Domain Bacteria Research Articles

Isolation, Identification and Phylogeny of Actinobacteria from Island Soils Using Different Isolation Methods

Actinobacteria are one of the most frequently studied prokaryotic groups within the Bacteria domain. In this study, soil samples collected from the islands of Burgazada, Büyükada, Gökçeada, Heybeliada, and Kınalıada were used to isolate, identify, and analyze the phylogeny of Actinobacteria. For the isolation studies, three different isolation methods and 11 different selective media were employed. As a result, a total of 103 bacterial strains were isolated. The molecular identification of the isolated strains was conducted using 16S rRNA gene region sequence analyses. These analyses revealed that the isolates belonged to 12 different genera within the Actinobacteria phylum. Comparison of the 16S rRNA gene sequences of the isolates with their closest relatives in the EzBioCloud database indicated a sequence similarity ranging between 95.76% and 100%. The isolation studies demonstrated that the standard dilution plate method was more effective for isolating both diverse genera and potential novel species. The data obtained through this method showed that 22 of the isolated strains, belonging to 8 different genera, have the potential to represent novel species. In conclusion, this study highlights that island soils are an important source for the discovery of new Actinobacteria species. Furthermore, it emphasizes the significance of such isolation studies in uncovering the rich biotechnological potential of Actinobacteria.

P1322 Gut microbiome and Virome dynamics between rural and urban population suggests the severity in ulcerative colitis patients

Abstract Background Ulcerative colitis (UC) is chronic, inflammatory disease of the colon mucosa. Gut microbiome dysbiosis is considered to play a significant role in UC pathogenesis. Apart from bacteria, viruses are the intricate part of the gut microbiome which are often neglected in 16s rRNA based metagenomic studies. Therefore, whole genome sequencing (WGS) based studies of gut meta-DNA should be implemented to identify the microorganisms of different domains (bacteria, and viruses) residing in the human gut. Methods Human gut microbiota composition was assessed at microbiome and virome profiling using WGS of fecal samples. The gut metagenomes were further evaluated for the human gut resistome study. Results The UC gut was enriched with the pathobionts such as Escherichia coli and Bacteroides sp. The beneficial microbe resides in perfect mutualism in the gut such as Prevotella sp CAG_279, Firmicutes bacterium CAG_129, Ruminococcus torques (degradation of resistant starch) were lower in abundance in UC. The gut microbiota composition of urbanized population was more similar to UC as they have lower abundance of Firmicutes, Faecalibacterium prausnitzii and Oscillibacter sp 57_20. The lower prevalence of Ruminococcus torques, a keystone taxa in UC urban participants, indicates the loss of physiological functions. The UC patients exhibited a dysbiotic virobiota, characterized by increase in viral abundance, particularly from the genera enterovirus (observed in enteric gut infections), lentivirus (observed in chronic gut diseases), and Betacoronavirus. In UC patients, meta-gut resistome was found to be dominated by antimicrobial resistant genes (ARGs) compared to healthy. The metagenome study revealed a higher prevalence of ARG genes in the rural population (378 in Healthy; 607 in UC) compared to the urban (340 in Healthy; 578 in UC). The maximum number of observed ARGs corresponds to E. coli corroborates with the presence of a higher number of E. coli bacteriophages. Bacteriophages were reported as the important contributor for the dissemination of ARGs. Conclusion Our findings suggest inevitable evidence that specific alterations of microbes residing in the gut are associated with the lifestyle changes; therefore, can be used for screening the UC cases. The pro-inflammatory nature of microorganisms may contribute to UC severity in the intestinal tract. The observed rural and urban differences are unlikely an artifact of the difference between their lifestyles; urbanization is actively transforming the gut microbiota of local communities at the expense of loss and decline of microbes associated with traditional lifestyles.

