earthworms, microorganisms, and the environment within forest ecosystems.

Cultivation of earthworms and analysis of associated bacterial communities during earthworms' growth using two types of agricultural wastes

Earthworm cultivation can effectively promote the resource utilization of agricultural waste. The efficient utilization of agricultural waste by earthworms mainly depends on the microbial communities in the guts. This study used silkworm excrement and cow manure as substrates for earthworm cultivation and investigated the associated bacterial communities during earthworms' growth. The survival rate of earthworms remained above 89% after 21 days of feeding with the two substrates. Proteobacteria, Actinobacteria, and Firmicutes constituted the predominant bacterial communities in earthworm growth, accounting for over 81% of the relative abundance in both guts and vermicompost. The bacteria richness and diversity in the foregut and midgut of earthworm were lower than those in the hindgut. The prediction function of intestinal bacterial communities of earthworms cultured with two substrates mainly involved biosynthesis, decomposition and energy production.

High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits

Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.

Impact of microplastics on nicosulfuron accumulation and bacteria community in soil-earthworms system

Microplastics (MPs) widely co-occur with various pollutants in soils. However, the data related to the impacts of MPs on terrestrial animal and microbial properties in pesticide-contaminated soils are few. In this study, the influence of MPs (0.01%, 0.1%, and 1%) on nicosulfuron concentrations in soil (10 µg/g) and earthworms were investigated, moreover, microbial community structure and diversity in soil and earthworm gut were also measured. After 30 days, the concentration of nicosulfuron in soil decreased to 1.27 µg/g, moreover, the residual concentration of nicosulfuron in soil (1%MPs and nicosulfuron) was only 44.8% of that in the single nicosulfuron treatment group. The accumulation of nicosulfuron in earthworms (1%MPs and nicosulfuron) was 7.37 µg/g, which was 1.82 times of that in the single nicosulfuron treatment group. In addition, 1% MPs decreased the richness and diversity of the soil and gut bacterial community in earthworms as well as altered microbial community composition, leading to the enrichment of specific microbial community. Our findings imply that MPs may change the migration of pesticides to terrestrial animal and as well as microbial diversity in earthworms and soil.

Epidermal microorganisms contributed to the toxic mechanism of nZVI and TCEP in earthworms by robbing metal elements and nutrients

Disrupting effects of pollutants on symbiotic microbiota have been regarded as an important mechanism of host toxicity, with most current research focusing on the intestinal microbiota. In fact, the epidermal microbiota, which participates in the nutrient exchange between hosts and environments, could play a crucial role in host toxicity via community changes. To compare the contributions of intestinal and epidermal symbiotic microorganisms to host toxicity, this study designed single and combined scenarios of soil contamination [nano zero-valent iron (nZVI) and tris (2-chloroethyl) phosphate (TCEP)], and revealed the coupling mechanisms between intestinal/epidermal symbiotic bacterial communities and earthworm toxicological endpoints. Microbiome analysis showed that 15% of intestinal microbes were highly correlated with host endpoints, compared to 45% of epidermal microbes showing a similar correlation. Functional comparisons revealed that key species on the epidermis were mainly heterotrophic microbes with genetic abilities to utilize metal elements and carbohydrate nutrients. Further verifications demonstrated that when facing the co-contamination of nZVI and TCEP, certain symbiotic microorganisms became dominant and consumed zinc, copper, and manganese along with saccharides and amino acids, which may be responsible for the nutritional deficiencies in the host earthworms. The findings can enrich the understanding of the coupling relationship between symbiotic microorganisms and host toxicity, highlighting the importance of epidermal microorganisms in host resistance to environmental pollution.

Elucidating response mechanisms at the metabolic scale of Eisenia fetida in typical oil pollution sites: A native driver in influencing carbon flow

