Survivability of Microbes in Natural Environments and Their Ecological Impacts

Devitalization of Bacteria in Composted Cattle Manure with Natural Additives and Risk for Environment

Nowadays, there is an effort to improve the effectiveness of the composting process, supported by the addition of various supplements to reduce soil nutrition losses and increase soil remediation. The aim of this study was to examine the devitalization effect of natural additives like zeolite-clinoptilolite and its combination with hydrated lime in composted cattle manure on indicator and pathogen bacteria. The composting process was running in three static piles of cattle manure mixed with wheat straw (control, zeolite-lime, and zeolite) for 126 days. Composted manure substrates were determined for physicochemical (temperature, pH, nitrogen and phosphorus content, C/N, organic matter, and moisture) and microbiological analyses (Salmonella spp., indicator bacteria). The effects of additives were reflected in changes in physicochemical factors, e.g., an increase in temperature (<53 °C) or pH (<9.3). According to Pearson correlation, these changes (pH, Nt, Pt) resulted in a significant decrease (p < 0.001) of indicator bacteria (two or three orders) in zeolite pile or zeolite-lime pile. Die-off of Salmonella spp. in the zeolite-lime pile was indicated within 41 days; in other piles, this occurred on day 63. Our results can aid in further optimizing the composting of cattle manure in order to lower environmental pollution and the risk of human infection.

Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov

A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HST, exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HST is most closely related to Virgibacillus halophilus 5B73CT, sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HST is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HST = DSM 115946T = NRRL B-65666T), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73CT = DSM 21623T = JCM 21758T = KCTC 13935T). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6T = DSM 22952T = CCM 7714T). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins.

IMPORTANCE

The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.

Where bacteria and eukaryotes meet

The international workshop "Interdisciplinary life of microbes: from single cells to multicellular aggregates," following a virtual preassembly in November 2021, was held in person in Dresden, from 9 to 13 November 2022. It attracted not only prominent experts in biofilm research but also researchers from broadly neighboring disciplines, such as medicine, chemistry, and theoretical and experimental biophysics, both eukaryotic and prokaryotic. Focused brainstorming sessions were the special feature of the event and are at the heart of this commentary.

Environmental processes and health implications potentially mediated by dust-borne bacteria

Understanding microbial migration and survival mechanisms in dust events (DEs) can elucidate genetic and metabolic exchange between environments and help predict the atmospheric pathways of ecological and health-related microbial stressors. Dust-borne microbial communities have been previously characterized, but the impact and interactions between potentially active bacteria within transported communities remain limited. Here, we analysed samples collected during DEs in Israel, using amplicon sequencing of the 16S rRNA genes and transcripts. Different air trajectories and wind speeds were associated not only with the genomic microbial community composition variations but also with specific 16S rRNA bacterial transcripts. Potentially active dust-borne bacteria exhibited positive interactions, including carbon and nitrogen cycling, biotransformation of heavy metals, degradation of organic compounds, biofilm formation, and the presence of pathogenic taxa. This study provides insights into the potential interactive relationships and survival strategies of microorganisms within the extreme dust environment.

Sustainable permeable biobarriers for atrazine removal in packed bed biofilm reactors

The synergy between two supported bacterial biofilms of S. equisimilis and P. putida and a sustainable biocarrier (raw pine) was studied, working both as biobarriers for the treatment of water contaminated with atrazine. Firstly, the effects of ATZ exposure on bacterial growth were evaluated, with Gram-positive S. equisimilis being a more tolerant bacterium to higher amounts of the herbicide. The bioremoval of ATZ by S. equisimilis concentrated biomass was then assessed, reaching around 83.5% after 15 days due to the potential degradation by the biomass and biosorption by the solids, with overlapping of both mechanisms. The optimization of bacterial biofilm attachment onto raw pine prior to bioremoval assays in lab-scale packed bed biofilm reactors was performed by varying initial biomass concentration, inocula growth time and hydrodynamic conditions. Lastly, the optimized biosystems were tested as sustainable remediation designs to treat water contaminated with the selected herbicide. Results reveal an added beneficial effect towards the bioremoval of atrazine using supported biofilms onto raw pine, reaching 90.42% and 79.71% by S. equisimilis and P. putida biofilms, respectively, over 58.31% increase when compared to sorption on fixed bed of pine. The coupling of biosorption/biodegradation favors the bioremoval process significantly.

