Corpse decomposition increases the diversity and abundance of antibiotic resistance genes in different soil types in a fish model

Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Effects of cadmium exposure on gut microbiota and antibiotic resistance genes in Haliotis diversicolor abalone

Heavy metals in soil, water, and industrial production can affect the antibiotic resistance of bacteria. Antibiotic resistance in gut microbiota has been extensively researched. The effects of cadmium (Cd) was investigated on the gut microbiota and antibiotic resistance genes (ARGs) of Haliotis diversicolor, a commercially important abalone species. By exposing H. diversicolor to four concentrations of Cd (0 μg L-1 (control), 6.5 μg L-1 (low), 42.25 μg L-1 (medium), and 274.63 μg L-1 (high)) for 30 and 60 days, 16 types of ARG (aadA-01, aadA-02, cfr, dfrA1, ermB, floR, folA, mecA, sul2, tetB-01, tetC-01, tetD-01, tetG-01, tetM-02, tetQ, vanC-01), and 1213 genus and 27 phylum microbiomes were detected. ARGs can be resistant to aminoglycoside, beta-lactamase, macrolide-lincosamide-streptogramin B, multidrug, florfenicol, macrolide, sulfonamides, tetracyclines, and vancomycin. Cadmium exposure significantly alters the abundance of tetC-01, tetB-01, tetQ, sul2, and aadA-01. About 5% (61) of genus-level microorganisms were significantly affected by Cd exposure. Microbiota alpha and beta diversities in the 60-day 42.25 μg L-1 Cd treatment differed significantly from those in other treatments. In addition, 26 pathogens were detected, and two pathogens (Vibrio and Legionella) were significantly affected by Cd exposure. Significant correlations between pathogens and ARGs increased with increased Cd concentration after 60 days of Cd exposure. Cadmium exposure may cause gut microbiota disturbance in H. diversicolor and increase the likelihood of ARG transfer to pathogens, increasing potential ecological and economic risks.

Metagenomics reveals the self-recovery and risk of antibiotic resistomes during carcass decomposition of wild mammals

Animal carcass decomposition may bring serious harm to the environment, including pathogenic viruses, toxic gases and metabolites, and antibiotic resistance genes (ARGs). However, how wild mammal corpses decomposition influence and change ARGs in the environment has less explored. Through metagenomics, 16S rRNA gene sequencing, and physicochemical analysis, this study explored the succession patterns, influencing factors, and assembly process of ARGs and mobile genetic elements (MGEs) in gravesoil during long-term corpse decomposition of wild mammals. Our results indicate that the ARG and MGE communities related to wildlife corpses exhibited a pattern of differentiation first and then convergence. Different from the farmed animals, the decomposition of wild animals first reduced the diversity of ARGs and MGEs, and then recovered to a level similar to that of the control group (untreated soil). ARGs and MGEs of the gravesoil are mainly affected by deterministic processes in different stages. MGEs and bacterial community are the two most important factors affecting ARGs in gravesoil. It is worth noting that the decomposition of wild animal carcasses enriched different high-risk ARGs at different stages (bacA, mecA and floR), which have co-occurrence patterns with opportunistic pathogens (Comamonas and Acinetobacter), thereby posing a great threat to public health. These results are of great significance for wildlife corpse management and environmental and ecological safety.

Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow

Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3--N 14.7% and NH4+-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.

Multiple effects of ZnO nanoparticles on goldfish (Carassius auratus): Skin mucus, gut microbiota and stable isotope composition

The skin and the gut are direct target tissues for nanoparticles, yet attention to effects of metal-based nanoparticles (MNPs) on these two and the discrepancy in these effects remain inadequate. Here, effects of ZnO nanoparticles (nZnO) on skin mucus and gut microbiota of goldfish (Carassius auratus) were investigated, as well as further elements turnover and metabolic variations. After 14 days of exposure, considerable variations in levels of biomarkers (protein, glucose, lysozyme and immunoglobulin M) in skin mucus demonstrated significant stress responses to nZnO. nZnO exposure significantly reduced the abundance of Cetobacterium in the gut while increased that of multiple pathogens, and further leading to down-regulation of pathways such as carbohydrate metabolism, translation, and replication and repair. Decreased δ¹⁵N values indicated declined N turnover in vivo, further demonstrating the negative effect of nZnO on metabolism in the organism. Integration analysis of each biomarker using the biomarker response index version 2 (IBRv2) revealed concentration-dependent effects of nZnO on skin mucus, while effects on physiology in vivo was not, demonstrating the discrepancy in the toxicity pathways and toxic effects of nZnO on different tissues. This work improved our understanding about the comprehensive toxicity of nZnO on aquatic organism.

