The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes

Unraveling the mystery of antibiotic resistance genes in green and red Antarctic snow

Antarctic snow is a thriving habitat for a diverse array of complex microorganisms, and can present in different colors due to algae blooms. However, the potential role of Antarctic snow as reservoirs for antibiotic resistance genes (ARGs) has not been studied. Using metagenomic sequencing, we studied ARGs in green-snow and red-snow on the Fildes Peninsula, Antarctica. Alpha and beta diversities of ARGs, as well as co-occurrence between ARGs and bacteria were assessed. The results showed that a total of 525 ARGs conferring resistance to 30 antibiotic classes were detected across the samples, with half of the ARGs presented in all samples. Green-snow exhibited a higher number of ARGs compared to red-snow. The most abundant ARGs conferring resistance to commonly used antibiotics, including disinfecting agents and antiseptics, peptide, isoniazid, MLS, fluoroquinolone, aminocoumarin, etc. Multidrug resistance genes stood out as the most diverse and abundant, with antibiotic efflux emerging as the dominant resistance mechanism. Interestingly, the composition of ARGs in green-snow markedly differed from that in red-snow, highlighting distinct ARG profiles. Beta-diversity partitioning showed a higher contribution of nestedness for ARG's variation in green-snow, while higher contribution of turnover in red-snow. Furthermore, the co-occurrence analysis between ARGs and bacteria unveiled intricate relationships, indicating that certain ARGs may have multiple potential hosts. The observed differences in co-occurrence networks between green-snow and red-snow suggested distinct host relationships between ARGs and bacteria in these colored snows. Given the increasing appearance of the colored snow around the world due to the climate change, the results shed light on the mystery and potential implication of ARGs in green and red Antarctic snow.

Antibiotic resistance genes in integrated surface ice, cryoconite, and glacier-fed stream in a mountain glacier in Central Asia

Glacier ice, cryoconite, and glacier-fed streams are interconnected features that have important implications for the dynamics and distribution of abiotic and biotic materials. However, the presence and behavior of antibiotic resistance genes (ARGs) within these glacial environments remained largely unexplored. Addressing this gap, we hypothesized that ARGs are widely distributed and exhibit distinct yet interconnected patterns of diversity and dynamics in these glacial environments. Here, we investigated ARGs in a mountain glacier in Central Asia. A total of 944 ARGs, spanning 22 antibiotic classes, were identified, with 633 ARGs shared across all three environments. Cryoconite exhibited the highest ARG richness, followed by ice, while stream biofilm displayed the lowest value. Exploring ARG profiles, we observed a consistent pattern in terms of antibiotic class and resistance mechanism across all three environments. Beta-lactam resistance genes exhibited the highest diversity, followed by multidrug, glycopeptide, and MLS. The predominant mechanisms were antibiotic inactivation, antibiotic efflux, and target alteration. The most prevalent ARG is cls, followed by mdfA, ropB, fabI, and macB. The similarity in ARG profiles between surface ice and cryoconite samples was more pronounced than their resemblance to stream biofilm samples. The variations of ARG profiles between any pair of environments were largely contributed by turnover component. Further insights into microbial interactions revealed 2328 significant associations between 80 OTUs and 356 ARGs, indicating complex relationships. Certain OTUs, including those from the genera Polaromonas, Ferruginibacter, Hymenobacter, Phormidesmis, Novosphingobium, and Polymorphobacter, were speculated as potential hosts for a variety of ARGs. Our findings underscore the intricate dynamics of antibiotic resistance in glacial ecosystems, emphasizing the need for a holistic understanding of ARG distribution, diversity, and associations across diverse environmental compartments. This research contributes valuable insights into the potential ecological implications of antibiotic resistance dissemination in cold environments, particularly as influenced by increasing climate change.