Microbes within the building envelope-a case study on the patterns of colonization and potential sampling bias

Humans are exposed to diverse communities of microbes every day. With more time spent indoors by humans, investigations into the communities of microbes inhabiting occupied spaces have become important to deduce the impacts of these microbes on human health and building health. Studies so far have given considerable insight into the communities of the indoor microbiota humans interact with, but mainly focus on sampling surfaces or indoor dust from filters. Beneath the surfaces though, building envelopes have the potential to contain environments that would support the growth of microbial communities. But due to design choices and distance from ground moisture, for example, the temperature and humidity across a building will vary and cause environmental gradients. These microenvironments could then influence the composition of the microbial communities within the walls. Here we present a case study designed to quantify any patterns in the compositions of fungal and bacterial communities existing in a building envelope and determine some of the key variables, such as cardinal direction, distance from floor or distance from wall joinings, that may influence any microbial community composition variation. By drilling small holes across walls of a house, we extracted microbes onto air filters and conducted amplicon sequencing. We found sampling height (distance from the floor) and cardinal direction the wall was facing caused differences in the diversity of the microbial communities, showing that patterns in the microbial composition will be dependent on sampling location within the building. By sampling beneath the surfaces, our approach provides a more complete picture of the microbial condition of a building environment, with the significant variation in community composition demonstrating a potential sampling bias if multiple sampling locations across a building are not considered. By identifying features of the built environment that promote/retard microbial growth, improvements to building designs can be made to achieve overall healthier occupied spaces.

Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals

Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.

Responses of compositions, functions, and assembly processes of bacterial and microeukaryotic communities to long-range voyages in simulated ballast water

Ballast water is one of the main vectors for the spread of harmful organisms among geologically isolated waters. However, the successional processes of microbial functions and assembly processes in ballast water during the long-term shipping voyage remain unclear. In this study, the compositions, ecological functions, community assembly, and potential environmental drivers of bacteria and microeukaryotes were investigated in simulated ballast water microcosms for 120 days. The results showed that the diversity and compositions of the bacterial and microeukaryotic communities varied significantly in the initial 40 days (T0∼T40 samples) and then gradually converged. The relative abundance of Proteobacteria showed a distinct tendency to decrease (87.90%-41.44%), while that of Ascomycota exhibited an increasing trend (6.35%-62.12%). The functional groups also varied significantly over time and could be related to the variations of the microbial community. The chemoheterotrophy and aerobic chemoheterotrophy functional groups for bacteria decreased from 44.80% to 28.02% and from 43.77% to 25.39%, respectively. Additionally, co-occurrence network analysis showed that the structures of the bacterial community in T60∼T120 samples were more stable than those in T0∼T40 samples. Stochastic processes also significantly affected the community assembly of bacteria and microeukaryotes. pH played the most significant role in driving the structures and assembly processes of the bacterial and microeukaryotic communities. The results of this study could aid in the understanding of variations in the functions and ecological processes of bacterial and microeukaryotic communities in ballast water over time and provide a theoretical basis for its management.

Microbial Interaction is Among the Key Factors for Isolation of Previous Uncultured Microbes

Pure cultivation of microbes is still limited by the challenges of microbial uncultivability, with most microbial strains unable to be cultivated under standard laboratory conditions. The experience accumulated from advanced techniques such as in situ cultivation has identified that microbial interactions exist in natural habitats but are absent in laboratory cultures. These microbial interactions are likely one of the key factors in isolating previously uncultured microbes. The need for better knowledge of the mechanisms operating in microbial interactions has led to various experiments that have utilized microbial interactions in different approaches to microbial cultivation. These new attempts to understand microbial interactions not only present a new perspective on microbial uncultivability but also provide an opportunity to access uncultured phylogenetically novel microbes with their potential biotechnology applications. In this review, we focus on studies of the mechanisms of microbial interaction where the growth of other microbes is affected. Additionally, we review some successful applications of microbial interactions in cultivation methods, an approach that can play an important role in the bioprospecting of untapped microbial resources.

Sustainable production and pharmaceutical applications of β-glucan from microbial sources

β-glucans are a large class of complex polysaccharides found in abundant sources. Our dietary sources of β-glucans are cereals that include oats and barley, and non-cereal sources can consist of mushrooms, microalgae, bacteria, and seaweeds. There is substantial clinical interest in β-glucans; as they can be used for a variety of diseases including cancer and cardiovascular conditions. Suitable sources of β-glucans for biopharmaceutical applications include bacteria, microalgae, mycelium, and yeast. Environmental factors including culture medium can influence the biomass and ultimately β-glucan content. Therefore, cultivation conditions for the above organisms can be controlled for sustainable enhanced production of β-glucans. This review discusses the various sources of β-glucans and their cultivation conditions that may be optimised to exploit sustainable production. Finally, this article discusses the immune-modulatory potential of β-glucans from these sources.

Humic Acid-Amended Formulation Improves Shelf-Life of Plant Growth-Promoting Rhizobacteria (PGPR) Under Laboratory Conditions

