Microbial Involvement Research Articles

The mechanism of dolomitization in a stromatolite mound in the late Cambrian Chaomidian Formation, Shandong Province, China

Clarifying the mechanism of dolomitization is of pivotal importance and represents a burning issue among geologists. A comprehensive model to define the genesis of dolomitization in the Cambrian Chaomidian Formation carbonates is still lacking. In the highly focused study, the advanced integration of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), clumped isotope and carbon/oxygen isotope analyses was used to reveal complex interactions between the genesis and dolomitization of a stromatolite mound in the late Cambrian Chaomidian Formation of China. The results show that the dolomite content increases from bottom to top, along with a shift in lithology from limestone to dolostone. Additionally, as we moved from the base to the summit of the stromatolite mound, the Fe, Mn, and Na contents increase with increasing Mg levels, whereas the δ13C and δ18O values became more positive. Conversely, the levels of Sr and total rare earth elements (REEs) gradually decreased. The dolomite grains in the stromatolite mound are micritic and euhedral to subhedral, with foggy cores and bright edges and low cation ordering. The stromatolite limestone, dolostone, and underlying lime mudstone samples exhibit similar REE patterns: light REE enrichment, heavy REE loss, negative δEu anomalies, and weak negative δCe anomalies. The δ13C and δ18O values fall within the late Cambrian seawater range, suggesting that dolomitizing fluids originated mainly from concentrated seawater and migrated from top to bottom. The δ18O values indicate lower dolomite formation temperatures than calcite formation temperatures, supporting dolomitization during the penecontemporaneous diagenetic stage. Petrographic evidence reveals the presence of pyrite, indicating sulfate-reducing bacterial activity during diagenesis. XPS analysis revealed similar organic functional groups in both the stromatolite limestone and the dolostone, including C-(C = O)-O, C–C/C-(C–H), C-O and C-N. However, the dolostone spectrum exhibited a larger C-OH/C-O peak area, suggesting significant microbial organic matter involvement in dolomite formation. While a kinetic obstacle is recognized as a primary cause of dolomite formation, this study also suggested that microbial activity weakened this obstacle during diagenesis. Thus, microbial metabolism or cyanobacterial decomposition facilitates dolomite formation during the penecontemporaneous diagenetic stage.

Acne and the cutaneous microbiome: A systematic review of mechanisms and implications for treatments.

Acne vulgaris is a pervasive skin disease characterized by inflammation of sebaceous units surrounding hair follicles. It results from the complex interplay between skin physiology and the intricate cutaneous microbiome. Current acne treatments, while effective, have major limitations, prompting a shift towards microbiome-based therapeutic approaches. This study aims to determine the relationship between acne and the cutaneous microbiome, assess the effects of current treatments on the cutaneous microbiome and explore the implications for developing new therapies. A systematic review was performed using PubMed and SCOPUS databases within the last 10 years. Methodological quality was assessed independently by two authors. The search retrieved 1830 records, of which 26 articles met the inclusion criteria. Meta-analysis of alpha diversity change was assessed using fixed and randomized effect models per therapeutic group. Eight studies pertain to the role of the cutaneous microbiome in acne, identifying C. acnes, S. aureus and S. epidermidis as key contributors through overproliferation, commensalism or dysbiosis. Eleven studies discuss current acne treatments, including doxycycline (1), topical benzoyl peroxide (BPO) (4), isotretinoin (2), sulfacetamide-sulfur (SSA) (2) and aminolevulinic acid-photodynamic therapy (ALA-PDT) (2), identified as modulating the cutaneous microbiome as a mechanism of efficacy in acne treatment. Seven studies discuss new treatments with topical probiotics, plant derivatives and protein derivatives, which contribute to acne clearance via modulation of dysbiosis, inflammatory markers and diversity indexes. A meta-analysis of the effects of existing therapeutics on the cutaneous microbiome identified benzoyl peroxide as the only treatment to facilitate significant change in diversity. Despite the heterogeneity of study types and microbiome classifications limiting the analysis, this review underscores the complexity of microbial involvement in acne pathogenesis. It delineates the effects of acne therapeutics on microbial diversity, abundance and composition, emphasizing the necessity for personalized approaches in acne management based on microbiome modulation.

