Mobile Elements Research Articles

Solid State Machinery of Multiple Dynamic Elements in a Metal-Organic Framework.

Engineering coordinated rotational motion in porous architectures enables the fabrication of molecular machines in solids. A flexible two-fold interpenetrated pillared Metal-Organic Framework precisely organizes fast mobile elements such as bicyclopentane (BCP) (107 Hz regime at 85 K), two distinct pyridyl rotors and E-azo group involved in pedal-like motion. Reciprocal sliding of the two sub-networks, switched by chemical stimuli, modulated the sizes of the channels and finally the overall dynamical machinery. Actually, iodine-vapor adsorption drives a dramatic structural rearrangement, displacing the two distinct subnets in a concerted piston-like motion. Unconventionally, BCP mobility increases, exploring ultra-fast dynamics (107 Hz) at temperatures as low as 44 K, while the pyridyl rotors diverge into a faster and slower dynamical regime by symmetry lowering. Indeed, one pillar ring gained greater rotary freedom as carried by the azo-group in a crank-like motion. A peculiar behavior was stimulated by pressurized CO2, which regulates BCP dynamics upon incremental site occupation. The rotary dynamics is intrinsically coupled to the framework flexibility as demonstrated by complementary experimental evidence (multinuclear solid-state NMR down to very low temperatures, synchrotron radiation XRD, gas sorption) and computational modelling, which helps elucidate the highly sophisticated rotor-structure interplay.

Host species of freshwater snails within the same freshwater ecosystem shapes the intestinal microbiome

BackgroundFreshwater snails are not only intermediate hosts for parasites but also an important part of the food chain as they convert plant biomass and humus into animal biomass. However, being widely distributed in freshwater environments, snails are highly affected by human activities, which makes their adaptation to altering environments challenging. The gut microbiome helps animals in their digestion, immune system, growth and adapting to changing environments. The effect of host species on intestinal microbial community has been poorly studied in snails.MethodsIn this study, single-molecule real-time sequencing technology (SMRT) was used to obtain full-length 16S rRNA genes to determine the intestinal microbiomes of three species of freshwater snails (SQ: Sinotaia quadrata, BU: Boreoelona ussuriensis, RP: Radix plicatula) with similar feeding habits in a same water environment.ResultsUnifrac PCoA (P<0.05), hierarchical cluster and Ternary analyses showed distinct and significant segregation of the intestinal microbiomes of the three hosts. The phyla Cyanobacteria, Proteobacteria, Firmicutes and Planctomycetota dominated snail guts, comprising 93.47%, 86.22%, and 94.34% of the total reads in SQ, BU and RP, respectively. Of these, only 25.26% of OTUs were identified up to species level, while 72.07% of OTUs were identified at the genus level. Although 72.94% of the total bacterial species (566) were common to three snails, significant differences were observed in terms of their abundance (P < 0.05). Several genera can help to determine the phenotype of the intestinal microbiota. In this case, Lelliottia contributed mainly to stress tolerance, biofilm formation, potential pathogenicity, mobile elements and facultatively anaerobic phenotypes in RP. Furthermore, Romboutsia and Clostridium_sensu_stricto_1 contributed to the anaerobic phenotype of SQ and RP, while Pirellula contributed to the aerobic phenotype in SQ. Moreover, PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) predicted 68 GH (glycoside hydrolase) genes, with these including monosaccharide-, disaccharide-, polysaccharide-, and starch-digesting enzyme genes as well as enzymes specific to aquatic plants. Many of the identified pathways were related to Infectious diseases and Xenobiotics biodegradation and metabolism, which expanded the resistance of freshwater snails.ConcludesLelliottia, Romboutsia, Clostridium_sensu_stricto_1, and Pirellula play an important role in the intestinal microbiota phenotype of the host snails. In general, the host species affects the structure of the gut microbial community, which in turn helps gastropods improve their environmental adaptability, but further study is still needed.