Plant growth-promoting rhizobacteria (PGPR) is a soil bacterium that positively impacts soil and crops. These microbes invade plant roots, promote plant growth, and improve crop yield production. Bacillus subtilis is a type of PGPR with a short shelf-life due to its structural and cellular components, with a non-producing resistance structure (spores). Therefore, optimum formulations must be developed to prolong the bacterial shelf-life by adding humic acid (HA) as an amendment that could benefit the microbes by providing shelter and carbon sources for bacteria. Thus, a study was undertaken to develop a biofertilizer formulation from locally isolated PGPR, using HA as an amendment. Four doses of HA (0, 0.01, 0.05, and 0.1%) were added to tryptic soy broth (TSB) media and inoculated with B. subtilis (UPMB10), Bacillus tequilensis (UPMRB9) and the combination of both strains. The shelf-life was recorded, and viable cells count and optical density were used to determine the bacterial population and growth trend at monthly intervals and endospores detection using the malachite green staining method. After 12 months of incubation, TSB amended with 0.1% HA recorded the highest bacterial population significantly with inoculation of UPMRB9, followed by mixed strains and UPMB10 at 1.8x107 CFUmL-1, 2.8x107 CFUmL-1and 8.9x106 CFUmL-1, respectively. Results showed that a higher concentration of HA has successfully prolonged the bacterial shelf-life with minimal cell loss. Thus, this study has shown that the optimum concentration of humic acid can extend the bacterial shelf-life and improve the quality of a biofertilizer.

Development of Decellularized Fish Skin Scaffold Decorated with Biosynthesized Silver Nanoparticles for Accelerated Burn Wound Healing

In this study, decellularized fish skin (DFS) scaffold decorated with silver nanoparticles was prepared for accelerating burn wound healing. The silver nanoparticles (AgNPs) synthesized by the green and facile method using Aloe vera leaf at different incubating times were characterized by using X-ray Diffraction (XRD), Fourier Transform Infrared (FT-IR) Spectroscopy, and Ultraviolet-Visible Spectroscopy (UV-Vis spectroscopy). The different characterizations confirmed that the sizes of AgNPs prepared by incubating for 6 hours and 12 hours were 29.1 nm and 35.2 nm, respectively. After that, the different concentrations of the smallest AgNPs were used to dope the DFS scaffold to determine the cell viability. Additionally, an agar well diffusion method was used to screen for antimicrobial activity. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were used to correlate the concentration of AgNPs with its bactericidal effect which was seen from 50 μg/ml. Then, the toxicity with human cells was investigated using a 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide (MTT) assay with no significant cell viability from the concentration of 50 μg/ml to 200 μg/ml compared to the cocultured and commercial treatments.

Comparative Genomics of Listeria Species Recovered from Meat and Food Processing Facilities

Listeria species (spp.) are contaminants that can survive in food, on equipment, and on food processing premises if appropriate hygiene measures are not used. Homologous stress tolerance genes, virulence gene clusters such as the prfA cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic Listeria spp. To enhance understanding of the genome evolution of virulence and virulence-associated properties, a comparative genome approach was used to analyze 41 genome sequences belonging to L. innocua and L. welshimeri isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette bcrABC and Tn6188_qac_1 disinfectant resistance determinant, and stress survival islets. These disinfectant-resistant genes were more frequently found in L. innocua (12%) than in L. welshimeri (2%). Several isolates representing the presumed nonpathogenic L. innocua still carried virulence-associated genes, including LGI2, LGI3, LIPI-3, and LIPI-4 which were absent in all L. welshimeri isolates. The mobile genetic elements identified were plasmids (pLGUG1 and J1776) and prophages (PHAGE_Lister_vB_LmoS_188, PHAGE_Lister_LP_030_3, PHAGE_Lister_A118, PHAGE_Lister_B054, and PHAGE_Lister_vB_LmoS_293). The results suggest that the presumed nonpathogenic isolates especially L. innocua can carry genes relevant to the strain's virulence and stress tolerance in the food and food processing facilities. IMPORTANCE This study provides genomic insights into the recently expanded genus in order to gain valuable information about the evolution of the virulence and stress tolerance properties of the genus Listeria and the distribution of these genetic elements pertinent to the pathogenic potential across Listeria spp. and clonal lineages in South Africa (SA).

Designing a Waste-Based Culture Medium for the Production of Plant Growth Promoting Microorganisms Based on Cladodes Juice from Opuntia ficus-indica Pruning

The production of beneficial microorganisms is the first step to obtain a commercial-based product for application in agriculture. In this study, prickly pear (Opuntia ficus-indica) pruning waste was evaluated as a raw material for the production of large amounts of Plant Growth Promoting Microorganisms (PGPMs) reducing the number of generated wastes. Specifically, five PGPMs constituting a synthetic microbial consortium with complementing plant growth-promoting traits were grown on a laboratory scale and, subsequently, on a pilot scale using a 21-L bioreactor. Primarily, the physical-chemical characterization of the culture medium obtained from the juice of Opuntia cladodes was carried out, revealing the presence of sugars and organic acids with different molar ratios. Compared to conventional media, the waste medium did not show significant differences in bacterial growth efficiency. Instead, the survival rates of the bacteria grown in cladodes juice media, after air-drying on zeolite or freeze-drying, were significantly higher than those observed when they were grown in conventional media. The present work is the first conducted on a pilot-scale that maximizes the production of PGPMs in submerged fermentation using cladodes juice from Opuntia, reducing both economic and environmental impacts associated with the generation of wastes.

