Metagenomics analysis reveals the distribution and communication of antibiotic resistance genes within two different red swamp crayfish Procambarus clarkii cultivation ecosystems

Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

Microcosm experiments revealed resistome coalescence of sewage treatment plant effluents in river environment

Sewage treatment plant (STP) effluents are important contributors of antibiotic resistance (AR) pollution in rivers. Effluent discharging into rivers causes resistome coalescence. However, their mechanisms and dynamic processes are poorly understood, especially for the effects of dilution, diffusion, and sunlight-induced attenuation on coalescence. In this study, we have constructed microcosmic experiments based on in-situ investigation to explore these issues. The first batch experiment revealed the effects of dilution and diffusion. The coverage of water coalesced resistomes ranged 66.26∼152.18 × /Gb and was positively correlated with effluent volume (Mann-Kendall test, p < 0.01). Principal coordinate analysis (PCoA) and source tracking analysis demonstrated that dilution and diffusion stepwise reduced AR pollution. The second batch experiment explored the temporal dynamics and sunlight attenuation on coalesced resistomes. Under natural light, the coverage and diversity of water resistomes posed decreasing trends, primarily attributed to drastic erasure of effluent traces. The proportion of effluent-specific ARGs in coalesced resistomes significantly declined over time (Spearman's r = -0.83 and -0.94 in coverage and richness). While under dark condition, the coverage and diversity increased. Sunlight radiation intensified the interactions between water and sediment resistomes, as evidenced by more shared ARGs and less dissimilarities across niches. Network analysis, metagenome-assembled genome (MAG) analysis and variation partitioning analysis (VPA) showed that microbiome controlled resistome coalescence, explaining 56.5% and 58.4% of resistomes in water and sediment, respectively. Biotic and abiotic factors synergistically explained 40% of water resistomes. This study offers a comprehensive understanding of AR transmission and provides theoretical bases for grasping AR pollution and developing effective suppression strategies.

The Role of Biogeography in Shaping Intestinal Flora and Influence on Fatty Acid Composition in Red Swamp Crayfish (Procambarus clarkii)

Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.

The fate of antibiotic resistance genes in the coastal lagoon with multiple functional zones

Coastal lagoons provide many important services to human society, but their year-round use for aquaculture introduces large amounts of sewage. The contamination of antibiotic resistance genes (ARGs) is therefore of great concern. In this study, 50 ARGs subtypes, two integrase genes (intl1, intl2), and 16S rRNA genes were detected by high-throughput quantitative PCR, and standard curves of all target genes were prepared for quantification. The occurrence and distribution of ARGs in a typical coastal lagoon (XinCun lagoon, China) were comprehensively explored. We detected 44 and 38 subtypes of ARGs in the water and sediment, respectively, and discuss the various factors influencing the fate of ARGs in the coastal lagoon. Macrolides-lincosamides-streptogramins B was the primary ARG type, and macB was the predominant subtype. Antibiotic efflux and antibiotic inactivation were the main ARG resistance mechanisms. The XinCun lagoon was divided into eight functional zones. The ARGs showed a distinct spatial distribution owing to the influence of microbial biomass and anthropogenic activity in different functional zones. Fishing rafts, abandoned fish ponds, the town sewage zone, and mangrove wetlands provided a large quantity of ARGs to the XinCun lagoon. Nutrients and heavy metals also significantly correlated with the fate of the ARGs, especially NO₂^--N and Cu, which cannot be ignored. It is noteworthy that lagoon-barrier systems coupled with persistent pollutant inputs result in coastal lagoons acting as a "buffer pool" for ARGs, which can then accumulate and threaten the offshore environment.

Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels

Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.

The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests

Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.

Distribution and influencing factors of antibiotic resistance genes of crayfish (Procambarus clarkii) intestine in main crayfish breeding provinces in China

The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO₃-N, pH and temperature), microbial alpha diversity and mobile genetic elements (MGEs) showed significant influence on ARGs profiles. Generally, our results illustrate that ARGs are prevalent in crayfish gut and may pose potential risk to human health, which will help develop targeted strategies for the risk management and assessment of ARGs in the aquaculture.

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.