The antibacterial activity of a prophage-encoded fitness factor is neutralized by two cognate immunity proteins

The human gastrointestinal tract is a competitive environment inhabited by dense polymicrobial communities. Bacteroides, a genus of Gram-negative anaerobes, are prominent members of this ecological niche. Bacteroides spp. uses a repertoire of mechanisms to compete for resources within this environment such as the delivery of proteinaceous toxins into neighbouring competitor bacteria and the ability to consume unique metabolites available in the gut. In recent work, Bacteroides stercoris gut colonization was linked to the activity of a prophage-encoded ADP-ribosyltransferase, which was found to stimulate the release of the metabolite inosine from host epithelial cells. This fitness factor, termed Bxa, shares a similar genomic arrangement to bacterial toxins encoded within interbacterial antagonism loci. Here, we report that Bxa also possesses antibacterial ADP-ribosyltransferase activity, raising the question of how Bxa-producing bacteria resist intoxication prior to Bxa's release from cells. To this end, we identify two cognate immunity proteins, Bsi and BAH, that neutralize Bxa's antibacterial activity using distinct mechanisms. BAH acts as an enzymatic immunity protein that reverses Bxa ADP-ribosylation whereas Bsi physically interacts with Bxa and blocks its ADP-ribosylation activity. We also find that the N-terminal domain of Bxa is dispensable for toxicity and homologous domains in other bacteria are fused to a diverse array of predicted toxins found throughout the Bacteroidaceae, suggesting that Bxa belongs to a broader prophage encoded polymorphic toxin system. Overall, this work shows that Bxa is a promiscuous ADP-ribosyltransferase and that B.stercoris possesses mechanisms to protect itself from the toxic activity of this prophage encoded fitness factor.

How Bacteria Establish and Maintain Outer Membrane Lipid Asymmetry.

Gram-negative bacteria build an asymmetric outer membrane (OM), with lipopolysaccharides (LPS) and phospholipids (PLs) occupying the outer and inner leaflets, respectively. This distinct lipid arrangement is widely conserved within the Bacteria domain and confers strong protection against physical and chemical insults. The OM is physically separated from the inner membrane and the cytoplasm, where most cellular resources are located; therefore, the cell faces unique challenges in the assembly and maintenance of this asymmetric bilayer. Here, we present a framework for how gram-negative bacteria initially establish and continuously maintain OM lipid asymmetry, discussing the state-of-the-art knowledge of specialized lipid transport machines that place LPS and PLs directly into their corresponding leaflets in the OM, prevent excess PL accumulation and mislocalization, and correct any lipid asymmetry defects. We critically assess current studies, or the lack thereof, and highlight important future directions for research on OM lipid transport, homeostasis, and asymmetry.

Origin of the Difference in Proton Transport Direction between Inward and Outward Proton-Pumping Rhodopsins.

ConspectusActive transport is a vital and ubiquitous process in biological phenomena. Ion-pumping rhodopsins are light-driven active ion transporters that share a heptahelical transmembrane structural scaffold in which the all-trans retinal chromophore is covalently bonded through a Schiff base to a conserved lysine residue in the seventh transmembrane helix. Bacteriorhodopsin from Halobacterium salinarum was the first ion-pumping rhodopsin to be discovered and was identified as an outward proton-pumping rhodopsin. Since the discovery of bacteriorhodopsin in 1971, many more ion-pumping rhodopsins have been isolated from diverse microorganisms spanning three domains (bacteria, archaea, and eukaryotes) and giant viruses. In addition to proton-pumping rhodopsins, chloride ion- and sodium ion-pumping rhodopsins have also been discovered. Furthermore, diversity of ion-pumping rhodopsins was found in the direction of ion transport; i.e., rhodopsins that pump protons inward have recently been discovered. Very intriguingly, the inward proton-pumping rhodopsins share structural features and many conserved key residues with the outward proton-pumping rhodopsins. However, a central question remains unchanged despite the increasing variety: how and why do the ion-pumping rhodopsins undergo interlocking conformational changes that allow unidirectional ion transfer within proteins? In this regard, it is an effective strategy to compare the structures and their evolutions in the proton-pumping processes of both inward and outward proton-pumping rhodopsins because the comparison sheds light on key elements for the unidirectional proton transport. We elucidated the proton-pumping mechanism of the inward and outward proton-pumping rhodopsins by time-resolved resonance Raman spectroscopy, a powerful technique for tracking the structural evolutions of proteins at work that are otherwise inaccessible.In this Account, we primarily review our endeavors in the elucidation of the proton-pumping mechanisms and determination factors for the transport directions of inward and outward proton-pumping rhodopsins. We begin with a brief summary of previous findings on outward proton-pumping rhodopsins revealed by vibrational spectroscopy. Next, we provide insights into the mechanism of inward proton-pumping rhodopsins, schizorhodopsins, obtained in our studies. Time-resolved resonance Raman spectroscopy provided valuable information about the structures of the retinal chromophore in the unphotolyzed state and intermediates of schizorhodopsins. As we ventured further into our investigations, we succeeded in uncovering the factors determining the directions of proton release and uptake in the retinal Schiff base. While it is intriguing that the proton-pumping rhodopsins actively transport protons against a concentration gradient, it is even more curious that proteins with structural similarities transport protons in opposite directions. Solving the second mystery led to solving the first. When we considered our findings, we realized that we would probably not have been able to elucidate the mechanism if we had studied only the outward pump. Our Account concludes by outlining future opportunities and challenges in the growing research field of ion-pumping rhodopsins, with a particular emphasis on elucidating their sequence-structure-function relationships. We aim to inspire further advances toward the understanding and creation of light-driven active ion transporters.

Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures.

Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp-Hcr) that catalyzes the conversion of NO2- to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp-Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰-49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3- and NO2- into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking.

Discovery and synthesis of leaderless bacteriocins from the Actinomycetota.

Leaderless bacteriocins are a unique class of bacteriocins that possess antimicrobial activity after translation and have few cases of documented resistance. Aureocin A53 and lacticin Q are considered two of the most well-studied leaderless bacteriocins. Here, we used in silico genome mining to search for novel aureocin A53-like leaderless bacteriocins in GenBank and MGnify. We identified 757 core peptides across 430 genomes with 75 species found currently without characterized leaderless bacteriocin production. These include putative novel species containing bacteriocin gene clusters (BGCs) from the genera Streptomyces (sp. NBC_00237) and Agrococcus (sp. SL85). To date, all characterized leaderless bacteriocins have been found within the phylum Bacillota, but this study identified 97 core peptides within the phylum Actinomycetota. Members of this phylum are traditionally associated with the production of antibiotics, such is the case with the genus Streptomyces. Actinomycetota is an underexplored phylum in terms of bacteriocin production with no characterized leaderless bacteriocin production to date. The two novel leaderless bacteriocins arcanocin and arachnicin from Actinomycetota members Arcanobacterium sp. and Arachnia sp., respectively, were chemically synthesized and antimicrobial activity was verified. These peptides were encoded in human gut (PRJNA485056) and oral (PRJEB43277) microbiomes, respectively. This research highlights the biosynthetic potential of Actinomycetota in terms of leaderless bacteriocin production and describes the first antimicrobial peptides encoded in the genera Arcanobacterium and Arachnia.IMPORTANCEBacteriocins are gathering attention as alternatives to current antibiotics given the increasing incidence of antimicrobial resistance. Leaderless bacteriocins are considered a commercially attractive subclass of bacteriocins due to the ability to synthesize active peptide and low levels of documented resistance. Therefore, in this work, we mined publicly available data to determine how widespread and diverse leaderless bacteriocins are within the domain of bacteria. Actinomycetota, known for its antibiotic producers but lacking described and characterized bacteriocins, proved to be a rich source of leaderless bacteriocins-97 in total. Two such peptides, arcanocin and arachnicin, were chemically synthesized and have antimicrobial activity. These bacteriocins may provide a novel source of novel antimicrobials that could aid in the development of future alternative antimicrobials and highlight that the Actinomycetota are an underexplored resource of bacteriocin peptides.

The rootstock genotype shapes the diversity of pecan (Carya illinoinensis) rhizosphere microbial community.