In search of poly-3-hydroxybutyrate (PHB): A comprehensive review unveiling applications and progress in fostering a sustainable bio-circular economy

The escalating demand for economical and durable materials has propelled plastics into an indispensable facet of daily human life, dominating commercial and industrial sectors. The global plastic production of 1.1 billion tons by 2050 exacerbates concerns. The COVID-19 pandemic has further intensified the issue, reaching an alarming 0.3–0.4 billion tons annually. Urgent action is imperative to curtail the drastic environmental impact. Various strategies, particularly microbial involvement in plastic production and degradation, must be implemented to address this. Poly-3-Hydroxybutyrate (PHB) microbial polyesters present a promising alternative to conventional plastics because of their biodegradable nature, thus offering a sustainable solution to plastic pollution. PHBs are employed in divergent industries, including agriculture, medicine, nanotechnology, food, and tissue engineering. This comprehensive review addresses the gap in the literature by encompassing a wide range of topics related to PHBs, their associated enzymes, metabolic pathways, and applications. It also provides an in-depth analysis, highlighting the significance of diverse microbial communities in both the synthesis and degradation of biopolymers. Strategies for augmenting PHA production and leveraging waste products for circular economy initiatives are also discussed, emphasizing the need for innovative solutions to address the global plastic crisis.Top of Form This review highlights two critical strategies for tackling plastic pollution: introducing alternative materials like bioplastics and leveraging biological recycling with microbial assistance. Adopting bio-based circular economy strategies, implementing comprehensive 6 R waste management practices, strengthening plastic pollution regulations, and raising social awareness can significantly improve eco-friendly plastic waste management, diminish pollution, and enhance socio-economic conditions, thus benefiting economies worldwide.

Biodegradability assessment of HDPE-based biocomposites: Influence of starch and fiber composition

This research aims to analyze the biodegradation dynamics of a tertiary composite blend, including High-Density Polyethylene (HDPE), starch and linen fiber, and their combined effect on decay processes in authentic environmental settings. It investigates the relationship between fiber content and decomposition rates, details the biodegradation mechanisms, and evaluates the reactive profiles of the involved constituents. Decay kinetics and the biodegradation mechanism of three formulations: HDPE60S40, HDPE60S20F20, and HDPE60S30F10, representing composites with 60 % HDPE, complemented by 40 %, 20 % starch and 20 %, 10 % linen fiber, respectively, are examined. HDPE60S30F10 is noted for its superior biodegradation rates, showing a 1.2 % weight loss in soil and 9.89 % in marine conditions and an increased resistance to shearing forces, whereas HDPE60S40 recorded a weight loss of 0,63 % in soil and 2.59 % in seawater against 1,7 % and 6.64 % in soil and seawtaer, respectively recorded with HDPE60S20F20. Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations complement these findings, presenting HDPE60S40 as the most rigid, HDPE60S20F20 as the most ductile with a bulk modulus of 13.34 GPa, and HDPE60S30F10 exhibiting the best shear resistance with a shear modulus of 12.48 GPa. Scanning Electron Microscopy (SEM) and Fourier-Transform Infrared Spectroscopy (FTIR) analyses confirm microbial involvement and significant surface erosion, particularly indicating particularly starch degradation. The results suggest that integrating linen fiber into the composites enhances biodegradation.

Contribution of Streptococcus pseudopneumoniae and Streptococcus salivarius to vocal fold mucosal integrity and function.

Structural changes to the vocal fold (VF) epithelium, namely, loosened intercellular junctions, have been reported in VF benign lesions. The potential mechanisms responsible for the disruption of cell junctions do not address the contribution of resident microbial communities to this pathological phenomenon. In this study, we focused on determining the relationship between Streptococcus pseudopneumoniae (SP), a dominant bacterial species associated with benign lesions, and Streptococcus salivarius (SS), a commensal bacterium, with human VF epithelial cells in our three-dimensional model of the human VF mucosa. This experimental system enabled direct deposition of bacteria onto constructs at the air/liquid interface, allowing for the assessment of bacterium-host interactions at the cellular, molecular and ultrastructural levels. Our findings demonstrate that SP disrupts VF epithelial integrity and initiates inflammation via the exported products HtrA1 and pneumolysin. In contrast, SS attaches to the VF epithelium, reduces inflammation and induces Mmp2-mediated apical desquamation of infected cells to mitigate the impact of pathogens. In conclusion, this study highlights the complexity of microbial involvement in VF pathology and potential VF mucosal restoration in the presence of laryngeal commensals.

