Horizontal Gene Transfer Research Articles

Comprehensive Genomic Analysis of Uropathogenic E. coli: Virulence Factors, Antimicrobial Resistance, and Mobile Genetic Elements.

Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates' genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies.

Viral diversity within marine biofilms and interactions with corrosive microbes

In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This means that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.

Phylogenetic diversity of Rhizobium species recovered from nodules of common beans (Phaseolus vulgaris L.) in fields in Uganda: R. phaseoli, R. etli, and R. hidalgonense.

A total of 75 bacterial isolates were obtained from nodules of beans cultivated across 10 sites in six agro-ecological zones in Uganda. Using recA gene sequence analysis, 66 isolates were identified as members of the genus Rhizobium, while 9 were related to Agrobacterium species. In the recA gene tree, most Rhizobium strains were classified into five recognized species. Phylogenetic analysis based on six concatenated sequences (recA-rpoB-dnaK-glnII-gyrB-atpD) placed 32 representative strains into five distinct Rhizobium species, consistent with the species groups observed in the recA gene tree: R. phaseoli, R. etli, R. hidalgonense, R. ecuadorense, and R. sophoriradicis, with the first three being the predominant. The rhizobial strains grouped into three nodC subclades within the symbiovar phaseoli clade, encompassing strains from distinct phylogenetic groups. This pattern reflects the conservation of symbiotic genes, likely acquired through horizontal gene transfer among diverse rhizobial species. The 32 representative strains formed symbiotic relationships with host beans, while the Agrobacterium strains did not form nodules and lacked symbiotic genes. Multivariate analysis revealed that species distribution was influenced by the environmental factors of the sampling sites, emphasizing the need to consider these factors in future effectiveness studies to identify effective nitrogen-fixing strains for specific locations.

High-throughput single-cell sequencing of activated sludge microbiome

Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.

Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.

Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.

Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci.

This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode "cargo" functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various Streptococcus mutans strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.IMPORTANCEOral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.

Biofilm-specific determinants of enterococci pathogen.

Amongst all Enterococcus spp., E. faecalis and E. faecium are most known notorious pathogen and their biofilm formation has been associated with endocarditis, oral, urinary tract, and wound infections. Biofilm formation involves a pattern of initial adhesion, microcolony formation, and mature biofilms. The initial adhesion and microcolony formation involve numerous surface adhesins e.g. pili Ebp and polysaccharide Epa. The mature biofilms are maintained by eDNA, It's worth noting that phage-mediated dispersal plays a prominent role. Further, the involvement of peptide pheromones in regulating biofilm maintenance sets it apart from other pathogens and facilitating the horizontal transfer of resistance genes. The role of fsr based regulation by regulating gelE expression is also discussed. Thus, we provide a concise overview of the significant determinants at each stage of Enterococcus spp. biofilm formation. These elements could serve as promising targets for antibiofilm strategies.

A plasmid-mediated type III secretion system associated with invasiveness and diarrheagenicity of Providencia rustigianii.

We have recently described a clinical isolate of Providencia rustigianii strain JH-1 carrying the genes for cytolethal distending toxin (CDT) in a conjugative plasmid. A cdtB mutant of strain JH-1, which lost CDT activity, was still found to retain invasiveness and diarrheagenicity. The strain was subjected to phenotypic and genetic analyses including whole genome sequencing (WGS) to explore the genetic determinants of the observed invasiveness and diarrheagenic properties. Analysis and annotation of WGS data revealed the presence of two distinct type III secretion systems (T3SS) in strain JH-1, one of which was located on the chromosome designated as cT3SS (3,992,833 bp) and the other on a mega-plasmid designated as pT3SS (168,819 bp). Comparative genomic analysis revealed that cT3SS is generally conserved in Providencia spp. but pT3SS was limited to a subset of Providencia spp., carrying cdt genes. Strain JH-1 was found to invade HeLa cells and induce fluid accumulation with characteristic pathological lesions in rabbit ileal loops. Remarkably, these phenomena were associated with the pT3SS but not cT3SS. The plasmid could be transferred by conjugation from strain JH-1 to other strains of P. rustigianii, Providencia rettgeri, and Escherichia coli with concomitant transfer of these virulence properties. This is the first report of a functional and mobile T3SS in P. rustigianii and its association with invasiveness and diarrheagenicity of this bacterium. These data suggest that P. rustigianii and other CDT-producing Providencia strains might carry T3SS and exert their diarrheagenic effect by exploiting the T3SS nano-machinery.IMPORTANCEThe precise mechanism of virulence of Providencia rustigianii is unclear, although some strains produce cytolethal distending toxin as a putative virulence factor. We have detected the presence of a type III secretion system (T3SS) for the first time on a plasmid in a P. rustigianii strain. Plasmid-mediated T3SS seems to be directly involved in virulence of P. rustigianii and may serve as a means of horizontal transfer of T3SS genes. Our results may have implication in understanding the mechanism of emergence of new pathogenic strains of P. rustigianii.