Phenotypic and resistome analysis of antibiotic and heavy metal resistance in the Antarctic bacterium Pseudomonas sp. AU10

Resistance to antibiotics and heavy metals in Antarctic bacteria has been investigated due to anthropogenic impact on the continent. However, there is still much to learn about the genetic determinants of resistance in native bacteria. In this study, we investigated antibiotic, heavy metal, and metalloid resistance in Pseudomonas sp. AU10, isolated from King George Island (Antarctica), and analyzed its genome to look for all the associated genetic determinants (resistome). We found that AU10 displayed resistance to Cr(VI), Cu(II), Mn(II), Fe(II), and As(V), and produced an exopolysaccharide with high Cr(VI)-biosorption capacity. Additionaly, the strain showed resistance to aminopenicillins, cefotaxime, aztreonam, azithromycin, and intermediate resistance to chloramphenicol. Regarding the resistome, we did not find resistance genes in AU10's natural plasmid or in a prophage context. Only a copper resistance cluster indicated possible horizontal acquisition. The mechanisms of resistance found were mostly efflux systems, several sequestering proteins, and a few enzymes, such as an AmpC β-lactamase or a chromate reductase, which would account for the observed phenotypic profile. In contrast, the presence of a few gene clusters, including the terZABCDE operon for tellurite resistance, did not correlate with the expected phenotype. Despite the observed resistance to multiple antibiotics and heavy metals, the lack of resistance genes within evident mobile genetic elements is suggestive of the preserved nature of AU10's Antarctic habitat. As Pseudomonas species are good bioindicators of human impact in Antarctic environments, we consider that our results could help refine surveillance studies based on monitoring resistances and associated resistomes in these populations.

Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules

Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.

A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42∘ S)

While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide–lincosamide–streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.

A mobile target

The global spread of antibiotic resistance could be due to a number of factors, and not just the overuse of antibiotics in agriculture and medicine as previously thought.

Whole genome analysis of Flavobacterium aziz-sancarii sp. nov., isolated from Ardley Island (Antarctica), revealed a rich resistome and bioremediation potential

Despite being one of the most isolated regions in the world, Antarctica is at risk of increased contamination with potentially toxic elements and other toxic chemicals through anthropogenic interventions. In this study, a psychrotolerant bacterium was isolated using the lake water collected from Ardley Island (Antarctica), which can grow at temperatures between 4 and 30 °C and pH values between 6.0 and 9.0. The isolate, named AC, had protease, amylase, and lipase activities with no NaCl tolerance and could degrade 1-5% diesel fuel. Multilocus sequence analysis (MLSA) using 16S rRNA, gyrB, tuf, and rpoD genes resulted in 92.91-98.6% sequence similarities between the isolate AC and other Flavobacterium spp. Whole genome analysis indicated that the genome length of Flavobacterium sp. AC is 5.8 Mbp with a GC content of 34.04% and 1274 genes predicted. The strain AC branched independently from other Flavobacterium spp. in the phylogenetic and phylogenomic trees and ranked a new species named Flavobacterium aziz-sancarii. Genome mining identified several cold-inducible genes, including stress-associated genes such as cold-shock proteins, chaperones, carotenoid biosynthetic genes, or oxidative-stress response genes. In addition, virulence, gliding motility, and biofilm-related genes were determined. Its genome contains 35 and 88 open-reading frames related to potentially toxic element and antibiotic resistance, respectively. F. aziz-sancarii showed a remarkable tolerance of Cr and Ni, with minimal inhibitory concentration values of 2.88 and 2.81 mM, respectively. Pb, Cu, and Zn exposure resulted in moderate toxicity (2.14-2.41 mM), while Cd showed the highest inhibitory effect in bacterial growth (0.74 mM). Antibiotic susceptibility testing indicated multidrug-resistant phenotype in correlation to in silico prediction of antibiotic resistance genes. Overall, our results contribute to biodiversity of Antarctica and provide new insights into resistome profile of Antarctic microorganisms. Additionally, the diesel degradation feature of F. aziz-sancarii offers potential use for the bioremediation of hydrocarbon-contaminated polar ecosystems.