Effect of Specific Spoilage Organisms on the Degradation of ATP-Related Compounds in Vacuum-Packed Refrigerated Large Yellow Croaker (Larimichthys crocea).

This study examined the spoilage potential of specific spoilage organisms on the degradation of adenosine triphosphate (ATP)-related compounds in vacuum-packed refrigerated large yellow croaker. The total viable count (TVC), ATP-related compounds and related enzymes of vacuum-packed refrigerated large yellow croaker inoculated with different bacteria (Pseudomonas fluorescens and Shewanella putrefaciens) were characterized using the spread plate method, high-performance liquid chromatography and assay kits, respectively. Results indicated that the TVC for both control and Shewanella putrefaciens groups reached spoilage levels at days 9 and 15, respectively. The changes of adenosine triphosphate (ATP), adenosine diphosphate (ADP), adenosine monophosphate (AMP) and adenosine deaminase activity across all groups showed no significant difference attributable to microbial growth. The results suggested that ATP to inosine monophosphate (IMP) degradation primarily occurs via fish's endogenous enzymes, with minimal microbial involvement. On day 12, the IMP content in fillets inoculated with Pseudomonas fluorescens (0.93 μmol/g) was half higher than in those inoculated with Shewanella putrefaciens (0.57 μmol/g). Both spoilage organisms facilitated IMP degradation, with Shewanella putrefaciens making a more substantial contribution. Analysis of K values and correlation coefficients revealed that Shewanella putrefaciens was the primary factor in the freshness loss of refrigerated vacuum-packed large yellow croaker. These findings offer a reference for understanding quality changes in refrigerated large yellow croaker, especially regarding umami degradation at the microbial level.

Microbial contribution to the formation of the Carboniferous sedimentary manganese deposits in northwestern China

There is an increasing consensus that microbes play a critical role in the genesis of sedimentary manganese (Mn) carbonate deposits. However, compelling evidence for the microbial involvement during sedimentary Mn metallogenesis remains insufficient, and the specific effects of microbial mediation need to be further elucidated. To advance our understanding of the microbial Mn metallogenesis, multi-scale petrographic observations and high-resolution mineralogical analyses (mainly based on Fourier transform infrared spectrometer and Raman spectroscopy) were conducted on the Carboniferous black shale-hosted Malkansu and limestone-hosted Zhaosu Mn ore deposits in northwestern China. Results show that the Mn ore samples are characterized by finely laminated texture with μm-scale cyclic variations of microbe-associated minerals including rhodochrosite, apatite, quartz, and organic matter as well. These features indicate the ubiquity of microbial mats during Mn mineralization. Microbial involvement is also supported by Mn carbonate aggregates with variable morphologies (filamentous with pearl necklace-like inner forms resembling vermiform morphologies and spheroidal, coccoid-like forms), as well as the annular organic matter that resembles bacterial cells. The cyclic occurrence of trace amounts of remnant Mn oxides verify that primary Mn accumulation took place under oxic bottom waters. The negative co-variation between Mn carbonates and organic matter on Raman profiles suggests that the former was formed during diagenesis via organic matter decomposition coupled with Mn oxide reduction. Combined with previous experimental simulations and natural observations, a two-step microbially mediated Mn metallogenic model is tentatively proposed for the studied Mn deposits: (1) Mn(II)-oxidizing bacteria effectively catalyzed the deposition of considerable Mn oxides under oxygenated bottom water columns, a process that was simultaneously sustained by oxygenic microbial mats such as cyanobacteria; (2) Buried Mn oxides were reduced by highly reactive organic matter sourced from dead biomats of Mn(II)-oxidizing bacteria and benthic phototrophs, a process mediated by Mn(IV)-reducing bacteria which not only promoted the reaction rate but also served as nucleation sites for Mn carbonate minerals. This model can also help to explain the occurrence of diverse authigenic accessory minerals (e.g., quartz, apatite, and talc) and remarkable enrichments of several specific elements (e.g., Co, Ce, and Mo) in the studied Mn ores, which were closely linked to the decomposed cells and extracellular polymeric substance (EPS). By comparing with previous microbial investigations on Mn deposits over geological history, we further highlight the fundamental role of microorganisms in regulating the formation of economic Mn carbonate deposits.

Clinical Presentation, Bacteriologic Findings and Possible Risk Factors for Ischemic Teat Necrosis in Cattle-A Case Series.