Complete Genome Sequence of a Copper-Resistant Xanthomonas campestris pv. campestris Strain Isolated from Broccoli in Mauritius Suggests Adaptive Gene Gain Through Horizontal Gene Transfer.

Bacterial adaptation is facilitated by the presence of mobile genetic elements and horizontal gene transfer of genes, such as those coding for virulence factors or resistance to antimicrobial compounds. A hybrid assembly of Nanopore MinIon long-read and Illumina short-read data was produced from a copper-resistant Xanthomonas campestris pv.campestris strain isolated from symptomatic broccoli leaves in Mauritius. We obtained a 5.2-Mb high-quality chromosome and no plasmid. We found four genomic islands, three of which were characterized as integrative conjugative elements or integrative mobilizable elements. These genomic islands carried type III effectors and the copper resistance copLABMGF system involved in pathogenicity and environmental adaptation, respectively.

Two birds with one stone: SGI1 can stabilize itself and expel the IncC helper by hijacking the plasmid parABS system.

The SGI1 family integrative mobilizable elements, which are efficient agents in distribution of multidrug resistance in Gammaproteobacteria, have a complex, parasitic relationship with their IncC conjugative helper plasmids. Besides exploiting the transfer apparatus, SGI1 also hijacks IncC plasmid control mechanisms to time its own excision, replication and expression of self-encoded T4SS components, which provides advantages for SGI1 over its helpers in conjugal transfer and stable maintenance. Furthermore, SGI1 destabilizes its helpers in an unknown, replication-dependent way when they are concomitantly present in the same host. Here we report how SGI1 exploits the helper plasmid partitioning system to displace the plasmid and simultaneously increase its own stability. We show that SGI1 carries two copies of sequences mimicking the parS sites of IncC plasmids. These parS-like elements bind the ParB protein encoded by the plasmid and increase SGI1 stability by utilizing the parABS system of the plasmid for its own partitioning, through which SGI1 also destabilizes the helper plasmid. Furthermore, SGI1 expresses a small protein, Sci, which significantly strengthens this plasmid-destabilizing effect, as well as SGI1 maintenance. The plasmid-induced replication of SGI1 results in an increased copy-number of parS-like sequences and Sci expression leading to strong incompatibility with the helper plasmid.

Laboratory domestication of Lactiplantibacillus plantarum alters some phenotypic traits but causes non-novel genomic impact.

Laboratory domestication has been negligibly examined in lactic acid bacteria (LAB). Lactiplantibacillus plantarum is a highly studied and industrially relevant LAB. Here, we passaged L. plantarum JGR2 in a complex medium to study the effects of domestication on the phenotypic properties and the acquisition of mutations. Lactiplantibacillus plantarum JGR2 was passaged in mMRS medium (deMan Rogossa Sharpe supplemented with 0.05%w/v L-cysteine) in three parallel populations for 70 days. One pure culture from each population was studied for various phenotypic properties and genomic alterations. Auto-aggregation of the evolved strains was significantly reduced, and lactic acid production and ethanol tolerance were increased. Other probiotic properties and antibiotic sensitivity were not altered. Conserved synonymous and non-synonymous mutations were observed in mobile element proteins (transposases), β-galactosidase, and phosphoketolases in all three isolates. The evolved strains lost all the repeat regions and some of the functions associated with them. Most of the conserved mutations were found in the genomes of other wild-type strains available in a public database, indicating the non-novel genomic impact of laboratory passaging. Laboratory domestication can affect the phenotypic and genotypic traits of L. plantarum and similar studies are necessary for other important species of LAB.