Previous investigations on the stress response patterns of earthworms (Eisenia fetida) in practical petroleum hydrocarbon (PH) contamination systems were less focused. Therefore, this study investigated the ecotoxicological effect of PH contamination on earthworms based on metabonomics and histological observation, followed by correlation analysis between the earthworm metabolism, PH types and concentrations, soil physicochemical characteristics, and the microbial community structures (i.e., diversity and abundance) and functions. The results showed that due to the abundant PH organics, the cell metabolism of earthworms shifts under PH contamination conditions, leading them to use organic acids as alternative energy sources (i.e., gluconeogenesis pathway). Simultaneously, biomarker metabolites related to cellular uptake, stress response, and membrane disturbance were identified. In addition, when compared to the controls, considerable epicuticle and cuticle layer disruption was observed, along with PH internalization. It was demonstrated that PH pollution preferentially influences the physiological homeostasis of earthworms through indirect (i.e., microbial metabolism regulation) than direct (i.e., direct interaction with earthworms) mechanisms. Moreover, the varied CO2 releasement was verified, which highlights the potential role of earthworms in influencing carbon transformation and corresponds with the considerably enriched energy metabolism-related pathway. This study indicated that PH contamination can induce a strong stress response in earthworms through both direct and indirect mechanisms, which in turn, substantially influences carbon transformation in PH contamination sites.

Synergistic effects of earthworms and cow manure under reduced chemical fertilization modified microbial community structure to mitigate continuous cropping effects on Chinese flowering cabbage

The substitution of chemical fertilizers with organic fertilizers is a viable strategy to enhance crop yield and soil quality. In this study, the aim was to investigate the changes in soil microorganisms, soil chemical properties, and growth of Chinese flowering cabbage under different fertilization treatments involving earthworms and cow manure. Compared with the control (100% chemical fertilizer), CE (30% reduction in chemical fertilizer + earthworms) and CFE (30% reduction in chemical fertilizer + cow dung + earthworms) treatments at soil pH 8.14 and 8.07, respectively, and CFC (30% reduction in chemical fertilizer + cow manure) and CFE treatments increased soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), and available potassium (AK) contents. Earthworms and cow manure promoted the abundance of Bacillus and reduced that of the pathogens Plectosphaerella and Gibberella. The mantle test revealed that pH was not correlated with the microbial community. Random forest analysis verified that AN, SOM, and TN were important factors that jointly influenced bacterial and fungal diversity. Overall, the synergistic effect of earthworms and cow manure increased soil fertility and microbial diversity, thereby promoting the growth and development of Chinese flowering cabbage. This study enhanced the understanding of how bioregulation affects the growth and soil quality of Chinese flowering cabbage, and thus provided a guidance for the optimization of fertilization strategies to maximize the yield and quality of Chinese flowering cabbage while reducing environmental risks.

The temporal profile of GH1 gene abundance and the shift in GH1 cellulase-producing microbial communities during vermicomposting of corn stover and cow dung

Vermicomposting is a promising method for corn stover management to achieve bioresource recovery and environmental protection. Most β-glucosidases, which limit the cellulose degradation rate during vermicomposting of corn stover, belong to glycoside hydrolase family 1 (GH1). This study was conducted with different earthworm densities to quantify the GH1 gene abundance and investigate the evolution of GH1 cellulase-producing microbial communities using qPCR and pyrosequencing. The results showed that β-glucosidase activity, GH1 gene abundance, TOC, and microbial communities carrying the GH1 gene were affected by processing time and earthworm density. After introducing earthworms, β-glucosidase activity increased to 1.90-2.13 U/g from 0.54 U/g. The GH1 gene abundance of treatments with earthworms (5.82E+09-6.70E+09 copies/g) was significantly higher than that of treatments without earthworms (2.48E+09 copies/g) on Day 45. Earthworms increased the richness of microbial communities. The relative abundances of Sphingobium and Dyadobacter, which are dominant genera harboring the GH1 gene, were increased by earthworms to peak values of 23.90% and 11.20%, respectively. Correlation analysis showed that Sphingobium, Dyadobacter, Trichoderma, and Starkeya were positively associated with β-glucosidases. This work sheds new light on the mechanism of cellulose degradation during vermicomposting at the molecular level.

Dynamics of bacterial community in the foregut and hindgut of earthworms with the nutrition supplied by kitchen waste during vermicomposting

Earthworm gut microbiota is vital in degrading bio-waste during vermicomposting. However, microbial dynamics in earthworm gut during this process are unclear. Thus, the aim is to firstly report the bacterial dynamics in both foregut and hindgut of earthworms over a 28 days' timeframe of vermicomposting by Eisenia foetida with the nutrition supplied by kitchen waste. Results showed that except the changing of the bacterial diversity, composition and structure, dynamics of the foregut and hindgut bacteria also differed during vermicomposting which related to the changes of nutrient provision. Day 3 was a turning point. The abundant bacteria of the top 20 % genera nearly did not overlap between the foregut and hindgut. In the end of vermicomposting, a remarkable stable bacterial structure appeared in the hindgut compared to somewhat muddled one in the foregut. Understanding the dynamics of earthworm gut microbiota enables the improvements to regulate the efficiency of organic waste vermicomposting.

