Bacterial Members Research Articles

Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress.

Microbiota that originate in the seed can have consequences for the education of the plant immune system, competitive exclusion of pathogens from the host tissue, and host access to critical nutrients. Our research objective was to investigate the consequences of the environmental conditions of the parent plant for bacterial seed microbiome assembly and transmission across plant generations. Using a fully factorial, three-generational experimental design, we investigated endophytic seed bacterial communities of common bean lines (Phaseolus vulgaris L.) grown in the growth chamber and exposed to either control conditions, drought, or excess nutrients at each generation. We applied 16S rRNA microbiome profiling to the seed endophytes and measured plant health outcomes. We discovered stable transmission of 22 bacterial members, regardless of the parental plant condition. This study shows the maintenance of bacterial members of the plant microbiome across generations, even under environmental stress. Overall, this work provides insights into the ability of plants to safeguard microbiome members, which has implications for crop microbiome management in the face of climate change.IMPORTANCESeed microbiomes initiate plant microbiome assembly and thus have critical implications for the healthy development and performance of crops. However, the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown, but this is critical information, given the intensifying stressors that crops face as the climate crisis accelerates. This study provides insights into the maintenance of plant microbiomes across generations, with implications for durable plant microbiome maintenance in agriculture on the changing planet.

Skin Bacterial and Fungal Microbiome Responses to Diet Supplementation and Rewilding in the Critically Endangered Southern Corroboree Frog.

The composition and dynamics of the skin bacterial and fungal microbiome is thought to influence host-pathogen defence. This microbial community is shaped by host captivity, diet, and microbial interactions between bacterial and fungal components. However, there remains little understanding of how specific micronutrients influence bacterial and fungal microbiome composition and their inter-domain interactions during rewilding of captive-bred animals. This study experimentally investigated the effect of dietary beta-carotene supplementation and subsequent field release on bacterial and fungal microbiome composition and dynamics using the Southern Corroboree frog (Pseudophryne corroboree) as a model system. We found large-scale diversification of bacterial communities post-release and similar diversification of fungal communities. The rewilded fungal mycobiome was more transient and demonstrated stronger temporal and micro-spatial fluctuations than the bacterial microbiome. Accounting for temporal and spatial factors, we found strong residual associations between bacterial members, yet limited evidence for inter-domain associations, suggesting that co-occurrence patterns between bacterial and fungal communities are largely a result of shared responses to the environment rather than direct interactions. Lastly, we found supplementation of dietary beta-carotene in captivity had no impact on post-release microbiome diversity, yet was associated with approximately 15% of common bacterial and fungal genera. Our research demonstrates that environmental factors play a dominant role over dietary beta-carotene supplementation in shaping microbiome diversity post-release, and suggest inter-domain interactions may also only exert a minor influence. Further research on the function and ecology of skin bacterial and fungal microbiomes will be crucial for developing strategies to support survival of endangered amphibian species.

Plastic Polymers and Antibiotic Resistance in an Antarctic Environment (Ross Sea): Are We Revealing the Tip of an Iceberg?

Microbial colonization of plastic polymers in Antarctic environments is an under-investigated issue. While several studies are documenting the spread of plastic pollution in the Ross Sea, whether the formation of a plastisphere (namely the complex microbial assemblage colonizing plastics) may favor the spread of antibiotic-resistant bacteria (ARB) in this marine environment is unknown yet. A colonization experiment was performed in this ecosystem, aiming at exploring the potential role of plastic polymers as a reservoir of antibiotic resistance. To this end, the biofilm-producing activity and the antibiotic susceptibility profiles of bacterial strains isolated from biofilms colonizing submerged polyvinylchloride and polyethylene panels were screened. The colonization experiment was carried out at two different sites of the Ross Sea, namely Road Bay and Tethys Bay. Most of bacterial isolates were able to produce biofilm; several multidrug resistances were detected in the bacterial members of biofilms associated to PVC and PE (also named as the plastisphere), as well as in the bacterial strains isolated from the surrounding water. The lowest percentage of ARB was found in the PE-associated plastisphere from the not-impacted (control) Punta Stocchino station, whereas the highest one was detected in the PVC-associated plastisphere from the Tethys Bay station. However, no selective enrichment of ARB in relation to the study sites or to either type of plastic material was observed, suggesting that resistance to antibiotics was a generalized widespread phenomenon. Resistance against to all the three classes of antibiotics assayed in this study (i.e., cell wall antibiotics, nucleic acids, and protein synthesis inhibitors) was observed. The high percentage of bacterial isolates showing resistance in remote environments like Antarctic ones, suffering increasing anthropic pressure, points out an emerging threat with a potential pathogenic risk that needs further deepening studies.