A bibliometric analysis of microbial forensics from 1984 to 2022: progress and research trends

Microbial forensics is a rapidly evolving discipline that has gained significant momentum in recent years. The study evaluated relevant results over the last four decades from 1984 to 2022 all over the world, aiming to analyze the growing trends and research orientations of microbial forensics. Using "microbial forensics" as the search topic in the Web of Science Core Collection, the systematic retrieval identified 579 documents relevant to the field and draw many statistical tables and maps to make the retrieval results visible. According to further bibliometric analysis, there are an increasing number of publications related to microbial forensics from the overall trend, with the highest number of publications recorded in 2021. In terms of the total number of articles, the USA and China were both the leading contributors to the field among 40 countries. The field has developed rapidly in recent years based on the development of next-generation sequencing. Over the course of its development, there are rich keywords in the research of scholars, which focus on diversity and identification. Moreover, despite the early hot topic being PCR (the use of PCR to probe microorganisms), in recent years, the topics, markers, and the potential application of microorganisms in forensic practice have become hot, which also indicates the future research directions of microbial forensic.

Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil

Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.

Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes

In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.

Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water

Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.

Corpse decomposition of freshwater economic fish leads to similar resistomes and the enrichment of high-risk antibiotic resistance genes in different water types

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Microbiota and mobile genetic elements influence antibiotic resistance genes in dust from dense urban public places

Many contaminants were carried by dust, a common environment media that is easy to contact with human beings, and antibiotic resistance genes (ARGs) as an emergency pollutant also harbor in dust and pose serious threats to human health especially those carried by opportunistic pathogens because inactivation of antibiotics caused by ARGs may enhance pathogenicity. Considering there is a gap of investigation of dust ARGs, 16 S rRNA gene sequences and high-throughput quantitative PCR were employed to obtain information of microbial communities and accumulated ARGs in dust from different urban places, including the malls, hospitals, schools and parks, to investigate the distribution and influencing factors of ARGs and discover the potential hosts of ARGs in dust. Here, 9 types of ARGs such as sulfonamide, tetracycline, and beta-lactamase and 71 subtypes of ARGs like sul1, tetM-01, and drfA1 were detected in dust. ARGs had varying distribution in different public places and seasons in dust. The abundances of total ARGs, MLSB and tetracycline genes were higher in spring than summer. The diversity of ARGs was highest in malls, follow by hospitals, schools, and parks. Additionally, multi-drug resistance genes in dust were more abundant in hospitals than in schools and parks. The microbes were distinguished as the most important driving factors for ARGs in dust, followed by the mobile genetic elements (MGEs) and different places, while dust physicochemical parameters only exert a negligible impact. Notably, several opportunistic pathogens like the Streptococcus, Vibrio, and Pseudomonas were inferred as potential hosts of high-risk ARGs such as mecA, tetM-02, and tetO-01 in dust because of strongly positive co-occurrence. These results imply that dust is likely an important reservoir of ARGs. We should realize that ARGs may be harbored in some opportunistic pathogens occur in dust and endanger human health because of dust contacting to human easily.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

Heavy rainfall accelerates the temporal turnover but decreases the deterministic processes of buried gravesoil bacterial communities

