Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome

Occurrence of antibiotic-resistant bacteria in the sea surface microlayer of coastal waters in the southern North Sea

The emergence of antibiotic-resistant bacteria in coastal waters is a global health problem posing potential risks to the health of humans who depend on coastal resources. Monitoring and increased efforts are needed to maintain the health of marine ecosystems. The sea surface microlayer (SML) is poorly studied for antibiotic resistance of the inhabiting bacteria. Therefore, we examined the antibiotic resistance patterns of 41 bacterial strains isolated from the SML in a harbor in the southern North Sea. The strains are affiliated with 17 genera typically found in the marine environment. Using the disc diffusion assay, we found extensive resistance, particularly to gentamycin, kanamycin, nalidixic acid, penicillin, sulfadimidine, and streptomycin. A broth microdilution assay showed high minimum inhibitory concentrations (MICs) for most isolates for amikacin, aztreonam, ceftazidime, cefepime, minocycline, and tobramycin. Genome analysis of three strains affiliated with the genera Pseudoseohaeicola, Nereida, and Vibrio, all showing a highly resistant phenotype, revealed the presence of 57, 42, and 90 genes, respectively, associated with antibiotic resistance. Over 50 % of these genes are multidrug efflux pumps. Our study shows that the SML in anthropogenic-influenced coastal regions harbors a wide diversity of antibiotic-resistant bacteria equipped with a broad range of multidrug efflux pumps.

Purification of aquaculture wastewater by macrophytes and biofilm systems: Efficient removal of trace antibiotics and enrichment of antibiotic resistance genes

The purification performance of aquaculture wastewater and the risk of antibiotic resistance genes (ARGs) dissemination in wetlands dominated by macrophytes remain unclear. Here, the purification effects of different macrophytes and biofilm systems on real aquaculture wastewater were investigated, as well as the distribution and abundance of ARGs. Compared to the submerged macrophytes, artificial macrophytes exhibited higher removal rates of TOC (58.80 ± 5.04 %), TN (74.50 ± 2.50 %), and TP (77.33 ± 11.66 %), and achieved approximately 79.92 % removal of accumulated trace antibiotics in the surrounding water. Additionally, the biofilm microbial communities on the surface of artificial macrophytes exhibited higher microbial diversity with fewer antibiotic-resistant bacteria (ARB) enrichment from the surrounding water. The absolute abundance of ARGs (sul1, sul2, and intI1) in the mature biofilm to be one to two orders of magnitude higher than that in the water. Although biofilms could decrease ARGs in the surrounding water by enriching ARB, the intricate network structure of biofilms further facilitated the proliferation of ARB and the dissemination of ARGs in water. Network analysis suggested that Proteobacteria and Firmicutes phyla were dominant and potential carriers of ARGs, contributing 69.00 % and 16.70 %, respectively. Our findings highlight that macrophytes and biofilm systems have great performance on aquaculture wastewater purification, but with high risk of ARGs.

Growth Suppression of a Robust Bacterium Methylobacterium extorquens by Porous Materials with Oxygen Functional Groups

Suppressing the growth of Methylobacterium species without the use of toxic chemicals has been a challenging task owing to their robustness against previous antimicrobial techniques. In this work, we prepared porous materials with various numbers and types of oxygen functional groups and investigated their ability to suppress the growth of Methylobacterium extorquens. It turned out that the number and type of oxygen functional groups in the porous materials greatly affected the growth of the bacterium. Three porous materials (resorcinol-formaldehyde gel (RF), hydrothermally treated RF (RFH), and Wakkanai siliceous shale (WS)) were tested, and RF exhibited the best performance in suppressing the growth of the bacterium. This performance is possibly due to abundant phenolic groups in the porous material.

Gut microbiota and transcriptome response of earthworms (Metaphire guillelmi) to polymyxin B exposure

Polymyxin B (PMB) has received widespread attention for its use as a last-line therapy against multidrug-resistant bacterial infection. However, the consequences of unintended PMB exposure on organisms in the surrounding environment remain inconclusive. Therefore, this study investigated the effects of soil PMB residue on the gut microbiota and transcriptome of earthworms (Metaphire guillelmi). The results indicated that the tested doses of PMB (0.01-100 mg/kg soil) did not significantly affect the richness and Shannon's diversity index of the earthworm gut microbiota, but PMB altered its community structure and taxonomic composition. Moreover, PMB significantly affected Lysobacter, Aeromonas, and Sphingomonas in the soil microbiota, whereas Pseudomonas was significantly impacted the earthworm gut microbiota. Furthermore, active bacteria responded more significantly to PMB than the total microbial community. Bacterial genera such as Acinetobacter and Bacillus were highly correlated with differential expression of some genes, including up-regulated genes associated with folate biosynthesis, sulphur metabolism, and the IL-17 signalling pathway, and downregulated genes involved in vitamin digestion and absorption, salivary secretion, other types of O-glycan biosynthesis, and the NOD-like receptor signalling pathway. These results suggest that adaptation to PMB stress by earthworms involves changes in energy metabolism, their immune and digestive systems, as well as glycan biosynthesis. The study findings help elucidate the relationship between earthworms and their microbiota, while providing a reference for understanding the environmental risks of PMB.