Deciphering roles of microbiota in arsenic biotransformation from the earthworm gut and skin

Biotransformation mediated by microbes can affect the biogeochemical cycle of arsenic. However, arsenic biotransformation mediated by earthworm-related microorganisms has not been well explored, especially the role played by earthworm skin microbiota. Herein, we reveal the profiles of arsenic biotransformation genes (ABGs) and elucidate the microbial communities of the earthworm gut, skin, and surrounding soil from five different soil environments in China. The relative abundance of ABGs in the earthworm skin microbiota, which were dominated by genes associated with arsenate reduction and transport, was approximately three times higher than that in the surrounding soil and earthworm gut microbiota. The composition and diversity of earthworm skin microbiota differed significantly from those of the soil and earthworm gut, comprising a core bacterial community with a relative abundance of 96% Firmicutes and a fungal community with relative abundances of 50% Ascomycota and 13% Mucoromycota. In addition, stochastic processes mainly contributed to the microbial community assembly across all samples. Moreover, fungal genera such as Vishniacozyma and Oomyces were important mediators of ABGs involved in the biogeochemical cycle of arsenic. This is the first study to investigate earthworm skin as a reservoir of microbial diversity in arsenic biotransformation. Our findings broaden the current scientific knowledge of the involvement of earthworms in the arsenic biogeochemical cycle.

Oxidative stress and DNA damage in earthworms induced by methyl tertiary-butyl ether in natural soils

Adverse effects of methyl tertiary-butyl ether (MTBE) have been noticed at different trophic levels by international researchers. However, there was unclear evidence about its effects on oxidative stress and DNA damage in earthworms. In this study, earthworms were cultivated in various doses of MTBE (0.0 mg/kg, 10.0 mg/kg, 30.0 mg/kg, and 60.0 mg/kg) contaminated agricultural soil for 7 days, 14 days, 21 days, and 28 days, respectively. The result showed that the reactive oxygen species (ROS) content of earthworms significantly increased in MTBE treatment groups compared to the control group. In MTBE treatment groups, the activities of superoxide dismutase, catalase, peroxidase, and glutathione S-transferase were significantly activated at the exposure of 7 days, which increased by 36.3-78.9%, 51.8-97.3%, 36.5-61.9%, and 12.0-54.8%, respectively. Then, the activities of these defense enzymes showed various changes following the changes in exposure times and MTBE concentrations. Especially in the 60.0 mg kg^-1 group, both antioxidant enzymes and GST were still significantly activated at the exposure of 14 days and then significantly inhibited at the exposure of 28 days. The analysis of olive tail moment showed significant DNA damage in the 10.0 mg kg^-1 group at the exposure of 28 days, and this damage in 30.0 mg/kg and 60.0 mg/kg groups was found at the exposure of 7 days. This result was consistent with the malondialdehyde accumulation in earthworms. Additionally, the analysis of IBRv2 showed the effects of MTBE treatments on earthworms in dose- and time-dependent manners. This study helps better to understand the effects of MTBE on soil invertebrate animals and provide theoretical support for soil protection in governing MTBE application.

Cow manure simultaneously reshaped antibiotic and metal resistome in the earthworm gut tract by metagenomic analysis

Earthworm conversion is an eco-friendly biological process that converts livestock waste into a benign nutrient-rich organic fertilizer. However, little is known about the impacts of earthworm-converted livestock manure on the antibiotic resistome in the earthworm gut microbiota. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift of antibiotic resistance genes (ARGs) in the earthworm gut-feeding on cow manure (CM)-by metagenomic analysis. The effects of copper (Cu) as a food addictive were also evaluated. CM substantially enriched the antibiotic resistome in the foregut and midgut, while it decreased in the hindgut. A similar trend was observed for metal resistance genes (MRGs). Notably, Cu in the CM had little effect on composition of ARGs and MRGs in earthworm gut. The earthworm gut microbiome altered by CM was responsible for the shift of ARGs and MRGs. In wormcast, Cu (100 and 300 mg/kg) significantly increased the abundance of ARGs and MRGs. Our study provides valuable insight into the response of ARGs and MRGs to CM in earthworm gut, and underscores the need for the judicious use of heavy metals as feed additives in livestock and poultry farming.