The influences of global climatic change require an understanding of changes in soil microbial communities under precipitation. However, little is known about how soil ("gravesoil") microbial communities associated with corpse decay respond to precipitation. Here, we explored the variations of temporal turnover and assembly in gravesoil bacterial communities in the Qinghai-Tibet Plateau ecosystem via controlled rainfall simulation experiments. In our experiments, rainfall intensity was set to 2.5 and 5 mm/3 days to simulate moderate and heavy rainfall, respectively, and sampling was conducted on the 4th, 11th, 18th, 32nd, 46th and 60th day. Our results showed precipitation significantly altered bacterial abundances and community structures. Analysis of time-decay relationships revealed that precipitation resulted in a divergent succession of gravesoil bacterial community structure and abundance changes of dominant phyla, such as Chloroflexi. Moreover, in the experimental groups, our results suggested that moderate rainfall increased the deterministic processes in the initial and mid periods, whereas heavy rainfall decreased these processes of gravesoil microbial community assembly in every period compared with those in the control group. The dispersal capacity induced by stochastic processes of gravesoil microbial communities decreased over time under moderate rainfall, whereas it initially increased and then decreased under heavy rainfall. This study highlights the influence of heavy rainfall on bacterial communities during corpse decay, which can provide some inferences for predicting changes in soil microbial communities under global climatic change.

Corpse decay of wild animals leads to the divergent succession of nrfA-type microbial communities

Animal carcasses introduce large amounts of nitrates and ammonium into the soil ecosystem. Some of this ammonium is transformed from nitrite through the nrfA-type microbial community. However, it is unclear how nrfA-type microorganisms respond to the decomposition of corpses. This study applied high-throughput sequencing to characterize the ecological succession of nrfA-type microbial communities in grassland soil. Our results showed that Cyclobacterium and Trueperella were the predominant genera for nrfA-type communities in soil with a decomposing corpse (experimental group), while Cyclobacterium and Archangium were dominant in soil without a corpse (control group). The alpha diversity indexes and the resistance and resilience indexes of the microbial communities initially increased and then decreased during decomposition. Compared with the control group, nrfA-encoding community structure in the experimental group gradually became divergent with succession and temporal turnover accelerated. Network analysis revealed that the microbial communities of the experimental group had more complex interactions than those of the control groups. Moreover, the bacterial community assembly in the experimental group was governed by stochastic processes, and the communities of the experimental group had a weaker dispersal capacity than those of the control group. Our results reveal the succession patterns of the nrfA-type microbial communities during degradation of wild animal corpses, which can offer references for demonstrating the ecological mechanism underlying the changes in the nrfA-type microbial community during carcass decay. KEY POINTS: • Corpse decay accelerates the temporal turnover of the nrfA-type community in soil. • Corpse decay changes the ecological succession of the nrfA-type community in soil. • Corpse decay leads to a complex co-occurrence pattern of the nrfA-type community in soil.

Animal Activities of the Key Herbivore Plateau Pika (Ochotona curzoniae) on the Qinghai-Tibetan Plateau Affect Grassland Microbial Networks and Ecosystem Functions

Plateau pikas (Ochotona curzoniae) are high-altitude model animals and famous "ecosystem engineers" on the Qinghai-Tibet Plateau. Pika activities may accelerate the degradation of alpine meadows. Nevertheless, little is known about the responses of bacterial, fungal, and archaeal communities, and ecosystem multifunctionality to pika perturbations. To address this question, we studied the impacts of only pika disturbance and combined disturbance (pika disturbance and grazing) on ecological networks of soil microbial communities and ecosystem multifunctionality. Our results demonstrated that Proteobacteria, Ascomycota, and Crenarchaeota were dominant in bacteria, fungi, and archaea, respectively. Bacteria, fungi, and archaea were all influenced by the combined disturbance of grazing and pika. Most fungal communities became convergent, while bacterial and archaeal communities became differentiated during the succession of surface types. In particular, the bacterial and fungal networks were less stable than archaeal networks. In response to the interference, cross-domain cooperation between bacterial and fungal communities increased, while competitive interactions between bacterial and archaeal communities increased. Pika disturbance at high intensity significantly reduced the ecosystem multifunctionality. However, the mixed effects of grazing and pika weakened such influences. This study revealed how pika activities affected microbial networks and ecosystem multifunctionality. These results provide insights to designing reasonable ecological management strategies for alpine grassland ecosystems.