Prokaryotes: the unseen majority

Single-cell view of deep-sea microbial activity and intracommunity heterogeneity

Microbial activity in the deep sea is cumulatively important for global elemental cycling yet is difficult to quantify and characterize due to low cell density and slow growth. Here, we investigated microbial activity off the California coast, 50-4000 m water depth, using sensitive single-cell measurements of stable-isotope uptake and nucleic acid sequencing. We observed the highest yet reported proportion of active cells in the bathypelagic (up to 78%) and calculated that deep-sea cells (200-4000 m) are responsible for up to 34% of total microbial biomass synthesis in the water column. More cells assimilated nitrogen derived from amino acids than ammonium, and at higher rates. Nitrogen was assimilated preferentially to carbon from amino acids in surface waters, while the reverse was true at depth. We introduce and apply the Gini coefficient, an established equality metric in economics, to quantify intracommunity heterogeneity in microbial anabolic activity. We found that heterogeneity increased with water depth, suggesting a minority of cells contribute disproportionately to total activity in the deep sea. This observation was supported by higher RNA/DNA ratios for low abundance taxa at depth. Intracommunity activity heterogeneity is a fundamental and rarely measured ecosystem parameter and may have implications for community function and resilience.

Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds

The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.

Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients

Viruses are the most abundant form of life on earth and play important roles in a broad range of ecosystems. Currently, two methods, whole genome shotgun metagenome (WGSM) and viral-like particle enriched metagenome (VLPM) sequencing, are widely applied to compare viruses in various environments. However, there is no critical assessment of their performance in recovering viruses and biological interpretation in comparative viral metagenomic studies. To fill this gap, we applied the two methods to investigate the stool virome in hepatocellular carcinoma (HCC) patients and healthy controls. Both WGSM and VLPM methods can capture the major diversity patterns of alpha and beta diversities and identify the altered viral profiles in the HCC stool samples compared with healthy controls. Viral signatures identified by both methods showed reductions of Faecalibacterium virus Taranis in HCC patients' stool. Ultra-deep sequencing recovered more viruses in both methods, however, generally, 3 or 5 Gb were sufficient to capture the non-fragmented long viral contigs. More lytic viruses were detected than lysogenetic viruses in both methods, and the VLPM can detect the RNA viruses. Using both methods would identify shared and specific viral signatures and would capture different parts of the total virome.

Environmental and ecological controls of the spatial distribution of microbial populations in aggregates

In microbial communities, the ecological interactions between species of different populations are responsible for the spatial distributions observed in aggregates (granules, biofilms or flocs). To explore the underlying mechanisms that control these processes, we have developed a mathematical modelling framework able to describe, label and quantify defined spatial structures that arise from microbial and environmental interactions in communities. An artificial system of three populations collaborating or competing in an aggregate is simulated using individual-based modelling under different environmental conditions. In this study, neutralism, competition, commensalism and concurrence of commensalism and competition have been considered. We were able to identify interspecific segregation of communities that appears in competitive environments (columned stratification), and a layered distribution of populations that emerges in commensal (layered stratification). When different ecological interactions were considered in the same aggregate, the resultant spatial distribution was identified as the one controlled by the most limiting substrate. A theoretical modulus was defined, with which we were able to quantify the effect of environmental conditions and ecological interactions to predict the most probable spatial distribution. The specific microbial patterns observed in our results allowed us to identify the optimal spatial organizations for bacteria to thrive when building a microbial community and how this permitted co-existence of populations at different growth rates. Our model reveals that although ecological relationships between different species dictate the distribution of bacteria, the environment controls the final spatial distribution of the community.

Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments

Marine microbial communities assemble along a sediment depth gradient and are responsible for processing organic matter. Composition of the microbial community along the depth is affected by various biotic and abiotic factors, e.g., the change of redox gradient, the availability of organic matter, and the interactions of different taxa. The community structure is also subjected to some random changes caused by stochastic processes of birth, death, immigration and emigration. However, the high-resolution shifts of microbial community and mechanisms of the vertical assembly processes in marine sediments remain poorly described. Archaeal and bacterial communities were analyzed based on 16S rRNA gene amplicon sequencing and metagenomes in the Bohai Sea sediment samples. The archaeal community was dominated by Thaumarchaeota with increased alpha diversity along depth. Proteobacteria was the dominant bacterial group with decreased alpha diversity as depth increased. Sampling sites and depths collectively affected the beta-diversity for both archaeal and bacterial communities. The dominant mechanism determining archaeal community assembly was determinism, which was mostly contributed by homogeneous selection, i.e., consistent selection pressures in different locations or depths. In contrast, bacterial community assembly was dominated by stochasticity. Co-occurrence networks among different taxa and key functional genes revealed a tight community with low modularity in the bottom sediment, and disproportionately more interactions among low abundant ASVs. This suggests a significant contribution to community stabilization by rare taxa, and suggests that the bottom layer, rather than surface sediments may represent a hotspot for benthic microbial interactions.

Impact of Plant-Beneficial Bacterial Inocula on the Resident Bacteriome: Current Knowledge and Future Perspectives

The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading to increased plant biomass and yield and improved plant health, as well as the ameliorated nutritional value of fruits and edible seeds. During the last decades, exciting, but heterogeneous, results have been obtained growing PGPB inoculated plants under controlled, stressful, and open field conditions. On the other hand, the possible impact of the PGPB deliberate release on the resident microbiota has been less explored and the little available information is contradictory. This review aims at filling this gap: after a brief description of the main mechanisms used by PGPB, we focus our attention on the process of PGPB selection and formulation and we provide some information on the EU regulation for microbial inocula. Then, the concept of PGPB inocula as a tool for rhizosphere engineering is introduced and the possible impact of bacterial inoculant on native bacterial communities is discussed, focusing on those bacterial species that are included in the EU regulation and on other promising bacterial species that are not yet included in the EU regulation.