Efficient conversion of hemicellulose into high-value product and electric power by enzyme-engineered bacterial consortia

As an abundant agricultural and forestry biomass resource, hemicelluloses are hard to be effectively degraded and utilized by microorganisms due to the constraints of membrane and metabolic regulations. Herein, we report a synthetic extracellular metabolic pathway with hemicellulose-degrading-enzymes controllably displayed on Escherichia coli surface as engineered bacterial consortia members for efficient utilization of xylan, the most abundant component in hemicellulose. Further, we develop a hemicellulose/O2 microbial fuel cell (MFC) configuring of enzyme-engineered bacterial consortia based bioanode and bacterial-displayed laccase based biocathode. The optimized MFC exhibited an open-circuit voltage of 0.71 V and a maximum power density (Pmax) of 174.33 ± 4.56 µW cm−2. Meanwhile, 46.6% (w/w) α-ketoglutarate was produced in this hemicellulose fed-MFC. Besides, the MFC retained over 95% of the Pmax during 6 days’ operation. Therefore, this work establishes an effective and sustainable one-pot process for catalyzing renewable biomass into high-value products and electricity in an environmentally-friendly way.

Regulation of root-associated microbiomes and root exudates by different tobacco species

BackgroundThe root-associated microbiomes are crucial in promoting plant growth and development through symbiotic interactions with their hosts. Plants may shape their microbiomes by secreting specific root exudates. However, the potential mechanisms how plant species determine root exudates and drive microbiome assembly have been little studied. In this study, three wild tobaccos and one cultivated tobacco were used to investigate the commonalities and differences of both root-associated microbiomes and root exudates.ResultsAmplicon sequencing results suggested that tobacco species significantly affected microbial communities in both the rhizosphere and root endosphere, with the strongest impact on the fungal community in the root endosphere. The microbial networks of wild tobacco species were more stable than that of the cultivated tobacco, and fungal members played a more important role in the networks of wild tobacco species, while bacterial members did so in the cultivated tobacco. The rhizosphere bacteria of wild tobacco species showed a higher functional diversity than that of the cultivated tobacco, while the bacteria in the root endosphere presented a contrary pattern. Metabolomics analysis showed significant differences in the composition and abundance of root exudates among the four tobacco species, and the greatest difference was found between the three wild species and the cultivated one. Correlation analysis showed the strongest correlation between metabolites and rhizosphere bacteria, in which O-benzoic acid (2-methoxybenzoic acid) had the most positive correlations with rhizosphere bacteria, while β-ureidoisobutenoic acid had the most negative correlations with rhizosphere bacteria. The rhizosphere bacteria Streptomyces, Hydrophilus and Roseobacter had the strongest positive correlations with metabolites, and the rhizosphere bacterium Nitrobacter had the most negative correlations with metabolites.ConclusionThis study revealed the differences of microbial communities and root exudates in the rhizosphere and root endosphere of four tobacco species, which can further improve our understanding of plant–microbiome interactions during crop domestication.Graphical

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution

Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.

Describing the Reproductive Microbiome of Tritrichomonas foetus Chronically Infected Bulls and Diagnostic Collection Device Performance.

Tritrichomonas foetus (T. foetus), the causative agent of bovine trichomoniasis, is an obligate protozoan parasite of the bovine reproductive tract and can be found on the penis, prepuce, and distal urethra of the bull and from the cranial vagina to the oviduct in the infected cow. To date, the microbiome of bulls infected with T. foetus has not been described. The objectives of this study were to (1) describe the preputial and penile microbiome of bulls chronically infected by T. foetus, (2) describe the seminal microbiome of T. foetus-infected bulls, and (3) evaluate different collection devices that could be used for sampling. Eleven bulls naturally infected with T. foetus were utilized for the collection of samples. Samples were obtained during the process of a routine breeding soundness exam utilizing either a dacron swab, pizzle stick, double-guarded swab, or semen collection. The preputial and seminal microbiome of T. foetus-infected bulls was dominated by bacterial members of the phyla Fusobacteriota, Firmicutes, Bacteroidota, Actinobacteria, and Campylobacterota. Semen collection yielded the most microbial diversity; however, there was no significant difference between the four methods (p ≥ 0.05). This study characterizes both the preputial and seminal microbial communities of bulls chronically infected by T. foetus.