The concept and essence of mobilization elements of tax policy

An important role in the transformation of the economy of the Russian Federation is played by tax policy, which has a significant impact on the market for goods, services, capital and labor. In this connection, the article analyzes the theoretical aspects of the formation of the state tax policy under the mobilization model of economic development. The subject of the study is tax policy as a tool for overcoming the economic crisis. The purpose of the study is to formulate principles for implementing tax policy in a mobilization economy, highlight its main elements and analyze their features. The methodology of the work is based on general logical and historical-legal methods of scientific research, which allows, taking into account historical experience, to propose a theoretical basis for modern tax policy in the conditions of a mobilization economy. The article provides a definition of the concept of tax policy in a mobilization economy. Based on the works of Russian scientists in the field of mobilization economics, the features of mobilization economics are highlighted for the purposes of forming tax policy. The study analyzes the historical experience of the Soviet Union in the period 1941-1945, on the basis of which the fundamental principles of tax policy in a mobilization economy are formulated. The article also develops a modern tax mechanism toolkit and describes its features. In addition, a comparison is made of tax regulation instruments for various models of economic development of economic macrosystems. An important part of the study is the structured and justified mobilization elements of tax policy. The solutions proposed in the study can be used in the practical implementation of tax policy in a mobilization economy.

Spatio-temporal variations in dissolved trace elements in peat bog porewaters impacted by dust inputs from open-pit mining activities in the Athabasca Bituminous Sands (ABS) region

Considerable volumes of dust are generated from open-pit bitumen mining operations in northern Alberta, Canada. The reactive mineral phases of these dust particles can potentially dissolve in acidic (pH < 4) bog waters. Their dissolution could release trace elements (TEs), which could eventually alter these bog ecosystems. The impact of dust dissolution on the abundance of TEs in the dissolved (<0.45 μm) fraction of porewaters from excavated pits (30–40 cm deep) in the ombrogenic zone of five peatlands was evaluated. Porewaters were collected from four bogs situated within 70 km of mines and upgraders in the Athabasca Bituminous Sands (ABS) region, Alberta, Canada, and from a reference bog situated 264 km away. Over two consecutive years, the dissolved concentrations of some conservative (Al, Th, Y) and mobile lithophile elements (Fe, Li, Mn, Sr), as well as the metals enriched in bitumen (V, Ni, Mo), all increased with proximity to the mining area, in the ABS region. These trends reflect the observed increase in dust deposition with proximity to the mining area from independent studies of snow, lichens, and Sphagnum moss. Contrarily, the impact of dust dissolution on the concentration of potentially toxic TEs (As, Cd, Pb, Sb, and Tl) was negligible. Thus, the elements which are more abundant in the porewaters near industry are either ecologically benign (e.g. Li and Sr) or essential micronutrients (e.g. Fe, Mn, Ni, and Mo). Manganese was the only element which was enriched by more than 10x at all sites near the mining area, compared to its concentration at the reference site. The enrichments of all other elements were <10x, indicating that anthropogenic dust emissions from mining areas have had only a modest effect on the TEs abundance in peat porewaters.

Large language models improve annotation of prokaryotic viral proteins.

Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches.

Genomic Characterization and Safety Assessment of Bifidobacterium breve BS2-PB3 as Functional Food.

Our group had isolated Bifidobacterium breve strain BS2-PB3 from human breast milk. In this study, we sequenced the whole genome of B. breve BS2-PB3, and with a focus on its safety profile, various probiotic characteristics (presence of antibiotic resistance genes, virulence factors, and mobile elements) were then determined through bioinformatic analyses. The antibiotic resistance profile of B. breve BS2-PB3 was also evaluated. The whole genome of B. breve BS2-PB3 consisted of 2,268,931 base pairs with a G-C content of 58.89% and 2,108 coding regions. The average nucleotide identity and whole-genome phylogenetic analyses supported the classification of B. breve BS2-PB3. According to our in silico assessment, B. breve BS2-PB3 possesses antioxidant and immunomodulation properties in addition to various genes related to the probiotic properties of heat, cold, and acid stress, bile tolerance, and adhesion. Antibiotic susceptibility was evaluated using the Kirby-Bauer disk-diffusion test, in which the minimum inhibitory concentrations for selected antibiotics were subsequently tested using the Epsilometer test. B. breve BS2-PB3 only exhibited selected resistance phenotypes, i.e., to mupirocin (minimum inhibitory concentration/MIC >1,024 μg/ml), sulfamethoxazole (MIC >1,024 μg/ml), and oxacillin (MIC >3 μg/ml). The resistance genes against those antibiotics, i.e., ileS, mupB, sul4, mecC and ramA, were detected within its genome as well. While no virulence factor was detected, four insertion sequences were identified within the genome but were located away from the identified antibiotic resistance genes. In conclusion, B. breve BS2-PB3 demonstrated a sufficient safety profile, making it a promising candidate for further development as a potential functional food.