Ischemic teat necrosis (ITN) is a growing problem in the dairy industry characterized by teat lesions, necrosis, pruritus and automutilation. Despite the economic and welfare consequences, there is no treatment, and the etiology of the disease remains poorly understood. The aim of this study was to investigate ITN by analyzing its clinical presentation, potential risk factors and microbial involvement. Methods included collection of milk and swab samples from affected cows over a period of one-and-a-half years and completion of questionnaires by veterinarians and farmers. Microbial testing included PCR testing for Treponema spp. and cultural testing by anaerobic and aerobic incubation on blood agar. The results showed a high and significant prevalence of Treponema spp. and Staphylococcus aureus in affected teats compared to non-ITN-affected control teats, indicating their potential role in the development of ITN. Other factors such as edema and milking practices also appear to contribute to the tissue damage. First-lactation and early-lactation heifers are particularly at risk. In conclusion, ITN appears to have a multifactorial etiology with both infectious and non-infectious factors playing a role. Further research is needed to better understand the complex interplay of these factors and to develop effective prevention and management strategies.

Inventarisasi Produk Pangan Fermentasi Lokal Pada Pasar Tradisional di Pontianak Sebagi Sumber Belajar Mikrobiologi

West Kalimantan, renowned for its abundant biological natural resources, often utilizes them in local food production through fermentation, representing indigenous knowledge passed down through generations. The involvement of microbes in changing a substrate to produce certain products is related to the use of microbes in life, and is one of the themes in the Microbiology course. The aim of this research is to inventory the types of traditional foods typical of West Kalimantan, and their relation to learning Microbiology. Data collection techniques to obtain facts are carried out through observation, interviews and documentation with sources. Data analysis was carried out in a qualitative descriptive manner. The research results showed that the types of traditional food found at the research location were cincalok, wet shrimp paste, salted mustard greens, tempoyak, jasam, and mandai. Based on the research results, it was concluded that there are six traditional food products which constitute local wisdom of ethnic groups in Pontianak. The process of making these food products utilizes bacteria that are naturally present, which means it involves the concept of microbiology, which indicates that it can be used as a learning resource for microbiology courses in the form of modules.

Development and application of a bioassay for assessing the dissipation rate of the synthetic strigolactone GR24 in soil

AbstractRoot parasitic weeds of the genera Striga, Orobanche, and Phelipanche cause enormous economic losses for farmers the world over. Germination of the seeds of these species requires a chemotropic signal in the form of strigolactones in the soil. Once a root parasitic weed germinates and becomes established, it draws nutrition from the host plants, leading to plant death and hence yield reduction. Despite the obvious importance of strigolactones, there is currently almost no information about the fate of strigolactones in the soil, although microbial involvement has been suggested. To begin to address this knowledge lacuna, we developed a bioassay—using the strigolactone synthetic analogue GR24—as a high‐throughput, inexpensive, and compact tool for monitoring the dissipation of strigolactones (GR24 in this case) in the soil by microorganisms and/or environmental conditions, including GR24 concentration, soil type, and temperature. As part of the bioassay, it was found that autoclaving the soil delayed the dissipation of GR24 versus sterilisation by gamma radiation and or no sterilisation. Analytical LC–MS/MS with a detection limit of 0.1 ppb confirmed this finding, with no GR24 being detected in non‐sterilised soil after 24 h. Application of the bioassay to monitor GR24 dissipation in soil showed that the higher the GR24 concentration the slower the degradation, and the higher the temperature, the faster the degradation. It also showed that the organic matter content of the soil affected the GR24 dissipation rate. These findings were also confirmed by analytical LC–MS/MS, indicating the applicability of the methodology for studies of root exudes.

Identification of bacterial dissimilatory antimonate reductase AnrA: genes and proteins involved in antimonate respiration and resistance in Geobacter sp. strain SVR.