Role of bacterial pathogens in microbial ecological networks in hydroponic plants.

Plant-associated microbial communities are crucial for plant growth and health. However, assembly mechanisms of microbial communities and microbial interaction patterns remain elusive across vary degrees of pathogen-induced diseases. By using 16S rRNA high-throughput sequencing technology, we investigated the impact of wildfire disease on the microbial composition and interaction network in plant three different compartments. The results showed that pathogen infection significantly affect the phyllosphere and rhizosphere microbial community. We found that the primary sources of microbial communities in healthy and mildly infected plants were from the phyllosphere and hydroponic solution community. Mutual exchanges between phyllosphere and rhizosphere communities were observed, but microbial species migration from the leaf to the root was rarely observed in severely infected plants. Moreover, wildfire disease reduced the diversity and network complexity of plant microbial communities. Interactions among pathogenic bacterial members suggested that Caulobacter and Bosea might be crucial "pathogen antagonists" inhibiting the spread of wildfire disease. Our study provides deep insights into plant pathoecology, which is helpful for the development of novel strategies for phyllosphere disease prediction or prevention.

Networking the desert plant microbiome, bacterial and fungal symbionts structure and assortativity in co-occurrence networks

In nature, microbes do not thrive in seclusion but are involved in complex interactions within- and between-microbial kingdoms. Among these, symbiotic associations with mycorrhizal fungi and nitrogen-fixing bacteria are namely known to improve plant health, while providing resources to benefit other microbial members. Yet, it is not clear how these microbial symbionts interact with each other or how they impact the microbiota network architecture. We used an extensive co-occurrence network analysis, including rhizosphere and roots samples from six plant species in a natural desert in AlUla region (Kingdom of Saudi Arabia) and described how these symbionts were structured within the plant microbiota network. We found that the plant species was a significant driver of its microbiota composition and also of the specificity of its interactions in networks at the microbial taxa level. Despite this specificity, a motif was conserved across all networks, i.e., mycorrhizal fungi highly covaried with other mycorrhizal fungi, especially in plant roots—this pattern is known as assortativity. This structural property might reflect their ecological niche preference or their ability to opportunistically colonize roots of plant species considered non symbiotic e.g., H. salicornicum, an Amaranthaceae. Furthermore, these results are consistent with previous findings regarding the architecture of the gut microbiome network, where a high level of assortativity at the level of bacterial and fungal orders was also identified, suggesting the existence of general rules of microbiome assembly. Otherwise, the bacterial symbionts Rhizobiales and Frankiales covaried with other bacterial and fungal members, and were highly structural to the intra- and inter-kingdom networks. Our extensive co-occurrence network analysis of plant microbiota and study of symbiont assortativity, provided further evidence on the importance of bacterial and fungal symbionts in structuring the global plant microbiota network.

Investigation into how Odontotermes obesus maintains a predominantly Termitomyces monoculture in their fungus combs suggests a potential partnership with both fungi and bacteria

Fungus-growing termites, like Odontotermes obesus, cultivate Termitomyces as their sole food source on fungus combs which are continuously maintained with foraged plant materials. This necessary augmentation also increases the threat of introducing non-specific fungi capable of displacing Termitomyces. The magnitude of this threat and how termites prevent the invasion of such fungi remain largely unknown. This study identifies these non-specific fungi by establishing the pan-mycobiota of O. obesus from the fungus comb and termite castes. Furthermore, to maximize the identification of such fungi, the mycobiota of the decaying stages of the unattended fungus comb were also assessed. The simultaneous assessment of the microbiota and the mycobiota of these stages identified possible interactions between the fungal and bacterial members of this community. Based on these findings, we propose possible interactions among the crop fungus Termitomyces, the weedy fungus Pseudoxylaria and some bacterial symbiotes. These possibilities were then tested with in vitro interaction assays which suggest that Termitomyces, Pseudoxylaria and certain potential bacterial symbiotes possess anti-fungal capabilities. We propose a multifactorial interaction model of these microbes, under the care of the termites, to explain how their interactions can maintain a predominantly Termitomyces monoculture.