Rhizosphere bacteria show a stronger response to antibiotic-based biopesticide than to conventional pesticides

The plant microbiota can substantially contribute to various functions related to host health, fitness, and productivity. Therefore, maintaining the integrity of the microbiota is beginning to be seen as a crucial factor in modern agriculture. Here, we evaluated the effects of two chemical pesticides (azoxystrobin and carbendazim) and an antibiotic-based biopesticide (wuyiencin) on the rhizosphere microbiome of tomato plants. It was found that all treatments resulted in changes in the bacterial community structure to varying degrees. The most pronounced changes were observed with the biopesticide, which resulted in an enrichment of Streptomyces in the microbiome. In contrast, the relative abundance of Actinobacteria decreased in samples that were treated with low and high dosages of carbendazim. Clostridia were enriched after the applications of azoxystrobin and wuyiencin. When functioning of the microbiome was assessed, it was shown that genes encoding multidrug efflux pumps and ABC transporters related to nutrient uptake were enriched. This enrichment is likely to overcome potentially negative effects linked to the exposure to the employed substances. The study provides new insights into the potential of different pesticides to modulate native plant microbiomes, and thus highlights the importance to include such evaluations when new active agents are developed.

Antibiotic-Induced Recruitment of Specific Algae-Associated Microbiome Enhances the Adaptability of Chlorella vulgaris to Antibiotic Stress and Incidence of Antibiotic Resistance

Insights into the symbiotic relation between eukaryotic hosts and their microbiome lift the curtain on the crucial roles of microbes in host fitness, behavior, and ecology. However, it remains unclear whether and how abiotic stress shapes the microbiome and further affects host adaptability. This study first investigated the effect of antibiotic exposure on behavior across varying algae taxa at the community level. Chlorophyta, in particular Chlorella vulgaris, exhibited remarkable adaptability to antibiotic stress, leading to their dominance in phytoplankton communities. Accordingly, we isolated C. vulgaris strains and compared the growth of axenic and nonaxenic ones under antibiotic conditions. The positive roles of antibiotics in algal growth were apparent only in the presence of bacteria. Results of 16S rRNA sequencing further revealed that antibiotic challenges resulted in the recruitment of specific bacterial consortia in the phycosphere, whose functions were tightly linked to the host growth promotion and adaptability enhancement. In addition, the algal phycosphere was characterized with 47-fold higher enrichment capability of antibiotic resistance genes (ARGs) than the surrounding water. Under antibiotic stress, specific ARG profiles were recruited in C. vulgaris phycosphere, presumably driven by the specific assembly of bacterial consortia and mobile genetic elements induced by antibiotics. Moreover, the antibiotics even enhanced the dissemination potential of the bacteria carrying ARGs from the algal phycosphere to broader environmental niches. Overall, this study provides an in-depth understanding into the potential functional significance of antibiotic-mediated recruitment of specific algae-associated bacteria for algae adaptability and ARG proliferation in antibiotic-polluted waters.

The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts

BACKGROUND

The microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated with Riccia temporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria and Burgenland, Austria combining qPCR analyses, amplicon sequencing and advanced microscopy.

RESULTS

Riccia spec. div. was colonized by a very high abundance of bacteria (10¹⁰ 16S rRNA gene copies per g of thallus) as well as archaea and fungi (10⁸ ITS copies per g of thallus). Each Riccia thallus contain approx. 1000 prokaryotic and fungal ASVs. The field type was the main driver for the enrichment of fungal taxa, likely due to an imprint on soil microbiomes by the cultivated crop plants. This was shown by a higher fungal richness and different fungal community compositions comparing liverwort samples collected from pumpkin fields, with those from corn fields. In contrast, bacterial communities linked to liverworts are highly specialized and the soil attached to them is not a significant source of these bacteria. Specifically, enriched Cyanobacteria, Bacteroidetes and Methylobacteria suggest a symbiotic interaction. Intriguingly, compared to the surrounding soil, the thallus samples were shown to enrich several well-known bacterial and fungal phytopathogens indicating an undescribed role of liverworts as potential reservoirs of crop pathogens.

CONCLUSIONS

Our results provide evidence that a stable bacterial community but varying fungal communities are colonizing liverwort thalli. Post-harvest, temporary agricultural biocrusts are important reservoirs for microbial biodiversity but they have to be considered as potential reservoirs for pathogens as well.