Phenotypic traits of carbon source utilization in environmental Salmonella strains isolated from river water

Salmonella in the environment have evolved genetically to maintain a stable cell metabolism. Nevertheless, a lack of common nutrients (such as glucose) causes these strains to metabolize alternative carbon sources. In this study, 21 strains of Salmonella Oranienburg isolated from subtropical river water were evaluated to compare their adaptation and preconditioning abilities for the consumption of environmental carbon sources (ECS). The results obtained in this study attributed important biological characteristics to the adaptation of the metabolism of Salmonella strains to diverse ECS; these characteristics include but are not limited to variations in plasticity and natural preconditioning in closely related microorganisms, such as environmental isolates belonging to the serotype Oranienburg.

Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism

Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD⁺/NADH ratio, generate more ATP through substrate-level phosphorylation, and accumulate biomass more rapidly. This novel, hybrid metabolism is dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally requires a flavin-binding extracellular lipoprotein (PplA) under laboratory conditions. It confers increased fermentation product yield, metabolic flux, and environmental acidification in laboratory media and during kale juice fermentation. The discovery of a single pathway that simultaneously blends features of fermentation and respiration in a primarily fermentative microorganism expands our knowledge of energy conservation and provides immediate biotechnology applications.

Bacteria produce the energy they need to live through two processes, respiration and fermentation. While respiration is often more energetically efficient, many bacteria rely on fermentation as their sole means of energy production. Respiration normally depends on the presence of small soluble molecules, such as oxygen, that can diffuse inside the cell, but some bacteria can use metals or other insoluble compounds found outside the cell to perform ‘extracellular electron transfer’.

Lactic acid bacteria are a large group of bacteria that have several industrial uses and live in many natural environments. These bacteria survive using fermentation, but they also carry a group of genes needed for extracellular electron transfer. It is unclear whether they use these genes for respiration or if they have a different purpose.

Tejedor-Sanz, Stevens et al. used a lactic acid bacterium called Lactiplantibacillus plantarum to study whether and how this group of bacteria use extracellular electron transfer. Analysis of L. plantarum and its effect on its surroundings showed that these bacteria use a hybrid process to produce energy: the cells use aspects of extracellular respiration to increase the yield and efficiency of fermentation. Combining these two approaches may allow L. plantarum to adapt to different environments and grow faster, allowing it to compete against other species.

Tejedor-Sanz, Stevens et al. provide new information on a widespread group of bacteria that are often used in food production and industry. The next step will be to understand how the hybrid system is controlled and how it varies among species. Understanding this process could result in new biotechnologies and foods that are healthier, produce less waste, or have different tastes and textures.

Enterococcal biofilm - a nidus for antibiotic resistance transfer?

Enterococci, important agents of hospital acquired infection, are listed on the WHO list of multi-drug resistant pathogens commonly encountered in hospital acquired infections are now of increasing importance, due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment and their presence is frequently used as an indicator of faecal pollution. Their success is related to their ability to survive within a broad range of habitats and the ease by which they acquire mobile genetic elements, including plasmids, from other bacteria. The enterococci are frequently present within a bacterial biofilm which provides stability and protection to the bacterial population along with an opportunity for a variety of bacterial interactions. Enterococci can accept extrachromosomal DNA both from within its own species and from other bacterial species and this is enhanced by the proximity of the donor and recipient strains. It is this exchange of genetic material that makes the role of biofilm such an important aspect of the success of enterococci. There remain many questions regarding the most suitable model systems to study enterococci in biofilm and regarding the transfer of genetic material including antibiotic resistance in these biofilms. This review focuses on some important aspects of biofilm in the context of horizontal gene transfer (HGT) in enterococci.

Evaluating comparative β-glucan production aptitude of Saccharomyces cerevisiae, Aspergillus oryzae, Xanthomonas campestris, and Bacillus natto

β-glucan is a natural polysaccharide derivative composed of a group of glucose monomers with β-glycoside bonds that can be synthesized intra- or extra-cellular by various microorganisms such as yeasts, bacteria, and moulds. The study aimed to discover the potential of various microorganisms such as Saccharomyces cerevisiae, Aspergillus oryzae, Xanthomonas campestris, and Bacillus natto in producing β-glucan. The experimental method used and the data were analyzed descriptively. The four microorganisms above were cultured under a submerged state in Yeast glucose (YG) broth for 120 h at 30 °C with 200 rpm agitation. During the growth, several parameters were examined including total population by optical density, the pH, and glucose contents of growth media. β-glucan was extracted using acid-alkaline methods from the growth media then the weight was measured. The results showed that S. cerevisiae, A. oryzae X. campestris, and B. natto were prospective for β-glucans production in submerged fermentation up to 120 h. The highest β-glucans yield was shown by B. natto (20.38%) with the β-glucans mass of 1.345 ± 0.08 mg and globular diameter of 600 μm. The highest β-glucan mass was achieved by A. oryzae of 82.5 ± 0.03 mg with the total population in optical density of 0.1246, a final glucose level of 769 ppm, the pH of 6.67, and yield of 13.97% with a globular diameter of 1400 μm.

pH Stress Mediated Alteration in Protein Composition and Reduction in Cytotoxic Potential of Gardnerella vaginalis Membrane Vesicles