Pecans (Carya illinoinensis), one of the most valuable native North American nut crops, are commonly propagated through grafting to preserve the desired characteristics from parent trees. Since successful cultivation of pecan trees relies on the interplay among scion varieties, rootstocks, and soil conditions, this study investigated the microbial change to communities in the soils and roots of southern (87MX5-1.7) and northern (Peruque) rootstocks in a rootstock test orchard. Both grafted with the 'Pawnee' scion cultivar. Bacterial 16S ribosomal RNA and fungal ITS were amplified from both roots and rhizosphere soils of the two 10-year-grafted trees, then sequenced and annotated into trophic and nutrient-related groups to characterize the rhizosphere microbiota. The Peruque roots had a higher relative abundance of saprotroph fungi, while 87MX5-1.7 exhibited higher levels of symbiotroph fungi and nitrogen fixation-related bacteria. Among them, the presence of symbiotroph fungi, particularly ectomycorrhizal fungi, notably differed between these two rootstocks, with a significantly higher presence observed in the root of 87MX5-1.7 compared to Peruque. This variation likely leads to divergent pathways of nutrient translocation: Peruque was in favor of multiple fungi (Russula and Inocybe) to gain nutrition, while 87MX5-1.7 preferred a specific domain of fungi (Tuber) and nitrogen fixation-related bacteria (Bradyrhizobia) to form beneficial symbiosis. Moreover, the presence of pathogens suggested a potential risk of Fusarium patch and snow molds in 87MX5-1.7, while canker and black foot disease pose threats in Peruque. The findings of this study suggest that rootstocks from different origins shape rhizosphere microbes differently, potentially affecting nutrient uptake and nut yield. Exploring rootstock-microbe combinations could provide insights into optimizing scion growth and ultimately increasing nut yield. By understanding how different rootstock-microbe interactions influence pecan tree development, growers can strategically select combinations that promote beneficial symbiotic relationships, enhancing nutrient uptake, disease resistance, and overall tree vigor.

Gradient of acid mine drainage regulates microbial community assembly and the diversity of species associated with native plants

Acid mine drainage (AMD) is considered as one of the most important global environmental challenges. Therefore, understanding the impact of AMD on the diversity of microbial communities associated with native plants is important for phytoremediation. In this study, the community assembly and microbial diversity associated with native plants growing along an AMD impact gradient was investigated using metabarcoding and high throughput iChip technique. The study revealed that across both domains of bacteria and fungi, richness and species diversity decreased according to AMD impact. Bacterial species diversity was more stratified according to the pH gradient than fungi, and the AMD impact on the plant-associated microbial diversity decreased towards the plant roots. The microbial community composition of the undisturbed site was significantly different from the AMD impacted sites, and the communities in the AMD impacted sites were further stratified according to the degree of impact. The overall microbial diversity was mediated by the AMD impact, niche differences and plant species differences. Dispersal limitation was the most important community assembly process in the undisturbed site, while the homogenous selection of Burkholderia, Actinospica, Puia and Bradyrhizobium increased along the AMD impact gradient. Differential abundance analysis further revealed that Umbelopsis, Burkholderia and Sphingomonas were among the biomarkers of the AMD impacted sites. Several strains of some of these responsive genera were subsequently isolated using the iChip. Overall, this study presents novel insight into the ecology of plant-associated microbial communities that are relevant for environmental monitoring and for enhancing the revegetation of AMD impacted sites.

Revisiting biochemical pathways for lead and cadmium tolerance by domain bacteria, eukarya, and their joint action in bioremediation.

With the advent rise is in urbanization and industrialization, heavy metals (HMs) such as lead (Pb) and cadmium (Cd) contamination have increased considerably. It is among the most recalcitrant pollutants majorly affecting the biotic and abiotic components of the ecosystem like human well-being, animals, soil health, crop productivity, and diversity of prokaryotes (bacteria) and eukaryotes (plants, fungi, and algae). At higher concentrations, these metals are toxic for their growth and pose a significant environmental threat, necessitating innovative and sustainable remediation strategies. Bacteria exhibit diverse mechanisms to cope with HM exposure, including biosorption, chelation, and efflux mechanism, while fungi contribute through mycorrhizal associations and hyphal networks. Algae, especially microalgae, demonstrate effective biosorption and bioaccumulation capacities. Plants, as phytoremediators, hyperaccumulate metals, providing a nature-based approach for soil reclamation. Integration of these biological agents in combination presents opportunities for enhanced remediation efficiency. This comprehensive review aims to provide insights into joint action of prokaryotic and eukaryotic interactions in the management of HM stress in the environment.

Crystal structure of guanosine 5'-monophosphate synthetase from the thermophilic bacterium Thermus thermophilus HB8.