Field-realistic dose of cefotaxime enhances potential mobility of β-lactam resistance genes in the gut microbiota of zebrafish (Danio rerio)

With large amounts of cephalosporin end up in natural ecosystems, water has been acknowledged as the large reservoir of β-lactam resistance over the past decades. However, there is still insufficient knowledge available on the function of the living organisms to the transmission of antibiotic resistance. For this reason, in this study, using adult zebrafish (Danio rerio) as animal model, exposing them to environmentally relevant dose of cefotaxime for 150 days, we asked whether cefotaxime contamination accelerated β-lactam resistance in gut microbiota as well as its potential transmission. Results showed that some of β-lactam resistance genes (βRGs) were intrinsic embedded in intestinal microbiome of zebrafish even without antibiotic stressor. Across cefotaxime treatment, the abundance of most βRGs in fish gut microbiome decreased apparently in the short term firstly, and then increased with the prolonged exposure, forming distinctly divergent βRG profiles with antibiotic-untreated zebrafish. Meanwhile, with the rising concentration of cefotaxime, the range of βRGs' host-taxa expanded and the co-occurrence relationships of mobile genetics elements (MGEs) with βRGs intensified, indicating the enhancement of βRGs' mobility in gut microbiome when the fish suffered from cefotaxime contamination. Furthermore, the path of partial least squares path modeling (PLS-PM) gave an integral assessment on the specific causality of cefotaxime treatment to βRG profiles, showing that cefotaxime-mediated βRGs variation was most ascribed to the alteration of MGEs under cefotaxime stress, followed by bacterial community, functioning both direct influence as βRG-hosts and indirect effects via affecting MGEs. Finally, pathogenic bacteria Aeromonas was identified as the critical host for multiple βRGs in fish guts, and its β-lactam resistance increased over the duration time of cefotaxime exposure, suggesting the potential spreading risks for the antibiotic-resistant pathogens from environmental ecosystems to clinic. Overall, our finding emphasized cefotaxime contamination in aquatic surroundings could enhance the β-lactam resistance and its transmission mobility in fish bodies.

Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa

Introduction

Every year, millions of deaths are associated with the increased spread of antimicrobial resistance genes (ARGs) in bacteria. With the increasing urbanization of the global population, the spread of ARGs in urban bacteria has become a more severe threat to human health.

Methods

In this study, we used metagenome-assembled genomes (MAGs) recovered from 1,153 urban metagenomes in multiple urban locations to investigate the fate and occurrence of ARGs in urban bacteria. Additionally, we analyzed the occurrence of these ARGs on plasmids and estimated the virulence of the bacterial species.

Results

Our results showed that multidrug and glycopeptide ARGs are ubiquitous among urban bacteria. Additionally, we analyzed the deterministic effects of phylogeny on the spread of these ARGs and found ARG classes that have a non-random distribution within the phylogeny of our recovered MAGs. However, few ARGs were found on plasmids and most of the recovered MAGs contained few virulence factors.

Discussion

Our results suggest that the observed non-random spreads of ARGs are not due to the transfer of plasmids and that most of the bacteria observed in the study are unlikely to be virulent. Additional research is needed to evaluate whether the ubiquitous and widespread ARG classes will become entirely prevalent among urban bacteria and how they spread among phylogenetically distinct species.

Chronicle of Research into Lichen-Associated Bacteria

Lichens are mutually symbiotic systems consisting of fungal and algal symbionts. While diverse lichen-forming fungal species are known, limited species of algae form lichens. Plasticity in the combination of fungal and algal species with different eco-physiological properties may contribute to the worldwide distribution of lichens, even in extreme habitats. Lichens have been studied systematically for more than 200 years; however, plasticity in fungal-algal/cyanobacterial symbiotic combinations is still unclear. In addition, the association between non-cyanobacterial bacteria and lichens has attracted attention in recent years. The types, diversity, and functions of lichen-associated bacteria have been studied using both culture-based and culture-independent methods. This review summarizes the history of systematic research on lichens and lichen-associated bacteria and provides insights into the current status of research in this field.

Trade-off for survival: Microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity

The environmental microbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen asa bioindicatororganism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native microbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.

Do microplastic biofilms promote the evolution and co-selection of antibiotic and metal resistance genes and their associations with bacterial communities under antibiotic and metal pressures?

Microplastic (MP) biofilms with heterogeneous bacterial compositions and structure have become a hotspot of antibiotic resistance genes (ARGs) in aquatic environments. The evolutionary features of ARGs and their related factors including class 1 integron (intI1), metal resistance genes (MRGs), and bacterial communities in MP biofilms under exogenous pressures and how they compared with natural substrates (NS) are unclear. The individual and combined pressures of sulfamethoxazole, tetracycline, and zinc were used to drive the dynamic evolution of ARGs, intI1, MRGs, and bacterial communities in the MP and NS biofilms. The exogenous pressures from the combined selection of sulfamethoxazole, tetracycline, and zinc and their increasing concentrations both significantly enhanced the abundances of ARGs on the MP compared to the NS. Meanwhile, the selective pressures resulted in obvious dissimilarities between the MP and NS bacterial communities. The core bacterial taxa and the co-occurrence patterns of ARGs and bacterial genera in the biofilms of MP and NS were obviously different, and more potential ARG host bacteria selectively colonized the MP. Metal pressure also enhanced the enrichment of ARGs in the MP biofilms by promoting the spread of intI1 via the co-selection mechanism.

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans

Following the advent of industrial-scale antibiotic production in the 1940s,¹ antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.^2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.⁴ However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.^4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.