The vagina of healthy women is predominantly colonized by lactobacilli but it also harbors a limited proportion of certain anaerobes such as Gardnerella vaginalis. An increase in G. vaginalis along with other anaerobes on account of perturbation in the vaginal microbiota is associated with bacterial vaginosis (BV). Although strategies adopted by G. vaginalis for survival and pathogenesis in a conducive environment (i.e., high vaginal pH, characteristic of BV) have been previously studied, the approaches potentially employed for adaptation to the low pH of the healthy vagina are unknown. In the present study, we investigated the effect of acidic stress on the modulation of the production and function of membrane vesicles (MVs) of G. vaginalis. pH stress led to a distortion of the bacterial cell morphology as well as an altered biogenesis of MVs, as revealed by transmission electron microscopy (TEM). Both qualitative and quantitative differences in protein content of MVs produced in response to pH stress were observed by flow cytometry. A significant change in the protein composition characterized by presence of chaperones despite a reduction in number of proteins was also noted in the stress induced MVs. Further, these changes were also reflected in the reduced cytotoxic potential toward vaginal epithelial cells. Although, these findings need to be validated in the in vivo settings, the modulation of G. vaginalis MV biogenesis, composition and function appears to reflect the exposure to acidic conditions prevailing in the host vaginal mileu in the absence of vaginal infection.

Interrogation of Bacillus anthracis SrtA active site loop forming open/close lid conformations through extensive MD simulations for understanding binding selectivity of SrtA inhibitors

Bacillus anthracis is a gram positive, deadly spore forming bacteria causing anthrax and these bacteria having the complex mechanism in the cell wall envelope, which can adopt the changes in environmental conditions. In this, the membrane bound cell wall proteins are said to progressive drug target for the inhibition of Bacillus anthracis. Among the cell wall proteins, the SrtA is one of the important mechanistic protein, which mediate the ligation with LPXTG motif by forming the amide bonds. The SrtA plays the vital role in cell signalling, cell wall formation, and biofilm formations. Inhibition of SrtA leads to rupture of the cell wall and biofilm formation, and that leads to inhibition of Bacillus anthracis and thus, SrtA is core important enzyme to study the inhibition mechanism. In this study, we have examined 28 compounds, which have the inhibitory activity against the Bacillus anthracis SrtA for developing the 3D-QSAR and also, compounds binding selectivity with both open and closed SrtA conformations, obtained from 100 ns of MD simulations. The binding site loop deviate in forming the open and closed gate mechanism is investigated to understand the inhibitory profile of reported compounds, and results show the closed state active site conformations are required for ligand binding specificity. Overall, the present study may offer an opportunity for better understanding of the mechanism of action and can be aided to further designing of a novel and highly potent SrtA inhibitors.

Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways

Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.

A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study

Diabetic foot infections (DFIs) are a major cause of hospitalization and can lead to lower extremity amputation. In this pilot study, we used a multiomics approach to explore the host–microbe complex within DFIs. We observed minimal differences in the overall microbial composition between PEDIS infection severities, however Staphylococcus aureus and Streptococcus genera were abundant and highly active in most mild to moderate DFIs. Further, we identified the significant enrichment of several virulence factors associated with infection pathogenicity belonging to both Staphylococcus aureus and Streptococcus. In severe DFIs, patients demonstrated a greater microbial diversity and differential gene expression demonstrated the enrichment of multispecies virulence genes suggestive of a complex polymicrobial infection. The host response in patients with severe DFIs was also significantly different as compared to mild to moderate DFIs. This was attributed to the enrichment of host genes associated with inflammation, acute phase response, cell stress and broad immune-related responses, while those associated with wound healing and myogenesis were significantly depleted.

The potential of cold-adapted microorganisms for biodegradation of bioplastics

Due to the extensive use of plastics, their quantity in the environment is constantly increasing, which creates a global problem. In the present study, we sought to isolate, test and identify Antarctic microorganisms which possess the ability to biodegrade bioplastics such as poly(ε-caprolactone) (PCL), poly(butylene succinate) (PBS) and poly(butylene succinate-co-butylene adipate) (PBSA) at low temperatures. 161 bacterial and 38 fungal isolates were isolated from 22 Antarctic soil samples. Among them, 92.16% of bacterial and 77.27% of fungal isolates formed a clear zone on emulsified PBSA, 98.04% and 81.82% on PBS and 100% and 77.27% on PCL as an additive to minimal medium at 20 °C. Based on the 16S and 18S rRNA sequences, bacterial strains were identified as species belonging to Pseudomonas and Bacillus and fungal strains as species belonging to Geomyces, Sclerotinia, Fusarium and Mortierella, while the yeast strain was identified as Hansenula anomala. In the biodegradation process conducted under laboratory conditions at 14, 20 and 28 °C, Sclerotinia sp. B11IV and Fusarium sp. B3'M strains showed the highest biodegradation activity at 20 °C (49.68% for PBSA and 33.7% for PCL, 45.99% for PBSA and 49.65% for PCL, respectively). The highest biodegradation rate for Geomyces sp. B10I was noted at 14 °C (25.67% for PBSA and 5.71% for PCL), which suggested a preference for lower temperatures (at 20 °C the biodegradation rate was only 11.34% for PBSA, and 4.46% for PCL). These data showed that microorganisms isolated from Antarctic regions are good candidates for effective plastic degradation at low temperatures.