Multi-element geochemical analyses on ultrafine soils in Western Australia – towards establishing abundance ranges in mineral exploration settings

In this study, we present summary statistics for multi-element soil geochemistry across Western Australia based on over 74 000 soil samples using the UltraFine+ ® method that extracts and analyses the clay (&lt;2 μ m) fraction of a soil sample. This method is a critical advancement for the detection of mobile element signatures for soil geochemical mineral exploration surveys in cover. However, existing estimates of background metal abundances acquired with other methods and on different sample media do not readily provide context for these analyses, as recovery from the fine fraction differs to that of whole-sample analysis. We therefore present herein the geochemical results for 52 elements, including precious, base and critical metals, as well as commonly associated pathfinder elements for Western Australian samples analysed during several research projects by the Commonwealth Scientific and Industrial Research Organisation (CSIRO). This dataset is separated by tectonic unit into the Eastern Goldfields Superterrane and the Youanmi Terrane in the Yilgarn Craton, the Pilbara Craton and Sylvania Inlier, the Gascoyne, Lamboo and Aileron Provinces, and the Bryah and Earaheedy Basins to provide exploration-relevant context in these areas. We discuss some of the general trends observed for 12 of these elements, as well as some considerations for the use of these data in comparison to other geochemical soil surveys and with regards to mineral exploration settings. The samples presented in this study are not evenly distributed across Western Australia and limited information is available to correlate whether lithology at depth is mineralized or barren. However, in the absence of other systematic datasets using the &lt;2 μ m-size fraction, these data present a suitable first-pass resource of element abundance ranges in areas of mineral exploration interest using the UltraFine+ ® method in some of the mineral-endowed areas of Western Australia. Supplementary material: Supplementary data A, UltraFine+ ® Soil Sampling Guide; B, UltraFine+ ® analyses results for available samples in Western Australia; C, Summary statistics of UltraFine+ ® analyses by simplified tectonic units; Supplementary Figure 1, Comparison of elemental mean values and uncertainties for ultrafine reference materials QC 320 and QC 422; Supplementary Figure 2, Violin plots of Ni, Cd, Mg and Au by simplified tectonic unit; Supplementary Figure 3, Location of soil samples in the Eastern Goldfields Superterrane analysed via UltraFine+ ® , and those collected as part of the NGSA and GSWA regolith programme; Supplementary Figure 4, Comparison of W, Al, Mg and Ca results from UltraFine+ ® , NGSA and GSWA analyses in the Eastern Goldfields Superterrane are available at https://doi.org/10.6084/m9.figshare.c.6919933

A transposon-based genetic marker for conspecific identity within the Bactrocera dorsalis species complex.