Metagenomic insights into the influence of thallium spill on sediment microbial community

Thallium (Tl) is an extremely toxic metal. The release of Tl into the natural environment can pose a potential threat to organisms. So far, information about the impact of Tl on indigenous microorganisms is still very limited. In addition, there has been no report on how sudden Tl spill influences the structure and function of the microbial community. Therefore, this study explored the response of river sediment microbiome to a Tl spill. Residual T1 in the sediment significantly decreased bacterial community diversity. The increase in the abundance of Bacteroidetes in all Tl- impacted sediments suggested the advantage of Bacteroidetes to resist Tl pressure. Under T1 stress, microbial genes related to carbon fixation and gene cysH participating in assimilatory sulfate reduction were down-regulated, while genes related to nitrogen cycling were up-regulated. After T1 spill, increase in both metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) was observed in Tl-impacted sediments. Moreover, the abundance of MRGs and ARGs was significantly correlated with sediment Tl concentration, implying the positive effect of Tl contamination on the proliferation of these resistance genes. Procrustes analysis suggested a significant congruence between profiles of MRGs and bacterial communities. Through LEfSe and co-occurrence network analysis, Trichococcus, Polaromonas, and Arenimonas were identified to be tolerant and resistant to Tl pollution. The colocalization analysis of contigs indicated the co-effects of selection and transfer for MRGs/ARGs were important reasons for the increase in the microbial resistance in Tl-impacted sediments. This study added new insights into the effect of Tl spill on microbial community and highlighted the role of heavy metal spill in the increase of both heavy metal and antibiotic resistance genes.

Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes

Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.

Source and acquisition of rhizosphere microbes in Antarctic vascular plants

Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.

Pseudomonas fluorescens Complex and Its Intrinsic, Adaptive, and Acquired Antimicrobial Resistance Mechanisms in Pristine and Human-Impacted Sites

Pseudomonas spp. are ubiquitous microorganisms that exhibit intrinsic and acquired resistance to many antimicrobial agents. Pseudomonas aeruginosa is the most studied species of this genus due to its clinical importance. In contrast, the Pseudomonas fluorescens complex consists of environmental and, in some cases, pathogenic opportunistic microorganisms. The records of antimicrobial-resistant P. fluorescens are quite scattered, which hinders the recognition of patterns. This review compiles published data on antimicrobial resistance in species belonging to the P. fluorescens complex, which were identified through phylogenomic analyses. Additionally, we explored the occurrence of clinically relevant antimicrobial resistance genes in the genomes of the respective species available in the NCBI database. Isolates were organized into two categories: strains isolated from pristine sites and strains isolated from human-impacted or metal-polluted sites. Our review revealed that many reported resistant phenotypes in this complex might be related to intrinsic features, whereas some of them might be ascribed to adaptive mechanisms such as colistin resistance. Moreover, a few studies reported antimicrobial resistance genes (ARGs), mainly β-lactamases. In-silico analysis corroborated the low occurrence of transferable resistance mechanisms in this Pseudomonas complex. Both phenotypic and genotypic assays are necessary to gain insights into the evolutionary aspects of antimicrobial resistance in the P. fluorescens complex and the possible role of these ubiquitous species as reservoirs of clinically important and transmissible ARGs.

Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements

Antibiotic resistance genes (ARGs) are undergoing a remarkably rapid geographic expansion in various ecosystems, including pristine environments such as Antarctica. The study of ARGs and environmental resistance genes (ERGs) mechanisms could provide a better understanding of their origin, evolution, and dissemination in these pristine environments. Here, we describe the diversity of ARGs and ERGs and the importance of mobile genetic elements as a possible mechanism for the dissemination of resistance genes in Antarctica. We analyzed five soil metagenomes from Deception Island in Antarctica. Results showed that detected ARGs are associated with mechanisms such as antibiotic efflux, antibiotic inactivation, and target alteration. On the other hand, resistance to metals, surfactants, and aromatic hydrocarbons were the dominant ERGs. The taxonomy of ARGs showed that Pseudomonas, Psychrobacter, and Staphylococcus could be key taxa for studying antibiotic resistance and environmental resistance to stress in Deception Island. In addition, results showed that ARGs are mainly associated with phage-type mobile elements suggesting a potential role in their dissemination and prevalence. Finally, these results provide valuable information regarding the ARGs and ERGs in Deception Island including the potential contribution of mobile genetic elements to the spread of ARGs and ERGs in one of the least studied Antarctic ecosystems to date.