Guanosine 5'-monophosphate (GMP) synthetase (GuaA) catalyzes the last step of GMP synthesis in the purine nucleotide biosynthetic pathway. This enzyme catalyzes a reaction in which xanthine 5'-monophosphate (XMP) is converted to GMP in the presence of Gln and ATP through an adenyl-XMP intermediate. A structure of an XMP-bound form of GuaA from the domain Bacteria has not yet been determined. In this study, the crystal structure of an XMP-bound form of GuaA from the thermophilic bacterium Thermus thermophilus HB8 (TtGuaA) was determined at a resolution of 2.20 Å and that of an apo form of TtGuaA wasdetermined at 2.10 Å resolution. TtGuaA forms a homodimer, and the monomer is composed of three domains, which is a typical structure for GuaA. Disordered regions in the crystal structure were obtained from the AlphaFold2-predicted model structure, and a model with substrates (Gln, XMP and ATP) was constructed for molecular-dynamics (MD) simulations. The structural fluctuations of the TtGuaA dimer as well as the interactions between the active-site residues were analyzed by MD simulations.

Tip extension and simultaneous multiple fission in a filamentous bacterium

Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such community-the human dental plaque biofilm-a network of filamentous Corynebacterium matruchotii cells forms the core of bacterial consortia known as hedgehogs, but the processes that generate these structures are unclear. Here, using live-cell time-lapse microscopy and fluorescent D-amino acids to track peptidoglycan biosynthesis, we report an extraordinary example of simultaneous multiple division within the domain Bacteria. We show that C. matruchotii cells elongate at one pole through tip extension, similar to the growth strategy of soil-dwelling Streptomyces bacteria. Filaments elongate rapidly, at rates more than five times greater than other closely related bacterial species. Following elongation, many septa form simultaneously, and each cell divides into 3 to 14 daughter cells, depending on the length of the mother filament. The daughter cells then nucleate outgrowth of new thinner vegetative filaments, generating the classic "whip handle" morphology of this taxon. Our results expand the known diversity of bacterial cell cycles and help explain how this filamentous bacterium can compete for space, access nutrients, and form important interspecies interactions within dental plaque.

Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest

The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.

Unraveling the spatio-temporal dynamics of soil and root-associated microbiomes in Texas olive orchards

Understanding the structure and diversity of microbiomes is critical to establishing olives in non-traditional production areas. Limited studies have investigated soil and root-associated microbiota dynamics in olives across seasons or locations in the United States. We explored the composition and spatiotemporal patterns of the olive-associated microbial communities and specificity in two niches (rhizosphere and root endosphere), seasons (spring, summer, and fall), and domains (bacteria and fungi) in the microbiome of the olive cultivar Arbequina across three olive orchards in Texas. Phylum Proteobacteria, followed by Actinobacteriota, dominated the bacterial populations in the rhizosphere and endosphere. Rubrobacter and Actinophytocola were dominant taxa in the rhizosphere and root endosphere at the genus level. Among fungal communities, phylum Ascomycota was prevalent in the rhizosphere and endosphere, while members of the Chaetomiaceae family outnumbered other taxa in the root endosphere. As per the alpha diversity indices, the rhizosphere at Moulton showed much higher richness and diversity than other places, which predicted a significant difference in rhizosphere between locations for bacterial diversity and richness. There was no significant variation in the bacterial diversity in the niches and the fungal diversity within the root endosphere between locations. Beta diversity analysis confirmed the effect of compartments—in influencing community differences. Microbial diversity was apparent within the endosphere and rhizosphere. The seasons influenced only the rhizosphere fungal diversity, contrasting the bacterial diversity in either niche. The research provided a comprehensive overview of the microbial diversity in olive trees' rhizosphere and root endosphere. The abundance and composition of OTUs associated with the rhizosphere soil of Arbequina suggest its role as a source reservoir in defining the potential endophytes.

Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota.

The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium, Candidatus Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production via the archaeal mevalonate pathway reconstituted in Escherichia coli cells, whereas that of phosphomevalonate dehydratase was confirmed by an in vitro assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in Candidatus P. breve, which probably involves horizontal gene transfer events.IMPORTANCEThe recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do.