Geobacter sp. strain SVR uses antimonate [Sb(V)] as a terminal electron acceptor for anaerobic respiration. Here, we visualized a possible key enzyme, periplasmic Sb(V) reductase (Anr), via active staining and non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that a novel dimethyl sulfoxide (DMSO) reductase family protein, WP_173201954.1, is involved in Anr. This protein was closely related with AnrA, a protein suggested to be the catalytic subunit of a respiratory Sb(V) reductase in Desulfuribacillus stibiiarsenatis. The anr genes of strain SVR (anrXSRBAD) formed an operon-like structure, and their transcription was upregulated under Sb(V)-respiring conditions. The expression of anrA gene was induced by more than 1 µM of antimonite [Sb(III)]; however, arsenite [As(III)] did not induce the expression of anrA gene. Tandem mass tag-based proteomic analysis revealed that, in addition to Anr proteins, proteins in the following categories were upregulated under Sb(V)-respiring conditions: (i) Sb(III) efflux systems such as Ant and Ars; (ii) antioxidizing proteins such as ferritin, rubredoxin, and thioredoxin; (iii) protein quality control systems such as HspA, HslO, and DnaK; and (iv) DNA repair proteins such as UspA and UvrB. These results suggest that strain SVR copes with antimony stress by modulating pleiotropic processes to resist and actively metabolize antimony. To the best of our knowledge, this is the first report to demonstrate the involvement of AnrA in Sb(V) respiration at the protein level. Furthermore, this is the first example to show high expression of the Ant system proteins in the Sb(V)-respiring bacterium.IMPORTANCEAntimony (Sb) exists mainly as antimonite [Sb(III)] or antimonate [Sb(V)] in the environment, and Sb(III) is more toxic than Sb(V). Recently, microbial involvement in Sb redox reactions has received attention. Although more than 90 Sb(III)-oxidizing bacteria have been reported, information on Sb(V)-reducing bacteria is limited. Especially, the enzyme involved in dissimilatory Sb(V) reduction, or Sb(V) respiration, is unclear, despite this pathway being very important for the circulation of Sb in nature. In this study, we demonstrated that the Sb(V) reductase (Anr) of an Sb(V)-respiring bacterium (Geobacter sp. SVR) is a novel member of the dimethyl sulfoxide (DMSO) reductase family. In addition, we found that strain SVR copes with Sb stress by modulating pleiotropic processes, including the Ant and Ars systems, and upregulating the antioxidant and quality control protein levels. Considering the abundance and diversity of putative anr genes in the environment, Anr may play a significant role in global Sb cycling in both marine and terrestrial environments.

Redox conditions of Datangpo-type manganese ores constrained by statistical analysis of pyrite framboids and iron isotopes

Datangpo-type manganese ores which originated in the Cryogenian Datangpo Formation, are overlaid and underlaid by Nantuo diamicite and Tiesi'ao silistones, respectively. A thorough understanding of the manganese mineralization process is currently limited by the continued uncertainty regarding the metallogenic redox condition of the Mn-bearing rock series. This study employed statistical analysis of pyrite framboid sizes and iron isotope (δ56Fe) to determine the redox conditions and constrain the mineralization process of Datangpo-type manganese ores in South China, considering the Gaolou in Chongqing, Yanglizhang in Guizhou, and Minle and Zhenxing in Hunan as examples. The results showed that Tiesi'ao siltstones mainly developed relatively larger diameter (7.29–7.68 μm) framboidal pyrites, whereas mudstones in the Datangpo Formation developed relatively smaller diameter (2.63–5.56 μm) framboidal pyrites. Furthermore, manganese ores produce non-framboidal pyrites. In three profiles, framboidal pyrite concentrations were found to be negatively correlated with Mn contents. These characteristics suggested that siltstones, mudstones, and manganese ores were deposited in oxic-anoxic, dysoxic-euxinic, and oxic-dysoxic conditions, respectively. The δ56Fe of whole rocks (δ56FeWR) exhibited a range from −0.73 ‰ to +0.48 ‰ (average of −0.32 ‰), whereas pyrite (δ56FePy) varied from +0.03 ‰ to +0.83 ‰ (average of +0.36 ‰). Furthermore, δ56FePy in manganese ore (average = +0.27 ‰) were lighter than those in mudstone (average = +0.49 ‰). The results of this study demonstrated that oxidation deposition played a role in pyrite formation, with manganese ores exhibiting more oxic conditions compared to mudstones. The findings of this study suggested that idiomorphic pyrite formation was similar to that of manganese ore, in which Mn precipitated in the form of manganese (hydro)oxides under oxic seawater, and then converted into rhodochrosite under anoxic sulfidic diagenetic conditions, with the involvement of microbes. This research has the potential to enhance comprehension regarding redox conditions and the regulation of sedimentary manganese ores via redox transformation.