Here we describe a molecular approach to assess conspecific identity that relies on the comparison of an evolved mutated transposable element sequence and its genomic insertion site in individuals from closely related species. This was explored with the IFP2 piggyBac transposon, originally discovered in Trichoplusia ni as a 2472bp functional element, that was subsequently found as mutated elements in seven species within the Bactrocera dorsalis species complex. In a B. dorsalis [Hendel] strain collected in Kahuku, Hawaii, a degenerate 2420bp piggyBac sequence (pBacBd-Kah) having ~ 94.5% sequence identity to IFP2 was isolated, and it was reasoned that common species, or strains within species, should share the same evolved element and its precise genomic insertion site. To test this assumption, PCR using primers to pBacBd-Kah and adjacent genomic sequences was used to isolate and compare homologous sequences in strains of four sibling species within the complex. Three of these taxa, B. papayae, B. philippinensis, and B. invadens, were previously synonymized with B. dorsalis, and found to share nearly identical pBacBd-Kah homologous elements (> 99% nucleotide identity) within the identical insertion site consistent with conspecific species. The fourth species tested, B. carambolae, considered to be a closely related yet independent species sympatric with B. dorsalis, also shared the pBacBd-Kah sequence and insertion site in one strain from Suriname, while another divergent pBacBd-Kah derivative, closer in identity to IFP2, was found in individuals from French Guiana, Bangladesh and Malaysia. This data, along with the absence of pBacBd-Kah in distantly related Bactrocera, indicates that mutated descendants of piggyBac, as well as other invasive mobile elements, could be reliable genomic markers for common species identity.

New insight into genesis of the Maojun laterite Fe–Mn deposit in the Lanshan area, Hunan Province, South China: Evidence from detailed mineralogical and geochemical studies

Laterite Fe–Mn deposits are widespread in South China, with the majority of Fe–Mn ore being present in residual quaternary clay beds. However, detailed geological data on the lateritization of low-iron-content carbonate rocks are rare. In this study, we present new results on the mineralogy and geochemistry, as well as a genetic model, of the Maojun laterite Fe–Mn deposit in the Lanshan area, Hunan Province, South China. The profile sequence of laterite consists of an eroded bedrock horizon at its base, an intermediate black–brown clay layer containing earthy Fe–Mn ore, and a reddish-brown clay layer with nodular ferromanganese ore in contact with reddish-brown or yellowish-brown clay on top. Field evidence and chemical analysis indicated that during lateritization, the Mn-Fe-containing carbonate rocks of the Huanggongtang (D2h) and Shetianqiao formations (D3s) saw a more significant removal of mobile elements (Mg, Ca, and Na) whilst insoluble elements (Fe, Mn, Si, Al, Pb, and Zn) exhibited persistent enrichment in situ. Discriminative diagrams of Fe–Mn mineralization, as well as the assemblage-related enrichment of Y, U, Mo, Pb, and Zn and depletion of high-field-strength elements Zr, Nb, and Th, imply that subsequent hydrothermal circulation overprinted on the previously formed hydrogenous deposit. Mineralogical studies conducted using XRD, EPMA, HR-TEM, and TIMA indicated the predominance of iron and manganese oxides; hematite, goethite, limonite, and hollandite were identified as major oxide phases and cryptomelane, pyrolusite, and coronadite were present in minute quantities. Similar minerals constitute the upper ferromanganese nodule horizons, although they possess distinct textures and concentrations. The mineralogy, geochemical associations, and Ti mass balance show a continuous vertical evolution from top to bottom in the lateritic profile. Ferromanganese concretions from the drenching zone with poorly crystallized Al–goethite, Al–hematite, limonite, Fe–kaolinite, Fe–Mn oxides and hollandite predominate in shallow parts, and microcrystalline hematite, goethite and hollandite were found in deeper layers. Mn2+ can be rapidly oxidized and precipitated on the surface of hematite and limonite as high-valence-state (Mn4+) manganese oxides and binds strongly with mobile elements (Ba, K, Pb, Zn, Ca, and Ni). Petrographical, mineralogical, and geochemical studies show that three stages comprised the formation of the Maojun laterite Fe–Mn deposit.

Insights into the genome of the ‘Loco’ Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae

BackgroundThe Peruvian ‘chanque’ or Chilean ‘loco’ Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes.ResultsUsing a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs.ConclusionThe information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.