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

Functional diversity of bacterial microbiota associated with the toxigenic benthic dinoflagellate Prorocentrum.

Interactions between bacterial microbiota and epibenthic species of the dinoflagellate Prorocentrum may define the onset and persistence of benthic harmful algal blooms (bHABs). Chemical ecological interactions within the dinoflagellate phycosphere potentially involve a complex variety of organic molecules, metabolites, and toxins, including undefined bioactive compounds. In this study, the bacterial diversity and core members of the dinoflagellate-associated microbiota were defined from 11 strains of three epibenthic Prorocentrum species, representing three geographically disjunct locations within Mexican coastal waters. Microbiota profiles in stable monoclonal Prorocentrum cultures were obtained by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. Thirteen classes of bacteria were identified among dinoflagellate clones, where Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia were consistently dominant. The bacterial community structure exhibited significantly different grouping by the location of origin of dinoflagellate clones. No significant diversity difference was found among free-living or unattached bacteria in the dinoflagellate culture medium (M) compared with those in closer association with the dinoflagellate host cells (H). Twelve taxa were defined as core members of the bacterial assemblage, representing the genera Algiphilus, Cohaesibacter, Labrenzia, Mameliella, Marinobacter, Marivita, Massilia, Muricauda, Roseitalea, and an unclassified member of the Rhodobacteraceae. The core members are inferred to significantly contribute to primary and secondary metabolic functions, but no direct correlation with dinoflagellate toxigenicity was apparent. Overall the bacterial profile and implied gene functionality indicated a suite of positive interactions, suggesting either mutualism or commensalism with the dinoflagellate. The further characterization and interpretation of specific gene functions and interactions between bacteria and dinoflagellates, such as epibenthic members of genus Prorocentrum, are key to understanding their role in toxigenesis and bHAB development.

Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer.

Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.

Adhesive interactions within microbial consortia can be differentiated at the single-cell level through expansion microscopy.

Investigating microbe-microbe interactions at the single-cell level is critical to unraveling the ecology and dynamics of microbial communities. In many situations, microbes assemble themselves into densely packed multi-species biofilms. The density and complexity pose acute difficulties for visualizing individual cells and analyzing their interactions. Here, we address this problem through an unconventional application of expansion microscopy, which allows for the 'decrowding' of individual bacterial cells within a multispecies community. Expansion microscopy generally has been carried out under isotropic expansion conditions and used as a resolution-enhancing method. In our variation of expansion microscopy, we carry out expansion under heterotropic conditions; that is, we expand the space between bacterial cells but not the space within individual cells. The separation of individual bacterial cells from each other reflects the competition between the expansion force pulling them apart and the adhesion force holding them together. We employed heterotropic expansion microscopy to study the relative strength of adhesion in model biofilm communities. These included mono and dual-species Streptococcus biofilms, and a three-species synthetic community (Fusobacterium nucleatum, Streptococcus mutans, and Streptococcus sanguinis) under conditions that facilitated interspecies coaggregation. Using adhesion mutants, we investigated the interplay between F. nucleatum outer membrane protein RadD and different Streptococcus species. We also examined the Schaalia-TM7 epibiont association. Quantitative proximity analysis was used to evaluate the separation of individual microbial members. Our study demonstrates that heterotropic expansion microscopy can 'decrowd' dense biofilm communities, improve visualization of individual bacterial members, and enable analysis of microbe-microbe adhesive interactions at the single-cell level.