Insights into the mechanisms of organic pollutant toxicity to earthworms: Advances and perspectives

Earthworms play positive ecological roles in soil formation, structure, and fertility, environmental protection, and terrestrial food chains. For this review, we searched the Web of Science database for articles published from 2011 to 2021 using the keywords "toxic" and "earthworm" and retrieved 632 publications. From the perspective of bibliometric analysis, we conducted a co-occurrence network analysis using the keywords "toxic" and "earthworm" to identify the most and least reported topics. "Eisenia fetida," "bioaccumulation," "heavy metals," "oxidative stress," and "pesticides" were the most common terms, and "microbial community," "bacteria," "PFOS," "bioaugmentation," "potentially toxic elements," "celomic fluid," "neurotoxicity," "joint toxicity," "apoptosis," and "nanoparticles" were uncommon terms. Additionally, in this review we highlight the main routes of organic pollutant entry into soil, and discuss the adverse effects on the soil ecosystem. We then systematically review the mechanisms underlying organic pollutant toxicity to earthworms, including oxidative stress, energy and lipid metabolism disturbances, neurological toxicity, intestinal inflammation and injury, gut microbiota dysbiosis, and reproductive toxicity. We conclude by discussing future research perspectives, focusing on environmentally relevant concentrations and conditions, novel data processing approaches, technologies, and detoxification and mitigation methods. This review has implications for soil management in the context of environmental pollution.

Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line

BACKGROUND

The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.

RESULTS

Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.

CONCLUSIONS

This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.

Metabolic response of earthworms (Pheretima guillemi) to silver nanoparticles in sludge-amended soil

Silver nanoparticles (AgNPs) can enter soils via the application of sludge and pose risks to soil invertebrates. However, current knowledge regarding the toxicity of AgNPs at environmentally relevant concentration is insufficient, especially at the molecular level. Therefore, we examined the effects of low-level AgNPs (7.2 mg kg^-1, dry weight) on the bioaccumulation, pathology and metabolism of earthworms (Pheretima guillemi). After exposure for 28 d, earthworms were dissected into digestive system and the rest of the body to explore the response of different body parts to AgNPs. Ag concentration in the digestive system of exposed group (2.5 mg kg^-1, dry weight) was significantly higher than that of the control group (0.5 mg kg^-1, dry weight). AgNPs exposure had no significant effects on the survival and growth, but induced intestinal damage and metabolic interference to earthworms relative to the control. Metabolomics analysis showed that AgNPs exposure disturbed the glycerophospholipid metabolism, glutathione metabolism and energy metabolism in the digestive system and the energy metabolism in the rest of the body. AgNPs exposure also induced lipid peroxidation in the digestive system. The different metabolic responses between two body parts highlighted the importance of the uptake routes of Ag. These results provide a biochemical insight for the risk assessment of low-level AgNPs in terrestrial environment.

Feasibility of vermicomposting combined with room drying for enhancing the stabilization efficiency of dewatered sludge

Vermicomposting is characterized by transforming organic waste into nutrient-rich organic fertilizer through the action of different earthworms and microorganisms. Although vermicomposting can recycle the excess sludge in an eco-friendly manner, the longer stabilization period has limited its industrial application. The present study sought to investigate a novel operation process of vermicomposting combined with room drying (VD) to improve the stabilization efficiency of dewatered sludge. Subsequently, the performance and efficiency of vermicomposting without room drying, room dry without vermicomposting, and VD for sludge stabilization were compared simultaneously. In the VD process, the sludge water content reduced from 60.8% to 1.64%, showing the highest electrical conductivity and lowest organic matter content, making the humus substances abundant in the final product. Moreover, the vermicomposting achieved the highest ammonia and nitrate content in final product. Additionally, the bacterial and eukaryotic abundances in the VD product were significantly higher (P < 0.01, i.e., 15.6% and 180.7%) than the vermicomposting product. The specific bacterial genus of Glutamicibacter, Chitinibacter, and Acidobacteria was dominated in the VD product. The Partial least squares-Path modeling (PLS-PM) results revealed that the maturity degree in the VD product was significantly associated with microbial component, and the organic form was strongly driven by the change in the physicochemical properties, which was contradictory to vermicomposting model. The study suggests that the VD process could shorten the vermicomposting period by rapidly accelerating the physical, chemical, and biological stabilization of sludge.