Transfer and accumulation of antibiotic resistance genes and bacterial pathogens in the mice gut due to consumption of organic foods

Over the last few decades, organic food demand has grown largely because of increasing personal health concerns. Organic farming introduces antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) into foods. However, potential effects of organic foods on the gut microbiome and ARGs have been overlooked. Using high-throughput quantitative PCR and 16S rRNA high-throughput sequencing technology, we examined 132 ARGs from major classes, eight transposase genes, universal class I integron-integrase gene (intI), clinical class I integron-integrase gene (cintI), and the bacterial community in mouse gut after 8 weeks with an either organic or inorganic lettuce and wheat diet. A total of 8 types of major ARGs and 10 mobile genetic elements (MGEs) were detected in mice gut, including tetracycline, multidrug, sulfonamide, aminoglycoside, beta-lactamase, chloramphenicol, MLSB and vancomycin resistance genes. We found that abundance and diversity of ARGs, mobile gene elements, and potential ARB in the gut increased with time after consumption of organic foods, whereas no significant changes were observed in inorganic treated groups. Moreover, MGEs, including IS613, Tp614 and tnpA_03 were found to play an important role in regulating ARG profiles in the gut microbiome following consumption of organic foods. Importantly, feeding organic food increased the relative abundance of the potentially antibiotic-resistant pathogens, Bacteroides and Streptococcus. Our results confirm that there is an increasing risk of ARGs and ARB in the gut microbiome, which highlights the importance of organic food industries taking into account the potential accumulation and transmission of ARGs as a risk factor.

The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein.

Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.

Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton.

Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.

Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont.

Many organisms have formed symbiotic relationships with nitrogen (N)-fixing bacteria to overcome N limitation. Diatoms in the family Rhopalodiaceae host unicellular, N-fixing cyanobacterial endosymbionts called spheroid bodies (SBs). Although this relationship is relatively young, SBs share many key features with older endosymbionts, including coordinated cell division and genome reduction. Unlike free-living relatives that fix N exclusively at night, SBs fix N largely during the day; however, how SB metabolism is regulated and coordinated with the host is not yet understood. We compared four SB genomes, including those from two new host species (Rhopalodia gibba and Epithemia adnata), to build a genome-wide phylogeny which provides a better understanding of SB evolutionary origins. Contrary to models of endosymbiotic genome reduction, the SB chromosome is unusually stable for an endosymbiont genome, likely due to the early loss of all mobile elements. Transcriptomic data for the R. gibba SB and host organelles addressed whether and how the allocation of transcriptional resources depends on light and nitrogen availability. Although allocation to the SB was high under all conditions, relative expression of chloroplast photosynthesis genes increased in the absence of nitrate, but this pattern was suppressed by nitrate addition. SB expression of catabolism genes was generally greater during daytime rather than at night, although the magnitude of diurnal changes in expression was modest compared to free-living Cyanobacteria. We conclude that SB daytime catabolism likely supports N-fixation by linking the process to host photosynthetic carbon fixation.

Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements.

Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.

RO-BIK—A robotic approach to developing dynamic architecture

This article presents a design proposal for a socially engaging, architecturally dynamic, and adaptable pavilion that fosters interaction among individuals. The pavilion aims to bridge the gap between open and enclosed spaces in university campuses or other cultural settings, maximizing their vibrancy. To achieve this objective, the design incorporates principles of robotics and data-driven analysis to examine the mechanics, form, and modes of interaction of mobile elements, expressed through computer-coded language. The article delves into the design process and highlights key features of the pavilion, emphasizing its adaptability to variable conditions and its capacity to guide and facilitate people’s movements and interactions. Furthermore, it explores the potential of motion within architecture by utilizing mechanics and programmability inspired by the Rubik’s Cube system. The article also provides the technical design of all components and focuses on the Multipurpose Path Planning (MTP) approach as a guiding principle for the RO-BIK project.

Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions

BackgroundEnterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.ResultsE. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans.ConclusionsOur study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.