Methane and nitrous oxide emissions and related microbial communities from mangrove stems on Qi'ao Island, Pearl River Estuary in China

Mangrove forests, crucial carbon-rich ecosystems, are increasingly vulnerable to soil carbon loss and greenhouse gas (GHG) emissions due to human disturbance. However, the contribution of mangrove trees to GHG emissions remains poorly understood. This study monitored CO2, CH4, and N2O fluxes from the stems of two mangrove species, native Kandelia obovata (KO) and exotic Sonneratia apetala (SA), at three heights (0.7 m, 1.2 m, and 1.7 m) during the dry winter period on Qi'ao Island, Pearl River Estuary, China. Heartwood samples were analyzed to identify potential functional groups related to gas fluxes. Our study found that tree stems acted as both sinks and sources for N2O (ranging from −9.49 to 28.35 μg m−2 h−1 for KO and from −6.73 to 28.95 μg m−2 h−1 for SA) and CH4. SA exhibited significantly higher stem CH4 flux (from −26.67 to 97.33 μg m−2 h−1) compared to KO (from −44.13 to 88.0 μg m−2 h−1) (P < 0.05). When upscaled to the community level, both species were net emitters of CH4, contributing approximately 4.68 % (KO) and 0.51 % (SA) to total CH4 emissions. The decrease in stem CH4 flux with increasing height, indicates a soil source. Microbial analysis in the heartwood using the KEGG database indicated aceticlastic methanogenesis as the dominant CH4 pathway. The presence of methanogens, methanotrophs, denitrifiers, and nitrifiers suggests microbial involvement in CH4 and N2O production and consumption. Remarkably, the dominance of Cyanobacteria in the heartwood microbiome (with the relative abundance of 97.5 ± 0.6 % for KO and 99.1 ± 0.2 % for SA) implies roles in carbon and nitrogen fixation for mangroves coping with nitrogen limitation in coastal wetlands, and possibly in CH4 production. Although the present study has limitations in sampling duration and area, it highlights the significant role of tree stems in GHG emissions which is crucial for a holistic evaluation of the global carbon sequestration capability of mangrove ecosystems. Future research should broaden spatial and temporal scales to enhance the accuracy of upscaling tree stem gas fluxes to the mangrove ecosystem level.

Impacts of rice terrace abandonment on soil ecosystem multifunctionality: Insights into reduced microbial diversity and exacerbated nitrogen limitation

Soil ecosystem multifunctionality (EMF) reflects the ability of soils to perform multiple ecological functions, and enzyme stoichiometry indicates microbial involvement in ecosystem nutrient cycling and energy balance. However, it remains unclear how the prevalence of terrace abandonment drives soil EMF and its relationship with microbial nutrient limitations. Soil samples were taken from rice terraces (RT), as well as from dry land (DLT) and forest land (FLT) formed after abandonment, and soil profiles were excavated to a depth of 0–120 cm. It was found that the soil EMF decreased significantly by 144.84% and 142.03%, respectively, in the DLT and FLT compared to RT. Soil EMF was not significantly different between DLT and FLT, and individual soil ecosystem functions were more similar. Microbial phosphorus limitation was observed in this study area, and the abandonment of RT resulted in a shift in microbial limitation from phosphorus to nitrogen, weakening microbial elemental homeostasis. Further analysis revealed that soil microbial diversity was the primary driver of decreased soil EMF, followed by enzyme stoichiometry. Therefore, soil microbial diversity may serve as a biological indicator of soil EMF quality. Overall, the abandonment of RT reduces soil EMF, but it is more beneficial to improve it by alleviating microbial nutrient limitation and fostering microbial diversity. Additionally, this study also highlights the significant impact of enzyme stoichiometry on soil EMF. More importantly, reducing the prevalence of abandoned terraces in mountainous and hilly areas contributes to sustainable soil resource management and cleaner agricultural production.

Grazing-driven shifts in soil bacterial community structure and function in a typical steppe are mediated by additional N inputs