Application of bacteriocins in food preservation and infectious disease treatment for humans and livestock: a review

Infectious diseases caused by bacteria that can be transmitted via food, livestock and humans are always a concern to the public, as majority of them may cause severe illnesses and death. Antibacterial agents have been investigated for the treatment of bacterial infections. Antibiotics are the most successful antibacterial agents that have been used widely for decades to ease human pain caused by bacterial infections. Nevertheless, the emergence of antibiotic-resistant bacteria has raised awareness amongst public about the downside of using antibiotics. The threat of antibiotic resistance to global health, food security and development has been emphasized by the World Health Organization (WHO), and research studies have been focused on alternative antimicrobial agents. Bacteriocin, a natural antimicrobial peptide, has been chosen to replace antibiotics for its application in food preservation and infectious disease treatment for livestock and humans, as it is less toxic.

Killing or inhibition actions of (a) antibiotics and (b) bacteriocin on gut microbiota.

Metabolt: An In-Situ Instrument to Characterize the Metabolic Activity of Microbial Soil Ecosystems Using Electrochemical and Gaseous Signatures

Metabolt is a portable soil incubator to characterize the metabolic activity of microbial ecosystems in soils. It measures the electrical conductivity, the redox potential, and the concentration of certain metabolism-related gases in the headspace just above a given sample of regolith. In its current design, the overall weight of Metabolt, including the soils (250 g), is 1.9 kg with a maximum power consumption of 1.5 W. Metabolt has been designed to monitor the activity of the soil microbiome for Earth and space applications. In particular, it can be used to monitor the health of soils, the atmospheric-regolith fixation, and release of gaseous species such as N₂, H₂O, CO₂, O₂, N₂O, NH₃, etc., that affect the Earth climate and atmospheric chemistry. It may be used to detect and monitor life signatures in soils, treated or untreated, as well as in controlled environments like greenhouse facilities in space, laboratory research environments like anaerobic chambers, or simulating facilities with different atmospheres and pressures. To illustrate its operation, we tested the instrument with sub-arctic soil samples at Earth environmental conditions under three different conditions: (i) no treatment (unperturbed); (ii) sterilized soil: after heating at 125 °C for 35.4 h (thermal stress); (iii) stressed soil: after adding 25% CaCl₂ brine (osmotic stress); with and without addition of 0.5% glucose solution (for control). All the samples showed some distinguishable metabolic response, however there was a time delay on its appearance which depends on the treatment applied to the samples: 80 h for thermal stress without glucose, 59 h with glucose; 36 h for osmotic stress with glucose and no significant reactivation in the pure water case. This instrument shows that, over time, there is a clear observable footprint of the electrochemical signatures in the redox profile which is complementary to the gaseous footprint of the metabolic activity through respiration.

Environmental Factors That Contribute to the Maintenance of Cryptococcus neoformans Pathogenesis

The ability of microorganisms to colonise and display an intracellular lifestyle within a host body increases their fitness to survive and avoid extinction. This host–pathogen association drives microbial evolution, as such organisms are under selective pressure and can become more pathogenic. Some of these microorganisms can quickly spread through the environment via transmission. The non-transmittable fungal pathogens, such as Cryptococcus, probably return into the environment upon decomposition of the infected host. This review analyses whether re-entry of the pathogen into the environment causes restoration of its non-pathogenic state or whether environmental factors and parameters assist them in maintaining pathogenesis. Cryptococcus (C.) neoformans is therefore used as a model organism to evaluate the impact of environmental stress factors that aid the survival and pathogenesis of C. neoformans intracellularly and extracellularly.

Alternative fate of glyoxylate during acetate and hexadecane metabolism in Acinetobacter oleivorans DR1