Metagenomic Analysis of Garden Soil-Derived Microbial Consortia and Unveiling Their Metabolic Potential in Mitigating Toxic Hexavalent Chromium

Soil microbial communities connect to the functional environment and play an important role in the biogeochemical cycle and waste degradation. The current study evaluated the distribution of the core microbial population of garden soil in the Varanasi region of Uttar Pradesh, India and their metabolic potential for mitigating toxic hexavalent chromium from wastewater. Metagenomes contain 0.2 million reads and 56.5% GC content. The metagenomic analysis provided insight into the relative abundance of soil microbial communities and revealed the domination of around 200 bacterial species belonging to different phyla and four archaeal phyla. The top 10 abundant genera in garden soil were Gemmata, Planctomyces, Steroidobacter, Pirellula, Pedomicrobium, Rhodoplanes, Nitrospira Mycobacterium, Pseudonocardia, and Acinetobacter. In this study, Gemmata was dominating bacterial genera. Euryarchaeota, Parvarchaeota, and Crenarchaeota archaeal species were present with low abundance in soil samples. X-ray photoelectric spectroscopy (XPS) analysis indicates the presence of carbon, nitrogen-oxygen, calcium, phosphorous, and silica in the soil. Soil-derived bacterial consortia showed high hexavalent chromium [Cr (VI)] removal efficiency (99.37%). The bacterial consortia isolated from garden soil had an important role in the hexavalent chromium bioremediation, and thus, this study could be beneficial for the design of a heavy-metal treatment system.

New globally distributed bacterial phyla within the FCB superphylum

Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.

The mud-dwelling clam Meretrix petechialis secretes endogenously synthesized erythromycin

Although lacking an adaptive immune system and often living in habitats with dense and diverse bacterial populations, marine invertebrates thrive in the presence of potentially challenging microbial pathogens. However, the mechanisms underlying this resistance remain largely unexplored and promise to reveal novel strategies of microbial resistance. Here, we provide evidence that a mud-dwelling clam, Meretrix petechialis, synthesizes, stores, and secretes the antibiotic erythromycin. Liquid chromatography coupled with mass spectrometry, immunocytochemistry, fluorescence in situ hybridization, RNA interference, and enzyme-linked immunosorbent assay revealed that this potent macrolide antimicrobial, thought to be synthesized only by microorganisms, is produced by specific mucus-rich cells beneath the clam's mantle epithelium, which interfaces directly with the bacteria-rich environment. The antibacterial activity was confirmed by bacteriostatic assay. Genetic, ontogenetic, phylogenetic and genomic evidence, including genotypic segregation ratios in a family of full siblings, gene expression in clam larvae, phylogenetic tree, and synteny conservation in the related genome region further revealed that the genes responsible for erythromycin production are of animal origin. The detection of this antibiotic in another clam species showed that the production of this macrolide is not exclusive to M. petechialis and may be a common strategy among marine invertebrates. The finding of erythromycin production by a marine invertebrate offers a striking example of convergent evolution in secondary metabolite synthesis between the animal and bacterial domains. These findings open the possibility of engineering-animal tissues for the localized production of an antibacterial secondary metabolite.

Maltodextrin-Coated Peppermint and Caraway Essential Oils Effects on Soil Microbiota

Essential oils exhibit strong antimicrobial effects that can serve as a substitute for synthetic pesticides. However, many reports mention the use of essential oils in protecting above-ground plant organs and storing raw materials and seeds, but only a few address the effects of treatments on soil microbiota. Regarding this, it is necessary to find a solution that will prevent the rapid degradation of oils in soil and extend the period of their action on the soil microbiota. The solution to this problem can be microencapsulation, where the choice of carrier plays a key role. In our experiment, maltodextrin was studied, often used in the microencapsulation of essential oils. It was examined independently in two doses (M1 and M2, with 50 and 200 g kg-1, respectively) and a combination with two essential oils known for their antimicrobial activity. We hypothesized that the selected microbial communities would react differently to the stress caused by maltodextrin-encapsulated essential oils. The serial dilution method assessed the number of colony-forming units (CFU) of bacteria, fungi, and actinomycetes. As the goal of microencapsulation was to prolong the effect of essential oils, their reaction was observed over a longer period. The soil microbial populations were examined in sandy and loamy soil at 1, 7, 14, and 78 days after encapsulated essential oils were mixed with the soil samples. In both types of soil, a significant increase in bacteria and actinomycetes was observed with maltodextrin in both doses. Encapsulated peppermint and caraway oils had different effects on microbes, both inhibitory and stimulatory. It is also important to note that peppermint with a smaller dose of maltodextrin significantly inhibited the growth of fungi in sandy soil in all measurements, as well as that caraway oil with a higher dose of maltodextrin significantly stimulated the growth of bacteria and actinomycetes in sandy soil. The higher dose of maltodextrin could explain this stimulation. Further research is recommended to test different doses of essential oils and maltodextrin, which would lead to the optimal dose of both wall and core materials.

Analysis of gut microbiota in patients with acute myocardial infarction by 16S rRNA sequencing

Background

An increasing number of studies have shown that gut microbiota are associated with human cardiovascular disease, but the characteristics of intestinal flora in patients with acute myocardial infarction (AMI) are still unclear. In this study, we aimed to investigate the difference of intestinal microflora between patients with AMI and healthy people, and to find the effect of percutaneous coronary intervention (PCI) on intestinal microflora.

Methods

A total of 60 stool samples and 60 peripheral blood samples were collected from 20 previously diagnosed AMI patients and 20 healthy people serving as controls. Gut microbiota communities were analyzed via 16 ribosomal RNA-sequencing (16S rRNA). Gut microbiota-derived metabolites, trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFA), in the blood were detected using stable isotope dilution high-performance liquid chromatography with on line electrospray ionization tandem mass spectrometry (LC/MS/MS).

Results

The results showed that a distinct pattern of gut microbiota was observed in AMI patients compared to healthy controls. AMI patients had lower microbiological richness but no significant change in diversity. Bacteroidetes and Verrucomicobia showed an upward trend, whereas Proteobacteria showed a downward trend in AMI patients. During a longitudinal study to compare the changes in bacteria before and after treatment, we found routine cardiac admission therapy 1 week after PCI surgery had no effect on the microbial community structure in patients. There were significantly higher levels of plasma TMAO in AMI patients' microbiota than that in the control group. Contrarily, there was no obvious change in SCFA.