Reshaping the root endophytic microbiota in plants to combat mercury-induced stress

Emerging evidence suggests that plants experiencing abiotic stress actively seek help from soil microbes. However, the empirical evidence supporting this strategy is limited, especially in response to heavy metal stress. We used integrated microbial community profiling and culture-based methods to investigate the interaction between mercury (Hg) stress, the entophytic root microbiome, and maize seedlings. The results of the pot experiment showed that soil Hg (20 mg/kg) strongly inhibited maize growth, indicating its strong phytotoxicity. Furthermore, Hg stress significantly altered the structure of the bacterial and fungal communities and enriched the potentially pathogenic Fusarium sp., suggesting that soil Hg stress may enhance the bio-stress induced by Fusarium species in maize. Additionally, soil Hg also led to the enrichment of beneficial bacterial members of Streptomyces, Lysobacter, and Sphingomonas (defined as differential species), which were also identified as keystone species in the Hg treatment by the analysis of co-occurrence networks. Therefore, it can be postulated that the members of Streptomyces, Lysobacter, and Sphingomonas function as stress-alleviating microbes. We successfully isolated the representatives of these stress-alleviating microbes. As expected, these strains mitigated the detrimental effects of Hg stess for the maize seedlings, suggesting that plants recruit the stress-alleviated microbiota to combat Hg stress. This study provides insights into the potential of manipulating the root microbiome to enhance plant growth in polluted environments.

Effects of packaging methods and temperature variations on the quality and microbial diversity of grouper (Epinephelus Lanceolatus) during cold storage

Microbial growth and its metabolism are the primary reasons for fish spoilage. In this study, the effects of temperature fluctuations and modified atmosphere packaging (MAP) on the quality and microbial diversity of grouper (Epinephelus lanceolatus) during cold storage were investigated. Fish fillets were packed in air packaging (AP), vacuum packaging (VP), MAP1 (40% CO2/55% N2/5% O2), and MAP2 (60% CO2/35% N2/5% O2), and stored at T1 (4 °C) and T2 (4–8 °C temperature fluctuations), respectively. Total viable counts (TVC), psychrophilic bacteria count, Pseudomonas count, and H2S-producing bacteria count all increased during cold storage. Pseudomonas, Serratia, and Carnobacterium were the dominant genera in AP, VP, and MAP2 at T1 storage, with relative abundances of 82.7%, 54.5%, and 57.3%, respectively. Temperature fluctuations accelerated the spoilage process of the grouper, and increased the relative abundance of Serratia in the samples, but had less effect on the composition of these spoilage bacterial members. The microbial community was more affected by the different gas atmospheres. MAP inhibited the growth of Pseudomonas and increased the relative abundance of Carnobacterium and Psychrobacter in the samples. Low temperature and MAP effectively suppressed the rise of pH, total volatile basic nitrogen (TVB-N), trimethylamine (TMA), thiobarbituric acid reactive substances (TBARs), and K values and maintained the water holding capacity (WHC) and sensory quality of the samples. Grouper had the longest shelf life under MAP2-T1 treatment. The MAP2-T1 samples maintained lower levels of TVB-N (151.8 mg/kg), TMA (7.6 mg/kg), TBARs (0.90 mg MDA/kg), and K value (48.5%) and higher levels of WHC (77.6%) on the 18th day, with a lower degree of spoilage compared to other samples.

Metaanalysis of Public Wastewater Metagenomes: Revealing the Influence of Climatic Variations on the Abundance of the Bacterial Members

As per the present trend, earth may experience severe hike in temperature by 2040. Therefore, global surveillance is required to combat against the upcoming climatic extremities. Emerging and re-emerging infectious diseases are part of the key pressing issues which can affect millions of people worldwide. Wastewater associated metagenomic data representing the wastewater samples collected from sewer networks in Newcastle (United Kingdom); Zimbabwe (Africa) and West Bengal (India), available in public databases were collected. It was observed that of the top 10 abundant genera, the prevalent genera in samples from United Kingdom, Africa, India were Desulfitobacterium, Prevotella, Sulfurospirillum respectively. By comparing all the three samples under study; it was observed that three microbial genera Bacteroides, Dechloromonas and Faecalibacterium were common throughout the samples. Metagenome-wide association studies were conducted to link microbes in the sample to the host disorders. Our study could predict overexpression of several enriched pathways like Vancomycin resistance, Platinum drug resistance across the samples. These findings prove efficacies of the community genomics approach to serve as a public health monitoring tool through detection of spatial variation as well as degree of commonness in wastewater bacterial profiles and also through the prediction of the pathogenic quantum of wastewater systems.