Herbivore grazing and nitrogen (N) fertilization affect soil microbial diversity and community composition both in direct and indirect pathways (e.g., via alterations in soil microenvironment and plant communities); however, their combination effects are still largely unexplored. We carried out a field study to investigate how soil abiotic properties, plant community composition and functional traits altered soil bacterial community structure and function in response to a long-term herbivore grazing (17-year sheep grazing with four stocking rates) and anthropogenic N inputs (6-year N addition with four levels) experiment. We show that a high stocking rate of 8.7 sheep ha−1 (SR8.7) decreased soil bacterial α- and β-diversity, while α- and β-diversity showed hump-shaped and saddle-shaped responses, respectively, with increasing N addition rate, reaching tipping points at the N application rate of 10 g N m−2 year−1 (N10). The synergistic effects of grazing and N addition induced the highest soil bacterial α-diversity at SR2.7 with N10. The contrasting effects of grazing and N addition induced higher soil bacterial β-diversity at SR8.7 with N20. Plant factors (e.g., aboveground biomass of Stipa bungeana and community-weighted mean carbon [CWM_C]), edaphic factors (e.g., soil moisture, pH, NO3−-N, and C:nutrients ratios) and their interactions were the most significant factors affecting the diversity and community composition of bacteria. Our structure equation model (SEM) shows that grazing-induced negative effects on soil pH and plant community composition indirectly increased the β-diversity of soil bacteria, while grazing-induced decreased CWM_C had positive effects on bacterial α-diversity and community structure. However, N addition indirectly increased β-diversity of soil bacteria via changes in soil NO3−-N and plant community composition, while N addition had negative impacts on bacterial α-diversity and community structure via variations in CWM_C. The interaction of grazing and N addition increased the complexity and stability of the bacterial network. Based on the KEGG database, grazing and N addition could accelerate the soil functional potential of C and N cycling. Our findings suggest that N application at a rate of <10 g N m−2 year−1 with a stocking rate of <5.3 sheep ha−1 could maintain the development of soil bacteria in supporting the most important ecosystem functions and services. Complex responses of soil microbes to grazing and N addition indicate the need for deeper investigations of the impacts of global change on microbial involvement in biogeochemical cycles.

Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism.

The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. In diverse individuals, variations in the gut microbiota can result in differences in microbe-drug interactions, underscoring the importance of personalized approaches in pharmacotherapy. However, previous studies on drug metabolism in the gut microbiota have been hampered by technical limitations. Nowadays, advances in biotechnological tools, such as microbially derived metabolism screening and microbial gene editing, have provided a deeper insight into the mechanism of drug metabolism by gut microbiota, moving us toward personalized therapeutic interventions. Given this situation, our review summarizes recent advances in the study of gut-microbiota-mediated drug metabolism and showcases techniques and models developed to navigate the challenges posed by the microbial involvement in drug action. Therefore, we not only aim at understanding the complex interaction between the gut microbiota and drugs and outline the development of research techniques and models, but we also summarize the specific applications of new techniques and models in researching gut-microbiota-mediated drug metabolism, with the expectation of providing new insights on how to study drug metabolism by gut microbiota.

The coupled effect of sediment resuspension and microbiota on phosphorus release and transformation in a simulated aquatic ecosystem

Plant microbial involvement in phosphorus (P) release and transformation during resuspension events in bottom aquatic systems remains poorly understood. Laboratory experiments were used in this study to explore the release and transformation of P from sediments and the microbiota involved. Dissolved and labile P were obtained by high-resolution dialysis and the diffusive gradients in thin films (DGT) technique, respectively. The bacterial community was investigated using a scanning electron microscope and 16S rRNA high throughput sequencing technique. Finally, the diffusion fluxes dynamics of phosphorus were calculated using the DGT-induced fluxes in sediments and soils (DIFS) model. These results showed that sustained disturbance can balance dissolved P concentrations in the resuspension layer (overlying water) and enhance the stability of P transformation and release processes. Notably, the bacterial community within the deeper sediment layer (Below 10 mm sediment depth) significantly influences P interception. Acidobacteria and Neobacteria were identified as the key bacterial genera responsible for phosphorus adsorption of plant roots at speeds of 150 rad/min (R150). In addition, as the sediment depths increased, a slower decrease in R curves fitted with the DIFS model, which indicated a continuous resupply process from solid phase to pore water, especially below R150. This study provides theoretical references for managing shallow lakes with frequent sediment resuspension.