Conclusions

The gut microbiota of patients with AMI differs from that of normal people, and the metabolic products of microflora are more abundant in the plasma of AMI than control cases. Microflora may act on the cardiovascular system through metabolites, and regulation of the microfloral structure may be used in the future treatment of cardiovascular diseases.

Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities

Microalgae that form phytoplankton live and die in a complex microbial consortium in which they co-exist with bacteria and other microorganisms. The dynamics of species succession in the plankton depends on the interplay of these partners. Bacteria utilize substrates produced by the phototrophic algae, while algal growth can be supported by bacterial exudates. Bacteria might also use chemical mediators with algicidal properties to attack algae. To elucidate whether specific bacteria play universal or context-specific roles in the interaction with phytoplankton, we investigated the effect of cocultured bacteria on the growth of 8 microalgae. An interaction matrix revealed that the function of a given bacterium is highly dependent on the cocultured partner. We observed no universally algicidal or universally growth-promoting bacteria. The activity of bacteria can even change during the aging of an algal culture from inhibitory to stimulatory or vice versa. We further established a synthetic phytoplankton/bacteria community with the centric diatom, Coscinodiscus radiatus, and 4 phylogenetically distinctive bacterial isolates, Mameliella sp., Roseovarius sp., Croceibacter sp., and Marinobacter sp. Supported by a Lotka-Volterra model, we show that interactions within the consortium are specific and that the sum of the pairwise interactions can explain algal and bacterial growth in the community. No synergistic effects between bacteria in the presence of the diatom was observed. Our survey documents highly species-specific interactions that are dependent on algal fitness, bacterial metabolism, and community composition. This species specificity may underly the high complexity of the multi-species plankton communities observed in nature. IMPORTANCE The marine food web is fueled by phototrophic phytoplankton. These algae are central primary producers responsible for the fixation of ca. 40% of the global CO2. Phytoplankton always co-occur with a diverse bacterial community in nature. This diversity suggests the existence of ecological niches for the associated bacteria. We show that the interaction between algae and bacteria is highly species-specific. Furthermore, both, the fitness stage of the algae and the community composition are relevant in determining the effect of bacteria on algal growth. We conclude that bacteria should not be sorted into algicidal or growth supporting categories; instead, a context-specific function of the bacteria in the plankton must be considered. This functional diversity of single players within a consortium may underly the observed diversity in the plankton.

Peptide-Grafted Nontoxic Cyclodextrins and Nanoparticles against Bacteriophage Infections

One of the biggest threats for bacteria-based bioreactors in the biotechnology industry is infections caused by bacterial viruses called bacteriophages. More than 70% of companies admitted to encountering this problem. Despite phage infections being such a dangerous and widespread risk, to date, there are no effective methods to avoid them. Here we present a peptide-grafted compounds that irreversibly deactivate bacteriophages and remain safe for bacteria and mammalian cells. The active compounds consist of a core (cyclodextrin or gold nanoparticle) coated with a hydrophobic chain terminated with a peptide selective for bacteriophages. Such peptides were selected via a phage display technique. This approach enables irreversible deactivation of the wide range of T-like phages (including the most dangerous in phage infections, phage T1) at 37 °C in 1 h. We show that our compounds can be used directly inside the environment of the bioreactor, but they are also a safe additive to stocks of antibiotics and expression inducers (such as isopropyl β-d-1-thiogalactopyranoside, i.e., IPTG) that cannot be autoclaved and are a common source of phage infections.

Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.

Horizontal gene transfer and ecological interactions jointly control microbiome stability

Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet, despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes in response to stressors. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for genes on mobile genetic elements with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies dramatically depending upon the identity of individual taxa, the mobility of the resistance gene, and the network of ecological interactions within the community. Nonmobile resistance genes can benefit susceptible taxa in cooperative communities yet damage those in competitive communities. Moreover, while the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can decrease the stability of the originally resistant donor taxon. We confirmed key theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together, these findings highlight the importance of the interplay between ecological interactions and horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.

Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax

Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages.

Microbial community metabolic alterations and resistance to metals and antibiotics driven by chronic exposition to multiple pollutants in a highly impacted tropical coastal bay

Microbial communities from Sepetiba Bay (SB, Rio de Janeiro, Brazil), characterized by 16S rRNA gene (V4-V5 region) sequencing analysis, were found to be correlated with the metallic contamination factor and the Quality Ratio (QR) index. Consistently, the predicted function of microbial communities, obtained with Tax4Fun2, showed that the functional patterns in SB internal sector under the highest anthropogenic pressure were different from that observed in the external sector with the lowest contamination level. Signal transduction, cellular community, membrane transport, and energy metabolism were among the KEGG pathways favored by metallic contamination in the SB internal sector, while lipid metabolism, transcription, and translation were among the pathways favored in the SB external sector. Noteworthy, the relative proportions of KEGG pathways and genes associated with metallic homeostasis showed significant differences according to the SB sectors, consistently with the ecological risk classification (QR index) of sediments. The functional prediction approach is an economically viable alternative and presents an overview of the main pathways/genes favored in the SB microbiota exposed to long-term pollution. In contrast, the microgAMBI, ecological status index based on bacterial community composition, was not consistent with the metallic contamination of SB, suggesting that this index requires improvements to be applied in tropical areas. Our study also revealed a strong correlation between metal resistance genes (MRG) and antibiotic resistance genes (ARG), indicating that MRG and ARG are co-selected by the metallic contamination prevailing in SB.

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait-trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait-trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.

Revealing CO2-Fixing SAR11 Bacteria in the Ocean by Raman-Based Single-Cell Metabolic Profiling and Genomics

The majority of marine microbes remain uncultured, which hinders the identification and mining of CO2-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO2-fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their 13C-bicarbonate (13C-HCO3-) intake via single-cell Raman spectra (SCRS) analysis. The target cells were then isolated by Raman-activated Gravity-driven Encapsulation (RAGE), and their genomes were amplified and sequenced at one-cell resolution. The single-cell metabolism, phenotype and genome are consistent. We identified a not-yet-cultured Pelagibacter spp., which actively assimilates 13C-HCO3-, and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO2 fixation, a complete gene set for a rhodopsin-based light-harvesting system, and the full genes necessary for carotenoid synthesis. The four proteorhodopsin (PR) genes identified in the Pelagibacter spp. were confirmed by heterologous expression in E. coli. These results suggest that hitherto uncultured Pelagibacter spp. uses light-powered metabolism to contribute to global carbon cycling.

Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly

Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup–Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.

Ecogenomics reveals viral communities across the Challenger Deep oceanic trench

Despite the environmental challenges and nutrient scarcity, the geographically isolated Challenger Deep in Mariana trench, is considered a dynamic hotspot of microbial activity. Hadal viruses are the least explored microorganisms in Challenger Deep, while their taxonomic and functional diversity and ecological impact on deep-sea biogeochemistry are poorly described. Here, we collect 13 sediment cores from slope and bottom-axis sites across the Challenger Deep (down to ~11 kilometers depth), and identify 1,628 previously undescribed viral operational taxonomic units at species level. Community-wide analyses reveals 1,299 viral genera and distinct viral diversity across the trench, which is significantly higher at the bottom-axis vs. slope sites of the trench. 77% of these viral genera have not been previously identified in soils, deep-sea sediments and other oceanic settings. Key prokaryotes involved in hadal carbon and nitrogen cycling are predicted to be potential hosts infected by these viruses. The detected putative auxiliary metabolic genes suggest that viruses at Challenger Deep could modulate the carbohydrate and sulfur metabolisms of their potential hosts, and stabilize host's cell membranes under extreme hydrostatic pressures. Our results shed light on hadal viral metabolic capabilities, contribute to understanding deep sea ecology and on functional adaptions of hadal viruses for future research.

Viruses, immunity and evolution

In this article, the evolution of viruses is analyzed in terms of their complexity. It is shown that the evolution of viruses is a partially directed process. The participation of viruses and mobile genetic elements in the evolution of other organisms by integration into the genome is also an a priori directed process. The high variability of genomes (including the genes of antibodies), which differs by orders of magnitude for various viruses and their hosts, is not a random process but is the result of the action of a molecular genetic control system. Herein, a model of partially directed evolution of viruses is proposed. Throughout the life cycle of viruses, there is an interaction of complex biologically important molecules that cannot be explained on the basis of classic laws. The interaction of a virus with a cell is essentially a quantum event, including selective long-range action. Such an interaction can be interpreted as the "remote key-lock" principle. In this article, a model of the interaction of biologically important viral molecules with cellular molecules based on nontrivial quantum interactions is proposed. Experiments to test the model are also proposed.

Acute resource pulses from periodical cicadas propagate to belowground food webs but do not affect tree performance

Acute resource pulses can have dramatic legacies for organismal growth, but the legacy effects of resource pulses on broader aspects of community structure and ecosystem processes are less understood. Mass emergence of periodical cicadas (Magicicada spp.) provides an excellent opportunity to shed light on the influence of resource pulses on community and ecosystem dynamics: the adults emerge every 13 or 17 years in vast numbers over much of eastern North America, with a smaller but still significant number becoming incorporated into forest food webs. To study the potential effects of such arthropod resource pulse on primary production and belowground food webs, we added adult cicada bodies to the soil surface surrounding sycamore trees and assessed soil carbon and nitrogen concentrations, plant-available nutrients, abundance and community composition of soil fauna occupying various trophic levels, decomposition rate of plant litter after 50 and 100 days, and tree performance for 4 years. Contrary to previous studies, we did not find significant cicada effects on tree performance despite observing higher plant-available nutrient levels on cicada addition plots. Cicada addition did change the community composition of soil nematodes and increased the abundance of bacterial- and fungal-feeding nematodes, while plant feeders, omnivores, and predators were not influenced. Altogether, acute resource pulses from decomposing cicadas propagated belowground to soil microbial-feeding invertebrates and stimulated nutrient mineralization in the soil, but these effects did not transfer up to affect tree performance. We conclude that, despite their influence on soil food web and processes they carry out, even massive resource pulses from arthropods do not necessarily translate to NPP, supporting the view that ephemeral nutrient pulses can be attenuated relatively quickly despite being relatively large in magnitude.

Network analysis reveals microbe-mediated impacts of aeration on deep sediment layer microbial communities

Over-aeration is a common remediation strategy for black and odorous water bodies, in which oxygen is introduced to impact aquatic microbial communities as an electron acceptor of high redox potential. In this study, black-odorous freshwater sediments were cultured for 9 weeks under aeration to investigate microbial covariations at different depths and time points. Based on community 16S rRNA gene sequencing, the microbial covariations were visualized using phylogenetic microbial ecological networks (pMENs). In the spatial scale, we identified smaller and more compact pMENs across all layers compared with the anaerobic control sediments, in terms of network size, average node connectivity, and modularity. The aerated middle layer had the most connectors, the least module hubs, a network hub, shorter average path length, and predominantly positive covariations. In addition, a significant sulfate accumulation in the aerated middle layer indicated the most intense sulfide oxidation, possibly because aeration prompted sediment surface Desulfobulbaceae, known as cable bacteria, to reach the middle layer. In the time scale, similarly, aeration led to smaller pMEN sizes and higher portions of positive covariations. Therefore, we conclude that elevated dissolved oxygen at the water-sediment interface may impact not only the surface sediment but also the subsurface and/or deep sediment microbial communities mediated by microorganisms, particularly by Desulfobulbaceae.

Viruses in Subsurface Environments

Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.

ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics

Compared with conventional comparative genomics, the recent studies in pan-genomics have provided further insights into species genomic dynamics, taxonomy and identification, pathogenicity and environmental adaptation. To better understand genome characteristics of species of interest and to fully excavate key metabolic and resistant genes and their conservations and variations, here we present ProPan (https://ngdc.cncb.ac.cn/propan), a public database covering 23 archaeal species and 1,481 bacterial species (in a total of 51,882 strains) for comprehensively profiling prokaryotic pan-genome dynamics. By analyzing and integrating these massive datasets, ProPan offers three major aspects for the pan-genome dynamics of the species of interest: 1) the evaluations of various species' characteristics and composition in pan-genome dynamics; 2) the visualization of map association, the functional annotation and presence/absence variation for all contained species' gene clusters; 3) the typical characteristics of the environmental adaptation, including resistance genes prediction of 126 substances (biocide, antimicrobial drug and metal) and evaluation of 31 metabolic cycle processes. Besides, ProPan develops a very user-friendly interface, flexible retrieval and multi-level real-time statistical visualization. Taken together, ProPan will serve as a weighty resource for the studies of prokaryotic pan-genome dynamics, taxonomy and identification as well as environmental adaptation.