Plasmid vector(s) in Bacillus thuringiensis harbor genes for insect pest control and for neglected infectious diseases in humans

Plasmids (circular DNA molecules) represent an ingenious strategy for horizontal gene transfer in prokaryotes and eukaryotic cells. Plasmids harbored in bacteria are responsible for the spread of traits such as antibiotic resistance, virulence factors, and the machinery for the horizontal gene transfer e.g., type IV secretion systems. Remarkably, Bacillus thuringiensis (Bt) cryptic plasmids encode and carry genes that, under the host environment, replicate and concomitate with sporulation, producing parasporal crystalline proteins of two major types, crystalline (Cry) and cytolytic (Cyt), the former toxic against different orders of insects such as Lepidopterans, Coleopterans, and Dipterans (Cry proteins, MW 50–130 KDa); Cyt proteins, produced by B. thuringiensis subspecies israelensis (Bti)(MW 27-kDa) are toxic against Dipterans, i.e., mosquitoes and black flies. The X-Ray tridimensional structure for both types of toxins, formed by three domains, mostly of beta sheets antiparallel (Domain II and Domain III) linked through loops of different lengths. Domain I is a bundle of alpha helices. This structure is characterized by five conserved blocks, implying a conservation in the mode of action. Cyt proteins possess two alpha helices and some beta sheets with a structure similar to the antimicrobial peptides. Indeed, the mode of action proposed is mediated by the toxin-lipid interaction that hypothetically could result in transmembrane ionic channel formation. Several pieces of evidence support the action of both toxins in insects and mammals. The question is to what extent these Bt/Bti plasmid-encoded Cry or Cyt genes can be applied as bioinsecticides individually or in combination with Lysinibacillus sphaericus. The feasibility of being considered a promising and safe biological strategy for crop pests and vector-borne neglected infectious diseases is an issue pinpointed in the present review.

An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host

A limited number of bacteria are able to colonize the nuclei of eukaryotes. ‘Candidatus Endonucleobacter’ infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that ‘Candidatus Endonucleobacter’ does not obtain most of its nutrition from nuclear DNA or RNA. Instead, ‘Candidatus Endonucleobacter’ upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7–13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that ‘Ca. Endonucleobacter’ acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.

Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes.

Caliciviruses have positive-sense RNA genomes, typically with short 5'-untranslated regions (5'UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5'UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200-300 codon-long ORF (designated ORF1*) that overlaps the 5'-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3'-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES's 3'-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF45, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1).

Possible horizontal gene transfer: Virectaria stellata (Sabiceeae-Rubiaceae), a new sandstone cliff species from the Republic of Guinea with stellate hairs recorded for the first time in the Rubiaceae

Virectaria (Sabiceeae-Cinchonoideae-Rubiaceae), is a morphologically isolated genus of tropical African herbs or subshrubs, occurring from Senegal to Tanzania. Virectaria stellata, a new species from Guinea, is published. It is a perennial herb, with stems becoming creeping and rooting, to 60 cm long. Virectaria stellata has stellate hairs, recorded here for the first time in the family Rubiaceae. We hypothesize that the stellate hairs of this species result not from mutation but from horizontal gene transfer (HGT) from an Acanthaceae, most likely Barleria, due to their common and perhaps uniquely shared microstructure. We briefly review literature on the control of the transition from simple to stellate hairs and on HGT in plants. Virectaria stellata is found in Forécariah and Kindia Prefectures in the Republic of Guinea. A Virectaria specimen without stellate hairs but otherwise similar to V. stellata was collected in Guinea, about 90 km to the North of the northernmost V. stellata collection. This specimen may represent a possible progenitor of V. stellata. The identification of this specimen requires further study. Virectaria stellata occurs in fissures in vertical sandstone rock at altitudes of 450 to 910 m, in sun or half-shade. An overview of sandstone endemic plant species in the vicinity of the new Virectaria is provided. No threats have been observed, therefore, Virectaria stellata is provisionally assessed here as Least Concern (LC).

Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.

Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.

Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture

Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 106 CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.

Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm

Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6–49.1 %) and tnpA-06 (0.27–7.5 %) were significantly increased in frozen soil, while Int3 (0.67–10.6 %) and tnpA-04 (11.1–19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.

Exosomes: Key Factors in Ovarian Cancer Peritoneal Metastasis and Drug Resistance.

Ovarian cancer remains a leading cause of death among gynecological cancers, largely due to its propensity for peritoneal metastasis and the development of drug resistance. This review concentrates on the molecular underpinnings of these two critical challenges. We delve into the role of exosomes, the nano-sized vesicles integral to cellular communication, in orchestrating the complex interactions within the tumor microenvironment that facilitate metastatic spread and thwart therapeutic efforts. Specifically, we explore how exosomes drive peritoneal metastasis by promoting epithelial-mesenchymal transition in peritoneal mesothelial cells, altering the extracellular matrix, and supporting angiogenesis, which collectively enable the dissemination of cancer cells across the peritoneal cavity. Furthermore, we dissect the mechanisms by which exosomes contribute to the emergence of drug resistance, including the sequestration and expulsion of chemotherapeutic agents, the horizontal transfer of drug resistance genes, and the modulation of critical DNA repair and apoptotic pathways. By shedding light on these exosome-mediated processes, we underscore the potential of exosomal pathways as novel therapeutic targets, offering hope for more effective interventions against ovarian cancer's relentless progression.

Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments

This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.

Linkage equilibrium between rare mutations.

Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here, we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination and discuss their implications for the rates of horizontal gene transfer in bacteria.

Comprehensive analysis reveals the differentiated influential mechanism of biodegradable and non-biodegradable microplastics on core microbial metabolisms and functional genes in an adsorption-biological coupling wastewater treatment system

The effects of different types of microplastics (MPs) on the wastewater treatment efficiency of an adsorption-biological coupling system were investigated. The distribution of the microbial community and metabolic pathways in the coupled system were also analyzed. Biodegradable polybutylene succinate microplastics (PBS MPs) were added to reactor A, while non-biodegradable polystyrene microplastics (PS MPs) was added to reactor B. The average chemical oxygen demand (COD) removal rates in reactor A with 0, 50, and 100 mg/L of MPs were 95.34 %, 89.13 %, and 86.08 %, respectively; the average COD removal rates in reactor B were 96.84 %, 88.43 %, and 87.02 %, respectively. The average total phosphorus (TP) removal rates in reactor A were 74.14 %, 38.94 %, and 36.45 %, respectively, while those in reactor B were 71.73 %, 39.50 %, and 33.09 %, respectively. In the two reactors, Proteobacteria had the highest relative abundance (53 %–62 %), followed by Actinobacteria. PS MPs inhibited the expression of quorum sensing genes by influencing SecA and SecY. Horizontal transfer genes illustrated that both MPs led to up-regulation of reactive oxygen species (ROS)-related functional genes. During glycolysis, the abundances of glucokinase (GLK), pyruvate kinase (PK), and phosphofructokinase (PFK) in reactor A were 0.0179 %, 0.0133 %, and 0.0387 % higher than that in reactor B, respectively. Meanwhile, in nitrogen metabolism, the abundance of key genes such as nasA (A: 40.8 % B: 37.9 %) was greater in reactor A than in reactor B.

Microbial bases of herbivory in beetles.

The ecological radiation of herbivorous beetles is among the most successful in the animal kingdom. It coincided with the rise and diversification of flowering plants, requiring beetles to adapt to a nutritionally imbalanced diet enriched in complex polysaccharides and toxic secondary metabolites. In this review, we explore how beetles overcame these challenges by coopting microbial genes, enzymes, and metabolites, through both horizontal gene transfer (HGT) and symbiosis. Recent efforts revealed the functional convergence governing both processes and the unique ways in which microbes continue to shape beetle digestion, development, and defense. The development of genetic and experimental tools across a diverse set of study systems has provided valuable mechanistic insights into how microbes spurred metabolic innovation and facilitated an herbivorous transition in beetles.