Transmission of tetracycline resistance genes and microbiomes from manure-borne black soldier fly larvae frass to rhizosphere soil and pakchoi endophytes

Manure treatment with black soldier fly larvae (BSFL) and BSFL frass application in crop land is a sustainable strategy; however, whether residual antibiotic resistance genes (ARGs) and their transmission risk are related to the manure BSFL treatment process is still unknown. In this paper, the effect of BSFL addition density on residual tetracycline resistance genes (TRGs) and transmission from frass to pakchoi was determined. The results showed that BSFL frass can provide sufficient nutrients for growth, improve the economic value of pakchoi, and reduce the risk of transmission of TRGs in chicken manure regardless of BSFL density. The potential hosts of the TRGs we detected were found in BSFL frass (Oblitimonas and Tissierella), rhizosphere soil (Mortierella and Fermentimonas), and pakchoi endophytes (Roseomonas). The present study concluded that BSFL frass produced by adding 100 BSFL per 100 g of chicken manure has the advantages of high value and low risk. These findings will provide important strategic guidance for animal manure disposal and theoretical support for preventing the transmission of TRGs in BSFL applications.

Antibiotic resistance genes and their links with bacteria and environmental factors in three predominant freshwater aquaculture modes

Rapid development of aquaculture industry and increasing demand of various inputs (especially antibiotics), are suspected to promote the occurrence and spread of ARGs in aquaculture related environments. However, the occurrences of ARGs under different freshwater aquaculture practices are rarely known. Here, we investigated the seasonal profiles of the main ARGs, intI1 and bacteria in waters from three kinds of predominant freshwater aquaculture practices around the Honghu Lake (China), as well as their co-occurrences and interrelationships with antibiotics, heavy metals and general water quality. The results indicate that quinolone resistance genes (qnrB), tetracycline resistance genes (tetB and tetX) and sulfonamide resistance genes (sul1 and sul2) were the top five predominant ARGs with seasonal variations of abundance. Fish ponds were of the highest absolute abundances of tested ARGs than the other two modes. Crayfish ponds and their adjacent ditches shared similar ARGs profile. Different subtypes of ARGs belonging to the same class of resistance were varied in abundances. Some bacteria were predicted to carry different ARGs, which indicating multi-antibiotic resistances. Moreover, the combined environmental factors (antibiotics, heavy metals and water quality) partially shaped the profiles of ARGs and bacteria composition. Overall, this study provides new comprehensive understanding on the characterization of ARGs contamination in different freshwater aquaculture practices from the perspectives of environmental chemistry, microbiology and ecology. The results would benefit the optimization of aquaculture practices toward environmental integrity and sustainability.

Occurrence of antibiotics and antibiotic resistance genes in cultured prawns from rice-prawn co-culture and prawn monoculture systems in China

Antibiotics and antibiotic resistance genes (ARGs) in the aquatic environment have raised great concerns, as the deleterious effects of residual antibiotics and the emergence of ARGs are challenges to aquaculture. This study analyzed feed, water, sediment and prawns' tissues from six culture ponds (integrated culture: rice-prawn pond; monoculture: prawn pond) in Tianjin, Northeast China. Eighteen types of antibiotics were detected in all ponds, which conferring to four classes of antibiotics including sulfonamides, tetracyclines, fluoroquinolones, macrolides. The mean log bioaccumulation factor (BAF) values for five antibiotics were analyzed in the hepatopancreas, muscle, and plasma, and we found the maximum Log BAF (1.45) for enrofloxacin in prawn plasma. Correlation analysis of antibiotic concentrations between the plasma and the other two tissues indicated that enrofloxacin, norfloxacin, and erythromycin levels in the hepatopancreas and muscle can be predicted by their plasma concentrations. We also conducted a hazard quotient analysis and found that the risk to human health of eating antibiotic-exposed prawns from the two types of aquaculture method was relatively low. Compared with monoculture, rice-prawn co-culture could significantly decrease the abundance of ARGs; additionally, significant correlations were detected among ARGs, antibiotics, and non-antibiotic environmental factors (e.g., total nitrogen, total ammonia nitrogen, and chemical oxygen demand) in prawn. The present study indicated that the rice-prawn co-culture system is more effective than monoculture for mitigating the bioaccumulation of antibiotics and the occurrence of ARGs in prawn.