Bacterial diversity in surface sediments of collapsed lakes in Huaibei, China

The collapse lake area due to coal mining in Huaibei shows high biodiversity, but the bacterial community composition and diversity in the lake sediments are still rarely studied. Therefore, based on 16S rRNA high-throughput sequencing and combined with analysis of environmental factors, we comparatively analyzed the bacterial community composition and diversity of surface sediments from East Lake (DH) and South Lake (NH) and Middle Lake (ZH) in the collapse lake area of Huaibei. The bacterial community compositions are significantly different in the sediments among Huaibei collapsed lakes, with DH having the largest number of species, and NH having a higher species diversity. Pseudomonadota is the most abundant phylum in the sediments of DH and NH, while the most abundant phyla in ZH are Bacteroidales, Chloroflexales, Acidobacteriales, and Firmicutes. Anaerolineae (24.05% ± 0.20%) is the most abundant class in the DH sediments, and Gammaproteobacteria (25.94% ± 0.40%) dominates the NH sediments, Bacteroidia (32.12% ± 1.32%) and Clostridia (21.98% ± 0.90%) contribute more than 50% to the bacteria in the sediments of ZH. Redundancy analysis (RDA) shows that pH, TN, and TP are the main environmental factors affecting the bacterial community composition in the sediments of the collapsed lake area. The results reveal the bacterial community composition and biodiversity in the sediments of the Huaibei coal mining collapsed lakes, and provide new insights for the subsequent ecological conservation and restoration of the coal mining collapsed lakes.

Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans

The human gut microbiota protects the host from invading pathogens and the overgrowth of indigenous opportunistic species via a process called colonization resistance. Here, we investigated the antagonistic activity of human gut bacteria towards Candida albicans, an opportunistic fungal pathogen that can cause severe infections in susceptible individuals. Coculture batch incubations of C. albicans in the presence of faecal microbiota from six healthy individuals revealed varying levels of inhibitory activity against C. albicans. 16S rRNA gene amplicon profiling of these faecal coculture bacterial communities showed that the Bifidobacteriaceae family, and Bifidobacterium adolescentis in particular, were most correlated with antagonistic activity against C. albicans. Follow-up mechanistic studies performed under anaerobic conditions confirmed that culture supernatants of Bifidobacterium species, particularly B. adolescentis, inhibited C. albicans in vitro. Fermentation acids (FA), including acetate and lactate, present in the bifidobacterial supernatants were important contributors to inhibitory activity. However, increasing the pH of both bacterial supernatants and mixtures of FA reduced their anti-Candida effects, indicating a combinatorial effect of prevailing pH and FA. This work, therefore, demonstrates potential mechanisms underpinning gut microbiome-mediated colonization resistance against C. albicans, and identifies particularly inhibitory components such as bifidobacteria and FA as targets for further study.

Zwitterionic surface chemistry enhances detachment of bacteria under shear

The ubiquitous nature of microorganisms, especially of biofilm-forming bacteria, makes biofouling a prevalent challenge in many settings, including medical and industrial environments immersed in liquid and subjected to shear forces. Recent studies have shown that zwitterionic groups are effective in suppressing bacteria and protein adhesion as well as biofilm growth. However, the effect of zwitterionic groups on the removal of surface-bound bacteria has not been extensively studied. Here we present a microfluidic approach to evaluate the effectiveness in facilitating bacteria detachment by shear of an antifouling surface treatment using (3-(dimethyl;(3-trimethoxysilyl)propyl)ammonia propane-1-sulfonate), a sulfobetaine silane (SBS). Control studies show that SBS-functionalized surfaces greatly increase protein (bovine serum albumin) removal upon rinsing. On the same surfaces, enhanced bacteria (Pseudomonas aeruginosa) removal is observed under shear. To quantify this enhancement a microfluidic shear device is employed to investigate how SBS-functionalized surfaces promote bacteria detachment under shear. By using a microfluidic channel with five shear zones, we compare the removal of bacteria from zwitterionic and glass surfaces under different shear rates. At times of 15 min, 30 min, and 60 min, bacteria adhesion on SBS-functionalized surfaces is reduced relative to the control surface (glass) under quiescent conditions. However, surface-associated bacteria on the SBS-functionalized glass and control show similar percentages of live cells, suggesting minimal intrinsic biocidal effect from the SBS-functionalized surface. Notably, when exposed to shear rates ranging from 104 to 105 s-1, significantly fewer bacteria remain on the SBS-functionalized surfaces. These results demonstrate the potential of zwitterionic sulfobetaine as effective antifouling coatings that facilitate the removal of bacteria under shear.

Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease Atherosclerosis

Accumulating evidence suggests an important role of gut microbiota in physiological processes of host metabolism as well as cardiometabolic disease. Recent advances in metagenomic and metabolomic research have led to discoveries of novel pathways in which intestinal microbial metabolism of dietary nutrients is linked to metabolic profiles and cardiovascular disease risk. A number of metaorganismal circuits have been identified by microbiota transplantation studies and experimental models using germ-free rodents. Many of these pathways involve gut microbiota-related bioactive metabolites that impact host metabolism, in particular lipid and glucose homeostasis, partly via specific host receptors. In this review, we summarize the current knowledge of how the gut microbiome can impact cardiometabolic phenotypes and provide an overview of recent advances of gut microbiome research. Finally, the potential of modulating intestinal microbiota composition and/or targeting microbiota-related pathways for novel preventive and therapeutic strategies in cardiometabolic and cardiovascular diseases will be discussed.

Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes

Freshwater microbes play a crucial role in the global carbon cycle. Anthropogenic stressors that lead to changes in these microbial communities are likely to have profound consequences for freshwater ecosystems. Using field data from the coordinated sampling of 617 lakes, ponds, rivers, and streams by citizen scientists, we observed linkages between microbial community composition, light and chemical pollution, and greenhouse gas concentration. All sampled water bodies were net emitters of CO₂, with higher concentrations in running waters, and increasing concentrations at higher latitudes. Light pollution occurred at 75% of sites, was higher in urban areas and along rivers, and had a measurable effect on the microbial alpha diversity. Genetic elements suggestive of chemical stress and antimicrobial resistances (IntI1, blaOX₅₈) were found in 85% of sites, and were also more prevalent in urban streams and rivers. Light pollution and CO₂ were significantly related to microbial community composition, with CO₂ inversely related to microbial phototrophy. Results of synchronous nationwide sampling indicate that pollution-driven alterations to the freshwater microbiome lead to changes in CO₂ production in natural waters and highlight the vulnerability of running waters to anthropogenic stressors.

Shift in Microbial Community Structure with Temperature in Deulajhari Hot Spring Cluster, Odisha, India

Hot springs are the reservoirs of novel hyperthermophilic and often mesophilic bacteria that provide information about the prevailing community structure. Here we analyzed the metagenome profile based 16S rRNA amplicon sequencing of the three different springs from Deulajhari hot spring cluster, S1, S2 and S3, having a range of temperature (43°C to 65°C), pH (7.14 – 8.10) and variation in N, P, K, TOC, Salinity, COD and TDS. These thermal spring clusters are covered with the dense vegetation of Pandanus and continuously enriched by plant leaf debris, thus resulting in a high amount of total organic carbon (TOC). The number of phyla varied among the springs: 20 in S1 (43°C), 18 in S2 (55°C) and 24 in S3 (65°C) from the 16S rRNA data. Out of the reported phyla in each spring, the most abundant were Chloroflexi, Proteobacteria, Chlorobi and Acidobacteria, which correlated with the temperature gradient. Various metabolic pathways such as ABC transporters, Two-component system, Purine metabolism were most abundantly present in the S2 sample compared to the other two. The CCA analysis revealed the correlation between physiochemical parameters and their functional annotation. The present study establishes the relation between the physiological parameters and the structural distribution of microbiota along the temperature gradient.

Diet, Microbes, and Cancer Across the Tree of Life: a Systematic Review

PURPOSE OF REVIEW

Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator between diet and cancers. Here, we review the work on cancer and the microbiome across species to search for broad patterns of susceptibility associated with different microbial species.

RECENT FINDINGS

Some microbes, such as Helicobacter bacteria, papillomaviruses, and the carnivore-associated Fusobacteria, consistently induce tumorigenesis in humans and other species. Other microbes, such as the milk-associated Lactobacillus, consistently inhibit tumorigenesis in humans and other species. We systematically reviewed over a thousand published articles and identified links between diet, microbes, and cancers in several species of mammals, birds, and flies. Future work should examine a larger variety of host species to discover new model organisms for human preclinical trials, to better understand the observed variance in cancer prevalence across species, and to discover which microbes and diets are associated with cancers across species. Ultimately, this could help identify microbial and dietary interventions to diagnose, prevent, and treat cancers in humans as well as other animals.

Bacterioplankton communities reveal horizontal and vertical influence of an Island Mass Effect

Coral reefs are highly productive ecosystems with distinct biogeochemistry and biology nestled within unproductive oligotrophic gyres. Coral reef islands have often been associated with a nearshore enhancement in phytoplankton, a phenomenon known as the Island Mass Effect (IME). Despite being documented more than 60 years ago, much remains unknown about the extent and drivers of IMEs. Here we utilized 16S rRNA gene metabarcoding as a biological tracer to elucidate horizontal and vertical influence of an IME around the islands of Mo'orea and Tahiti, French Polynesia. We show that those nearshore oceanic stations with elevated chlorophyll a included bacterioplankton found in high abundance in the reef environment, suggesting advection of reef water is the source of altered nearshore biogeochemistry. We also observed communities in the nearshore deep chlorophyll maximum (DCM) with enhanced abundances of upper euphotic bacterioplankton that correlated with intrusions of low-density, O₂ rich water, suggesting island influence extends into the DCM.

Microbial communities on plastic particles in surface waters differ from subsurface waters of the North Pacific Subtropical Gyre

The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.

The healthy equine uterus harbors a distinct core microbiome plus a rich and diverse microbiome that varies with geographical location

The goal of this study was to understand the composition and existence of the resident uterine microbiome in healthy mares and to establish the presence of a core microbiome for the healthy equine uterus. We analyzed the microbiomes of 35 healthy mares that are long-time residents of three farms in Oklahoma, Louisiana, and Australia as well as that of 19 mares purchased from scattered owners in the Southern Mid-Western states of the United States. Over 6 million paired-end reads of the V4 region of the 16S rRNA gene were obtained resulting in 19,542 unique Amplicon Sequence Variants (ASVs). ASVs were assigned to 17 known phyla and 213 known genera. Most abundant genera across all animals were Pseudomonas (27%) followed by Lonsdalea (8%), Lactobacillus (7.5%), Escherichia/Shigella (4.5%), and Prevotella (3%). Oklahoma and Louisiana samples were dominated by Pseudomonas (75%). Lonsdalea (28%) was the most abundant genus in the Australian samples but was not found in any other region. Microbial diversity, richness, and evenness of the equine uterine microbiome is largely dependent on the geographical location of the animal. However, we observed a core uterine microbiome consisting of Lactobacillus, Escherichia/Shigella, Streptococcus, Blautia, Staphylococcus, Klebsiella, Acinetobacter, and Peptoanaerobacter.

Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean

The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.

Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family

Rod-shaped bacteria typically elongate and divide by transverse fission. However, several bacterial species can form rod-shaped cells that divide longitudinally. Here, we study the evolution of cell shape and division mode within the family Neisseriaceae, which includes Gram-negative coccoid and rod-shaped species. In particular, bacteria of the genera Alysiella, Simonsiella and Conchiformibius, which can be found in the oral cavity of mammals, are multicellular and divide longitudinally. We use comparative genomics and ultrastructural microscopy to infer that longitudinal division within Neisseriaceae evolved from a rod-shaped ancestor. In multicellular longitudinally-dividing species, neighbouring cells within multicellular filaments are attached by their lateral peptidoglycan. In these bacteria, peptidoglycan insertion does not appear concentric, i.e. from the cell periphery to its centre, but as a medial sheet guillotining each cell. Finally, we identify genes and alleles associated with multicellularity and longitudinal division, including the acquisition of amidase-encoding gene amiC2, and amino acid changes in proteins including MreB and FtsA. Introduction of amiC2 and allelic substitution of mreB in a rod-shaped species that divides by transverse fission results in shorter cells with longer septa. Our work sheds light on the evolution of multicellularity and longitudinal division in bacteria, and suggests that members of the Neisseriaceae family may be good models to study these processes due to their morphological plasticity and genetic tractability.