Potential of artificial soil preparation for vegetation restoration using red mud and phosphogypsum

Red mud and phosphogypsum have long been a focus and challenge in global industrial waste management, and their low-cost and large-scale utilization technology has always been an urgent need. This study is based on the strong acid-base neutralization reaction between red mud and phosphogypsum, which contain an elemental composition similar to that of natural soil, red mud itself has characteristic of clay minerals, and other auxiliary materials (i.e. rice husk powder, bentonite, fly ash, polyacrylamide flocculant and microbial suspension) were added, so as to explore the potential of synergistically prepared artificial soil for vegetation restoration. The results showed that the artificial soils exhibited physicochemical characteristics (e.g., pH, moisture content, cation exchange capacity) similar to those of natural soil, along with abundant organic matter, nitrogen, phosphorus, and potassium contents, meeting the growth requirements of plants. The artificial soils were able to support favorable growth of suitable plants (e.g., sunflower, wheat, rye grass), accumulating high levels of diverse enzymatic activities, comparable to those in natural soils (e.g., catalase, urease, phosphatase), or even surpassing natural soils (e.g., sucrase), and rich microorganism communities, such as Cyanobacteria, Proteobacteria, Actinobacteria in the bacteria domain, and Ascomycota in the fungi domain, were initially developed. It's suggested that preparing 1 ton of artificial soil entails synergistic consumption of 613.7 kg of red mud and 244.6 kg of phosphogypsum, accounting for mass proportions of 61.4 % and 24.5 %, respectively. In future, more evaluations on the leaching loss of nutrients and alkalinity and the environmental risks of heavy metals should be conducted to more references for the artificial soil application. In summary, the preparation of artificial soil is a very simple, efficient, scalable and low-cost collaborative resource utilization scheme of red mud and phosphogypsum, which has great potential for vegetation restoration in some places such as tailings field and soil-deficient depression.

Unlocking potential: Exploring the methane production potential in anaerobic co-digestion of cassava wastewater and glycerol

This study aimed at evaluating the feasibility of CH4 production in a mesophilic (30 °C) single-stage anaerobic co-digestion of cassava wastewater (CW) and glycerol in an anaerobic fluidized bed reactor (AFBR) with mixing ratio of 50 % / 50 % CW/Gly on a (chemical oxygen demand)COD basis. Thus, the following strategy was used: increasing the organic loading rate (OLR) (1–20 g COD.L−1.d−1) by increasing the substrate concentration (1–20 g COD.L−1) and applying a hydraulic detention time (HRT) of 24 h. The AFBR presented a maximum methane (CH4) content of 88.38±1.94 % and a CH4 yield (MY) of 293.48±18.37 mL of CH4.mL−1CODrem in the OLR of 1 g COD.L−1.d−1 and the maximum methane production rate (MPR) of 62.09±2.75 mL of CH4.L−1.h−1 in the OLR of 20 g COD.L−1.d−1. The conversion of glycerol and carbohydrates remained above 91±0.54 % and 82±2.79 %, respectively, and the COD conversion was above 80±0.65 %. The main metabolites were HAc, HPr, HBu, EtOH and HVa. The most abundant genera identified in the AFBR were Izemoplasmatales and Enterobacteriaceae for the bacteria domain, and Methanosaeta, Methanobacterium for the archaea domain. The single-stage system is robust and can operate with higher OLR without reducing the efficiency of wastewater treatment and CH4 production.

Metagenomic Analyses Reveal Gut Microbial Profiles of Cnaphalocrocis medinalis Driven by the Infection of Baculovirus CnmeGV.

The composition of microbiota in the digestive tract gut is essential for insect physiology, homeostasis, and pathogen infection. Little is known about the interactions between microbiota load and oral infection with baculoviruses. CnmeGV is an obligative baculovirus to Cnaphalocrocis medinalis. We investigated the impact of CnmeGV infection on the structure of intestinal microbes of C. medinalis during the initial infection stage. The results revealed that the gut microbiota profiles were dynamically driven by pathogen infection of CnmeGV. The numbers of all the OTU counts were relatively higher at the early and later stages, while the microbial diversity significantly increased early but dropped sharply following the infection. The compositional abundance of domain bacteria Firmicutes developed substantially higher. The significantly enriched and depleted species can be divided into four groups at the species level. Fifteen of these species were ultimately predicted as the biomarkers of CnmeGV infection. CnmeGV infection induces significant enrichment of alterations in functional genes related to metabolism and the immune system, encompassing processes such as carbohydrate, amino acid, cofactor, and vitamin metabolism. Finally, the study may provide an in-depth analysis of the relationship between host microbiota, baculovirus infection, and pest control of C. medinalis.