The influence of Helicobacter pylori, proton pump inhibitor, and obesity on the gastric microbiome in relation to gastric cancer development

Helicobacter pylori infection is still the main risk factor for the development of gastric cancer (GC). We explore the scientific evidence for the role of the gastric microbiome beyond Helicobacter pylori (H. pylori) in gastric carcinogenesis. The composition of the gastric microbiome in healthy individuals, in presence and absence of H. pylori infection, in proton pump inhibitor (PPI)-users, obese individuals, and GC patients was investigated. Possible mechanisms for microbial involvement, limitations of available research and options for future studies are provided.A common finding amongst studies was increased levels of Streptococcus, Prevotella, Neisseria, and Actinomyces in healthy individuals or those with H. pylori-negative gastritis. In PPI-users the risk for GC increases with the treatment duration, and the gastric microbiome shifts, with the most consistent increase in the genus Streptococcus. Similarly, in obese individuals, Streptococcus was the most abundant genus, with an increased risk for cardia GC. The genera Streptococcus, Lactobacillus and Prevotella were found to be more prominent in GC patients in multiple studies. Potential mechanisms of non-H. pylori microbiota contributing to GC are linked to lipopolysaccharide production, contribution to inflammatory pathways, and the formation of N-nitroso compounds and reactive oxygen species.In conclusion, the knowledge of the gastric microbiome in GC is mainly descriptive and based on sequencing of gastric mucosal samples. For a better mechanistic understanding of microbes in GC development, longitudinal cohorts including precancerous lesions, different regions in the stomach, and subtypes of GC, and gastric organoid models for diffuse and intestinal type GC should be employed.

Labile carbon inputs boost microbial contribution to legacy mercury reduction and emissions from industry-polluted soils

Soils is a crucial reservoir influencing mercury (Hg) emissions and soil-air exchange dynamics, partially modulated by microbial reducers aiding Hg reduction. Yet, the extent to which microbial engagements contribute to soil Hg volatilization remains largely unknown. Here, we characterized Hg-reducing bacterial communities in natural and anthropogenically perturbed soil environments and quantified their contribution to soil Hg(0) volatilization. Our results revealed distinct Hg-reducing bacterial compositions alongside elevated mercuric reductase (merA) gene abundance and diversity in soils adjacent to chemical factories compared to less-impacted ecosystems. Notably, solely industry-impacted soils exhibited increased merA gene abundance along Hg gradients, indicating microbial adaption to Hg selective pressure through quantitative changes in Hg reductase and genetic diversity. Microcosm studies demonstrated that glucose inputs boosted microbial involvement and induced 2–8 fold increments in cumulative Hg(0) volatilization in industry-impacted soils. Microbially-mediated Hg reduction contributed to 41.6% of soil Hg(0) volatilization in industry-impacted soils under 25% water-holding capacity and glucose input conditions over a 21-day incubation period. Alcaligenaceae, Moraxellaceae, Nitrosomonadaceae and Shewanellaceae were identified as potential contributors to Hg(0) volatilization in the soil. Collectively, our study provides novel insights into microbially-mediated Hg reduction and soil-air exchange processes, with important implications for risk assessment and management of industrial Hg-contaminated soils.

Lesional skin of seborrheic dermatitis patients is characterized by skin barrier dysfunction and correlating alterations in the stratum corneum ceramide composition.

Seborrheic dermatitis (SD) is a chronic inflammatory skin disease characterized by erythematous papulosquamous lesions in sebum rich areas such as the face and scalp. Its pathogenesis appears multifactorial with a disbalanced immune system, Malassezia driven microbial involvement and skin barrier perturbations. Microbial involvement has been well described in SD, but skin barrier involvement remains to be properly elucidated. To determine whether barrier impairment is a critical factor of inflammation in SD alongside microbial dysbiosis, a cross-sectional study was performed in 37 patients with mild-to-moderate facial SD. Their lesional and non-lesional skin was comprehensively and non-invasively assessed with standardized 2D-photography, optical coherence tomography (OCT), microbial profiling including Malassezia species identification, functional skin barrier assessments and ceramide profiling. The presence of inflammation was established through significant increases in erythema, epidermal thickness, vascularization and superficial roughness in lesional skin compared to non-lesional skin. Lesional skin showed a perturbed skin barrier with an underlying skewed ceramide subclass composition, impaired chain elongation and increased chain unsaturation. Changes in ceramide composition correlated with barrier impairment indicating interdependency of the functional barrier and ceramide composition. Lesional skin showed significantly increased Staphylococcus and decreased Cutibacterium abundances but similar Malassezia abundances and mycobial composition compared to non-lesional skin. Principal component analysis highlighted barrier properties as main discriminating features. To conclude, SD is associated with skin barrier dysfunction and changes in the ceramide composition. No significant differences in the abundance of Malassezia were observed. Restoring the cutaneous barrier might be a valid therapeutic approach in the treatment of facial SD.