Rod-shaped bacteria typically elongate and divide by transverse fission, but a few species are known to divide longitudinally. Here, the authors use genomic, phylogenetic and microscopy techniques to shed light on the evolution of cell shape, multicellularity and division mode within the family Neisseriaceae.

Culturomics, a potential approach paving the way toward bacteriotherapy

The human microbiota has been extensively studied over the past decade to describe its role in health and diseases. Numerous studies showed the presence of bacterial imbalance in a variety of human health conditions, suggesting great potential for the development of bacteriotherapies. Identifying mechanisms involving the human microbiota has been very challenging due to the complex data generated by molecular approaches and the limited number of organisms isolated by culture and described. This review summarizes the efforts done to describe the human microbiota through culturomics and the advancements in culturing the organisms residing at different body sites.

Research progress on the relationship between intestinal microecology and intestinal bowel disease

Intestinal microecology is the main component of human microecology. Intestinal microecology consists of intestinal microbiota, intestinal epithelial cells, and intestinal mucosal immune system. These components are interdependent and establish a complex interaction network that restricts each other. According to the impact on the human body, there are three categories of symbiotic bacteria, opportunistic pathogens, and pathogenic bacteria. The intestinal microecology participates in digestion and absorption, and material metabolism, and inhibits the growth of pathogenic microorganisms. It also acts as the body's natural immune barrier, regulates the innate immunity of the intestine, controls the mucosal barrier function, and also participates in the intestinal epithelial cells' physiological activities such as hyperplasia or apoptosis. When the steady‐state balance of the intestinal microecology is disturbed, the existing core intestinal microbiota network changes and leads to obesity, diabetes, and many other diseases, especially irritable bowel syndrome, inflammatory bowel disease (IBD), and colorectal malignancy. Intestinal diseases, including tumors, are particularly closely related to intestinal microecology. This article systematically discusses the research progress on the relationship between IBD and intestinal microecology from the pathogenesis, treatment methods of IBD, and the changes in intestinal microbiota.

Effect of Climate on Bacterial and Archaeal Diversity of Moroccan Marine Microbiota

The Moroccan coast is characterized by a diversity of climate, reflecting a great richness and diversity of fauna and flora. By this, marine microbiota plays a fundamental role in many biogeochemical processes, environmental modifications, and responses to temperature changes. To date, no exploration by high-throughput techniques has been carried out on the characterization of the Moroccan marine microbiota. The objective of this work is to study the diversity and metabolic functions of MMM from the Moroccan coast (Atlantic and Mediterranean) according to the water source (WS) and the type of climate (CT) using the approach high-throughput sequencing of the 16SrRNA gene. Four water samples of twelve sampling sites from the four major climates along the Moroccan coastline were collected, and prokaryotic DNA was extracted. V4 region of 16S rRNA gene was amplified, and the product PCR was sequenced by Illumina Miseq. The β-diversity and α-diversity indices were determined to assess the species richness and evenness. The obtained results were analyzed by Mothur and R software. A total of twenty-eight Bacterial phyla and twelve Archaea were identified from the samples. Proteobacteria, Bacteroidetes, and Cyanobacteria are the three key bacterial phyla, and the Archaeal phyla identified are: Euryarchaeota, Nanoarchaeaeota, Crenarchaeota, Hydrothermarchaeota, Asgardaeota, Diapherotrites, and Thaumarchaeota in the Moroccan coastline and the four climates studied. The whole phylum are involved in marine biogeochemical cycles, and through their functions they participate in the homeostasis of the ocean in the presence of pollutants or stressful biotic and abiotic factors. In conclusion, the obtained results reported sufficient deepness of sequencing to cover the majority of Archaeal and Bacterial genera in each site. We noticed a strong difference in microbiota diversity, abundance, and taxonomy inter- and intra-climates and water source without significant differences in function. To better explore this diversity, other omic approaches can be applied such as the metagenomic shotgun, and transcriptomic approaches allowing a better characterization of the Moroccan marine microbiota and to understand the mechanisms of its adaptation and its impacts in/on the ecosystem.

The past, present, and future of antibiotics

Antibiotics have transformed modern medicine. They are essential for treating infectious diseases and enable vital therapies and procedures. However, despite this success, their continued use in the 21st century is imperiled by two orthogonal challenges. The first is that the microbes targeted by these drugs evolve resistance to them over time. The second is that antibiotic discovery and development are no longer cost-effective using traditional reimbursement models. Consequently, there are a dwindling number of companies and laboratories dedicated to delivering new antibiotics, resulting in an anemic pipeline that threatens our control of infections. The future of antibiotics requires innovation in a field that has relied on highly traditional methods of discovery and development. This will require substantial changes in policy, quantitative understanding of the societal value of these drugs, and investment in alternatives to traditional antibiotics. These include narrow-spectrum drugs, bacteriophage, monoclonal antibodies, and vaccines, coupled with highly effective diagnostics. Addressing the antibiotic crisis to meet our future needs requires considerable investment in both research and development, along with ensuring a viable marketplace that encourages innovation. This review explores the past, present, and future of antimicrobial therapy.

Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt

The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe³⁺, napAB to reduce NO₃⁻ to NO₂⁻, hydAB to produce H₂ and genes sirA, phsABC and ttrABC to reduce SO₃²⁻, S₂O₃²⁻ and S₄O₆²⁻, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe³⁺ and promote the oxidation of Fe²⁺ in the presence of NO₃⁻ under anaerobic conditions. Production of H₂ has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe³⁺ and NO₃⁻, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S₄O₆²⁻ and S₂O₃²⁻ as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.