The glyoxylate shunt (GS), involving isocitrate lyase (encoded by aceA) and malate synthase G (encoded by glcB), is known to play important roles under several conditions including oxidative stress, antibiotic defense, or certain carbon source metabolism (acetate and fatty acids). Comparative growth analyses of wild type (WT), aceA, and glcB null-strains revealed that aceA, but not glcB, is essential for cells to grow on either acetate (1%) or hexadecane (1%) in Acinetobacter oleivorans DR1. Interestingly. the aceA knockout strain was able to grow slower in 0.1% acetate than the parent strain. Northern Blot analysis showed that the expression of aceA was dependent on the concentration of acetate or H₂O₂, while glcB was constitutively expressed. Up-regulation of stress response-related genes and down-regulation of main carbon metabolism-participating genes in a ΔaceA mutant, compared to that in the parent strain, suggested that an ΔaceA mutant is susceptible to acetate toxicity, but grows slowly in 0.1% acetate. However, a ΔglcB mutant showed no growth defect in acetate or hexadecane and no susceptibility to H₂O₂, suggesting the presence of an alternative pathway to eliminate glyoxylate toxicity. A lactate dehydrogenase (LDH, encoded by a ldh) could possibly mediate the conversion from glyoxylate to oxalate based on our RNA-seq profiles. Oxalate production during hexadecane degradation and impaired growth of a ΔldhΔglcB double mutant in both acetate and hexadecane-supplemented media suggested that LDH is a potential detoxifying enzyme for glyoxylate. Our constructed LDH-overexpressing Escherichia coli strain also showed an important role of LDH under lactate, acetate, and glyoxylate metabolisms. The LDH-overexpressing E. coli strain, but not wild type strain, produced oxalate under glyoxylate condition. In conclusion, the GS is a main player, but alternative glyoxylate pathways exist during acetate and hexadecane metabolism in A. oleivorans DR1.

Taxonomic and Functional Annotation of Termite Degraded Butea monosperma (Lam.) Kuntze (Flame of the Forest)

Background:

Butea monosperma is an economically and medicinally important plant that grows all over India, however, the plant is highly susceptible to termite attack. The present study unravelled the bacterial community composition and their functional attributions from the termite degraded Butea.

Methods:

Total genomic DNA from termite degraded Butea monosperma samples was extracted and subjected to sequencing on Illumina's Miseq. The raw and unassembled reads obtained from high-throughput sequencing were used for taxonomic and functional profiling using different online and stand-alone softwares. Moreover, to ascertain the effect of different geographical locations and environmental factors, comparative analysis was performed using four other publically available metagenomes.

Results:

The higher abundance of Actinobacteria (21.27%), Proteobacteria (14.18%), Firmicutes (10.46%), and Bacteroidetes (4.11%) was found at the phylum level. The genus level was dominated by Bacillus (4.33%), Gemmatimonas (3.13%), Mycobacterium (1.82%), Acidimicrobium (1.69%), Thermoleophilum (1.23%), Nocardioides (1.44%), Terrimonas and Acidithermus (1.09%) and Clostridium (1.05%). Functional annotation of the termite degraded B. monosperma metagenome revealed a high abundance of ammonia oxidizers, sulfate reducers, dehalogenators, nitrate reducers, sulfide oxidizers, xylan degraders, nitrogen fixers and chitin degraders.

Conclusion:

The present study highlights the significance of the inherent microbiome of the degraded Butea shaping the microbial communities for effective degradation of biomass and different environmental toxicants. The unknown bacterial communities present in the sample can serve as enzyme sources for lignocelluloses degradation for biofuel production.

Wastewater-Agar as a selection environment: A first step towards a fungal in-situ bioaugmentation strategy

Viable and metabolically active fungi in toxic mixed liquors, treating landfill leachates and municipal wastewaters, were identified by culture depending methods. A selective culture medium consisting of wastewater and agar (WA) restrained fungi that could be randomly present (94% of the 51 taxa retrieved on WA were sample-specific), overcoming the problem of fast growing fungi or mycoparasite fungi. Moreover, WA allowed the isolation of fungi with a possible role in the degradation of pollutants typically present in the two wastewaters. Phoma medicaginis var. medicaginis, Chaetomium globosum, and Geotrichum candidum were mainly found in municipal wastewater, whereas Pseudallescheria boydii, Scedosporium apiospermum, Aspergillus pseudodeflectus, and Scopulariopsis brevicaulis were typical of landfill leachate.

Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides

Algal polysaccharides are an important bacterial nutrient source and central component of marine food webs. However, cellular and ecological aspects concerning the bacterial degradation of polysaccharide mixtures, as presumably abundant in natural habitats, are poorly understood. Here, we contextualize marine polysaccharide mixtures and their bacterial utilization in several ways using the model bacterium Alteromonas macleodii 83-1, which can degrade multiple algal polysaccharides and contributes to polysaccharide degradation in the oceans. Transcriptomic, proteomic and exometabolomic profiling revealed cellular adaptations of A. macleodii 83-1 when degrading a mix of laminarin, alginate and pectin. Strain 83-1 exhibited substrate prioritization driven by catabolite repression, with initial laminarin utilization followed by simultaneous alginate/pectin utilization. This biphasic phenotype coincided with pronounced shifts in gene expression, protein abundance and metabolite secretion, mainly involving CAZymes/polysaccharide utilization loci but also other functional traits. Distinct temporal changes in exometabolome composition, including the alginate/pectin-specific secretion of pyrroloquinoline quinone, suggest that substrate-dependent adaptations influence chemical interactions within the community. The ecological relevance of cellular adaptations was underlined by molecular evidence that common marine macroalgae, in particular Saccharina and Fucus, release mixtures of alginate and pectin-like rhamnogalacturonan. Moreover, CAZyme microdiversity and the genomic predisposition towards polysaccharide mixtures among Alteromonas spp. suggest polysaccharide-related traits as an ecophysiological factor, potentially relating to distinct 'carbohydrate utilization types' with different ecological strategies. Considering the substantial primary productivity of algae on global scales, these insights contribute to the understanding of bacteria-algae interactions and the remineralization of chemically diverse polysaccharide pools, a key step in marine carbon cycling.