Functional diversity of YbbN/CnoX proteins: Insights from a comparative analysis of three thioredoxin-like oxidoreductases from Pseudomonas aeruginosa, Xylella fastidiosa and Escherichia coli

YbbN/CnoX are proteins that display a Thioredoxin (Trx) domain linked to a tetratricopeptide domain. YbbN from Escherichia coli (EcYbbN) displays a co-chaperone (holdase) activity that is induced by HOCl. Here, we compared EcYbbN with YbbN proteins from Xylella fastidiosa (XfYbbN) and from Pseudomonas aeruginosa (PaYbbN). EcYbbN presents a redox active Cys residue at Trx domain (Cys63), 24 residues away from SQHC motif (SQHC[N24]C) that can form mixed disulfides with target proteins. In contrast, XfYbbN and PaYbbN present two Cys residues in the CXXC (CAPC) motif, while only PaYbbN shows the Cys residue equivalent to Cys63 of EcYbbN. Our phylogenetic analysis revealed that most of the YbbN proteins are in the bacteria domain of life and that their members can be divided into four groups according to the conserved Cys residues. EcYbbN (SQHC[N24]C), XfYbbN (CAPC[N24]V) and PaYbbN (CAPC[N24]C) are representatives of three sub-families. In contrast to EcYbbN, both XfYbbN and PaYbbN: (1) reduced an artificial disulfide (DTNB) and (2) supported the peroxidase activity of Peroxiredoxin Q from X. fastidiosa, suggesting that these proteins might function similarly to the canonical Trx enzymes. Indeed, XfYbbN was reduced by XfTrx reductase with a high catalytic efficiency (kcat/Km = 1.27 x 107 M−1 s−1), similar to the canonical XfTrx (XfTsnC). Furthermore, EcYbbN and XfYbbN, but not PaYbbN displayed HOCl-induced holdase activity. Remarkably, EcYbbN gained disulfide reductase activity while lost the HOCl-activated chaperone function, when the SQHC was replaced by CQHC. In contrast, the XfYbbN CAPA mutant lost the disulfide reductase activity, while kept its HOCl-induced chaperone function. In all cases, the induction of the holdase activity was accompanied by YbbN oligomerization. Finally, we showed that deletion of ybbN gene did not render in P. aeruginosa more sensitive stressful treatments. Therefore, YbbN/CnoX proteins display distinct properties, depending on the presence of the three conserved Cys residues.

Novel sterol binding domains in bacteria.

Sterol lipids are widely present in eukaryotes and play essential roles in signaling and modulating membrane fluidity. Although rare, some bacteria also produce sterols, but their function in bacteria is not known. Moreover, many more species, including pathogens and commensal microbes, acquire or modify sterols from eukaryotic hosts through poorly understood molecular mechanisms. The aerobic methanotroph Methylococcus capsulatus was the first bacterium shown to synthesize sterols, producing a mixture of C-4 methylated sterols that are distinct from those observed in eukaryotes. C-4 methylated sterols are synthesized in the cytosol and localized to the outer membrane, suggesting that a bacterial sterol transport machinery exists. Until now, the identity of such machinery remained a mystery. In this study, we identified three novel proteins that may be the first examples of transporters for bacterial sterol lipids. The proteins, which all belong to well-studied families of bacterial metabolite transporters, are predicted to reside in the inner membrane, periplasm, and outer membrane of M. capsulatus, and may work as a conduit to move modified sterols to the outer membrane. Quantitative analysis of ligand binding revealed their remarkable specificity for 4-methylsterols, and crystallographic structures coupled with docking and molecular dynamics simulations revealed the structural bases for substrate binding by two of the putative transporters. Their striking structural divergence from eukaryotic sterol transporters signals that they form a distinct sterol transport system within the bacterial domain. Finally, bioinformatics revealed the widespread presence of similar transporters in bacterial genomes, including in some pathogens that use host sterol lipids to construct their cell envelopes. The unique folds of these bacterial sterol binding proteins should now guide the discovery of other proteins that handle this essential metabolite.