Chitosan Nanoparticle Encapsulation of Antibacterial Essential Oils

Chitosan is the most suitable encapsulation polymer because of its natural abundance, biodegradability, and surface functional groups in the form of free NH₂ groups. The presence of NH₂ groups allows for the facile grafting of functionalized molecules onto the chitosan surface, resulting in multifunctional materialistic applications. Quaternization of chitosan's free amino is one of the typical chemical modifications commonly achieved under acidic conditions. This quaternization improves its ionic character, making it ready for ionic-ionic surface modification. Although the cationic nature of chitosan alone exhibits antibacterial activity because of its interaction with negatively-charged bacterial membranes, the nanoscale size of chitosan further amplifies its antibiofilm activity. Additionally, the researcher used chitosan nanoparticles as polymeric materials to encapsulate antibiofilm agents (such as antibiotics and natural phytochemicals), serving as an excellent strategy to combat biofilm-based secondary infections. This paper provided a summary of available carbohydrate-based biopolymers as antibiofilm materials. Furthermore, the paper focuses on chitosan nanoparticle-based encapsulation of basil essential oil (Ocimum basilicum), mandarin essential oil (Citrus reticulata), Carum copticum essential oil ("Ajwain"), dill plant seed essential oil (Anethum graveolens), peppermint oil (Mentha piperita), green tea oil (Camellia sinensis), cardamom essential oil, clove essential oil (Eugenia caryophyllata), cumin seed essential oil (Cuminum cyminum), lemongrass essential oil (Cymbopogon commutatus), summer savory essential oil (Satureja hortensis), thyme essential oil, cinnamomum essential oil (Cinnamomum zeylanicum), and nettle essential oil (Urtica dioica). Additionally, chitosan nanoparticles are used for the encapsulation of the major essential components carvacrol and cinnamaldehyde, the encapsulation of an oil-in-water nanoemulsion of eucalyptus oil (Eucalyptus globulus), the encapsulation of a mandarin essential oil nanoemulsion, and the electrospinning nanofiber of collagen hydrolysate-chitosan with lemon balm (Melissa officinalis) and dill (Anethum graveolens) essential oil.

A CURE for Physiological Characterization of Bacterioplankton in Liquid Culture

Bacterial characterization is an important aspect of microbiology that includes experimentally determining growth rates, environmental conditions conducive to growth, and the types of energy sources microorganisms can use. Researchers use this information to help understand and predict an organism's ecological distribution and environmental functions. Microbiology students generally conduct bacterial characterization experiments in their coursework; however, they are frequently restricted to model organisms without ecological relevance and already well-studied physiologies. We present a course-based undergraduate research experience (CURE) curriculum to involve students in characterization of previously untested, ecologically relevant aquatic free-living bacteria (bacterioplankton) cultures to identify the usable nutrient substrates, as well as the temperature and salinity ranges conducive to growth. Students use these results to connect their organism's physiology to the isolation environment. This curriculum also exposes students to advanced microbiology methods such as flow cytometry for measuring cell concentrations, teaches them to use the programming language R for data plotting, and emphasizes scientific communication through writing, speaking, poster creation/presentation, and social media. This CURE is an attractive introduction to scientific research and was successfully tested with 187 students in three semesters at two different universities. Students generated reproducible growth data for multiple strains across these different deployments, demonstrating the utility of the curriculum for research support.

Comparative study of methods for detecting extraterrestrial life in exploration mission of Mars and the solar system

The detection and analysis of extraterrestrial life are important issues of space science. Mars is among the most important planets to explore for extraterrestrial life, owing both to its physical properties and to its ancient and present environments as revealed by previous exploration missions. In this paper, we present a comparative study of methods for detecting extraterrestrial life and life-related substances. To this end, we have classified and summarized the characteristics targeted for the detection of extraterrestrial life in solar system exploration mission and the methods used to evaluate them. A summary table is presented. We conclude that at this moment (i) there is no realistic single detection method capable of concluding the discovery of extraterrestrial life, (ii) no single method has an advantage over the others in all respects, and (iii) there is no single method capable of distinguishing extraterrestrial life from terrestrial life. Therefore, a combination of complementary methods is essential. We emphasize the importance of endeavoring to detect extraterrestrial life without overlooking possible alien life forms, even at the cost of tolerating false positives. Summaries of both the targets and the detection methods should be updated continuously, and comparative studies of both should be pursued. Although this study assumes Mars to be a model site for the primary environment for life searches, both the targets and detection methods described herein will also be useful for searching for extraterrestrial life in any celestial environment and for the initial inspection of returned samples.

First principles of terrestrial life: exemplars for potential extra-terrestrial biology

The search for life elsewhere in the universe represents not only a potential expansion of our knowledge regarding life, but also a clarification of the first principles applicable to terrestrial life, which thus restrict the very search for extra-terrestrial life. Although there are no exact figures for how many species have existed throughout Earth's total history, we can still make inferences about how the distribution of this life has proceeded through a bell curve. This graph shows the totality of life, from its origin to its end. The system enclosing life contains a number of first principles designated the walls of minimal complexity and adaptive possibility, the fence of adaptation, and right-skewed extension. In this discussion of life, a framework will be formulated that, based on the dynamic relationship between mesophiles and extremophiles, will be imposed on exoworlds in order to utilize the graph's predictive power to analyze how extra-terrestrial life could unfold. In this framework the evolutionary variation does not depend on the specific biochemistry involved. Once life is 'up and running,' the various biochemical systems that can constitute terrestrial and extra-terrestrial life will have secondary significance. The extremophilic tail represents a range expansion in which all habitat possibilities are tested and occupied. This tail moves to the right not because of the biochemistry constitutions of organisms, but because it can do nothing else. Thus, it can be predicted that graphs of terrestrial and extra-terrestrial life will be similar overall. A number of other predictions can be made; for example, for worlds in which the atmospheric disequilibrium is approaching equilibrium, it is predicted that life may still be present because the extremophilic range expansion is stretched increasingly farther to the right. Because life necessarily arises at a left wall of minimal complexity, it is predicted that any origin of cellular life will have a close structural resemblance to that of the first terrestrial life. Thus, in principle, life may have originated more than once on Earth, and still exist. It is also predicted that there may be an entire subset of life existing among other domains that we do not see because, in an abstract sense, we are inside the graph. If we view the graph in its entirety, this subset appears very much like a vast supra-domain of life.