Different Metabolomic Responses to Carbon Starvation between Light and Dark Conditions in the Purple Photosynthetic Bacterium, Rhodopseudomonas palustris

Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark. After starvation for 5 d in the light, cells showed increases in the amount of ATP and the NAD⁺/NADH ratio. Decreases in the amounts of most metabolites related to glycolysis and the TCA cycle in energy-rich starved cells suggest the active utilization of these metabolites for the modification of cellular components. Starvation in the dark induced the consumption of cellular compounds such as amino acids, indicating that the degradation of these cellular components produced ATP in order to maintain viability under energy-poor conditions. The present results suggest that intracellular energy levels alter survival strategies under carbon-starved conditions through metabolism.

Increase of Salt Tolerance in Carbon-Starved Cells of Rhodopseudomonas palustris Depending on Photosynthesis or Respiration

Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after carbon starvation under photosynthetic conditions in comparison with anaerobic and aerobic dark conditions. Tolerance to a treatment with high concentration of salt (2.5 M NaCl for 1 h) was largely increased after starvation under anaerobically light and aerobically dark conditions. The starved cells under the conditions of photosynthesis or aerobic respiration contained high levels of cellular ATP, but starvation under the anaerobic dark conditions resulted in a decrease of cellular ATP contents. To observe the large increase of the salt tolerance, incubation of starved cells for more than 18 h under illumination was needed. These results suggest that the ATP-dependent rearrangement of cells induced salt tolerance.

Changes in the Vibrio harveyi Cell Envelope Subproteome During Permanence in Cold Seawater

Previous work demonstrated that physiological, morphological, and gene expression changes as well as the time-dependent entry into the viable but not culturable (VBNC) state are used by Vibrio species to survive and cope with diverse stress conditions including seasonal temperature downshifts and starvation. To learn more about the nature and specific contribution of membrane proteins to cell adaptation and survival, we analyzed variations in the protein composition of cell envelope and related them to morphological and physiological changes that were taking place during the long-term permanence of Vibrio harveyi in seawater microcosm at 4 °C. We found that after 21 days of permanence, nearly all population (ca. 99 %) of V. harveyi acquired the VBNC phenotype. Although the size of V. harveyi cells gradually decreased during the incubation time, we found that this morphological change was not directly related to their entry into the VBNC state. Our proteomic study revealed that the level of membrane proteins playing key roles in cellular transport, maintenance of cell structure, and in bioenergetics processes remained unchanged along starvation at low temperature, thus suggesting that V. harveyi might need these proteins for the long-term survival and/or for the resuscitation process. On a contrary, the level of two proteins, elongation factor Tu (EF-TU) and bacterioferritin, greatly increased reaching the maximal values by the end of the incubation period. We further discuss the above data with respect to the putative roles likely exerted by membrane proteins during transition to and maintaining of the VBNC state.

Cultural, Transcriptomic, and Proteomic Analyses of Water-Stressed Cells of Actinobacterial Strains Isolated from Compost: Ecological Implications in the Fed-Batch Composting Process

This study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (FBC) process by comparing culturability and stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (CTC). The FBC reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. During this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of operation. The plate counts of aerobic chemoorganotrophic bacteria were 3.2-fold higher than CTC-positive (CTC+) counts on average at the fully acclimated stage (after 7 weeks of operation), in which Actinobacteria predominated, as shown by lipoquinone profiling and cultivation methods. When the actinobacterial isolates from the FBC process were grown under aw stress, no significant differences were observed in culturability among the cultures, whereas CTC stainability decreased with reductions in aw levels. A cDNA microarray-based transcriptomic analysis of a representative isolate showed that many of the genes involved in cellular metabolism and genetic information processing were down-regulated by aw stress. This result was fully supported by a proteomic analysis. The results of the present study suggest that, in low aw mature compost, the metabolic activity of the community with Actinobacteria predominating is temporarily reduced to a level that hardly reacts with CTC; however, these bacteria are easily recoverable by exposure to a high aw culture medium. This may be a plausible reason why acclimated FBC reactors in which Actinobacteria predominate yields higher plate counts than CTC+ counts.

Wake me when it's over - Bacterial toxin-antitoxin proteins and induced dormancy

Toxin-antitoxin systems are encoded by bacteria and archaea to enable an immediate response to environmental stresses, including antibiotics and the host immune response. During normal conditions, the antitoxin components prevent toxins from interfering with metabolism and arresting growth; however, toxin activation enables microbes to remain dormant through unfavorable conditions that might continue over millions of years. Intense investigations have revealed a multitude of mechanisms for both regulation and activation of toxin-antitoxin systems, which are abundant in pathogenic microorganisms. This minireview provides an overview of the current knowledge regarding type II toxin-antitoxin systems along with their clinical and environmental implications.