Human gut microbiota and their production of endocannabinoid-like mediators are directly affected by a dietary oil

ABSTRACT Dietary omega-3 polyunsaturated fatty acids (n-3 PUFAs) and the gut microbiome affect each other. We investigated the impact of supplementation with Buglossoides arvensis oil (BO), rich in stearidonic acid (SDA), on the human gut microbiome. Employing the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we simulated the ileal and ascending colon microbiomes of four donors. Our results reveal two distinct microbiota clusters influenced by BO, exhibiting shared and contrasting shifts. Notably, Bacteroides and Clostridia abundance underwent similar changes in both clusters, accompanied by increased propionate production in the colon. However, in the ileum, cluster 2 displayed a higher metabolic activity in terms of BO-induced propionate levels. Accordingly, a triad of bacterial members involved in propionate production through the succinate pathway, namely Bacteroides, Parabacteroides, and Phascolarctobacterium, was identified particularly in this cluster, which also showed a surge of second-generation probiotics, such as Akkermansia, in the colon. Finally, we describe for the first time the capability of gut bacteria to produce N-acyl-ethanolamines, and particularly the SDA-derived N-stearidonoyl-ethanolamine, following BO supplementation, which also stimulated the production of another bioactive endocannabinoid-like molecule, commendamide, in both cases with variations across individuals. Spearman correlations enabled the identification of bacterial genera potentially involved in endocannabinoid-like molecule production, such as, in agreement with previous reports, Bacteroides in the case of commendamide. This study suggests that the potential health benefits on the human microbiome of certain dietary oils may be amenable to stratified nutrition strategies and extend beyond n-3 PUFAs to include microbiota-derived endocannabinoid-like mediators.

Characterization and identification of long-chain hydrocarbon-degrading bacterial communities in long-term chronically polluted soil in Ogoniland: an integrated approach using culture-dependent and independent methods

Escalating oil consumption has resulted in an increase in accidental spills of petroleum hydrocarbons, causing severe environmental degradation, notably in vulnerable regions like the Niger Delta. Complex mixture of these hydrocarbons particularly long-chain alkanes presents unique challenges in restoration of polluted environment due to their chemical properties. This study aimed to investigate the long-chain hydrocarbon-degrading bacterial communities within long-term chronically polluted soil in Ogoniland, by utilizing both traditional cultivation methods and modern culture-independent techniques. Results revealed that surface-polluted soil (SPS) and subsurface soil (SPSS) exhibit significantly higher total organic carbon (TOC) ranging from 5.64 to 5.06% and total petroleum hydrocarbons (TPH) levels ranging from 36,775 ppm to 14,087 ppm, compared to unpolluted soil (UPS) with 1.97% TOC and 479 ppm TPH, respectively. Analysis of carbon chain lengths reveals the prevalence of longer-chain alkanes (C20-28) in the surface soil. Culture-dependent methods, utilizing crude oil enrichment (COE) and paraffin wax enrichment (PWE), yield 47 bacterial isolates subjected to a long-chain alkane degradation assay. Twelve bacterial strains demonstrate significant degradation abilities across all enriched media. Three bacterial members, namely Pseudomonas sp. (almA), Marinomonas sp. (almA), and Alteromonas (ladA), exhibit genes responsible for long-chain alkane degradation, demonstrating efficiency between 50 and 80%. Culture-independent analysis reveals that surface SPS samples exhibit greater species richness and diversity compared to subsurface SPSS samples. Proteobacteria dominates as the phylum in both soil sample types, ranging from 22.23 to 82.61%, with Firmicutes (0.2–2.22%), Actinobacteria (0.4–3.02%), and Acidobacteria (0.1–3.53%) also prevalent. Bacterial profiles at genus level revealed that distinct variations among bacterial populations between SPS and SPSS samples comprising number of hydrocarbon degraders and the functional predictions also highlight the presence of potential catabolic genes (nahAa, adh2, and cpnA) in the polluted soil. However, culture-dependent analysis only captured a few of the dominant members found in culture-independent analysis, implying that more specialized media or environments are needed to isolate more bacterial members. The findings from this study contribute valuable information to ecological and biotechnological aspects, aiding in the development of more effective bioremediation applications for restoring oil-contaminated environments.

Understanding and exploring the diversity of soil microorganisms in tea (Camellia sinensis) gardens: toward sustainable tea production.

Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.