Microbial Activity Research Articles

Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections

Preoperative identification of causal organism(s) is crucial for effective prosthetic joint infection treatment. Herein, we explore the clinical application of a novel metatranscriptomic (MT) workflow, CSI-Dx, to detect pathogens associated with prosthetic joint infection. MT provides insight into transcriptionally active microbes, overcoming limitations of culture-based and available molecular methods. This study included 340 human synovial fluid specimens subjected to CSI-Dx and traditional culture-based methods. Exploratory analyses were conducted to determine sensitivity and specificity of CSI-Dx for detecting clinically-relevant taxa. Our findings provide insights into the active microbial community composition of synovial fluid from arthroplasty patients and demonstrate the potential clinical utility of CSI-Dx for aiding prosthetic joint infection diagnosis. This approach offers potential for improved sensitivity and acceptable specificity compared to synovial fluid culture, enabling detection of culturable and non-culturable microorganisms. Furthermore, CSI-Dx provides valuable information on antimicrobial resistance gene expression. While further optimization is needed, integrating metatranscriptomic technologies like CSI-Dx into routine clinical practice can revolutionize prosthetic joint infection diagnosis by offering a comprehensive and active snapshot of associated pathogens.

Synergistic impact of tank mixing pendimethalin and pyroxasulfone on soil enzymatic and microbial dynamics.

A field experiment was carried out during the Rabi 2022-23 at Punjab Agricultural University, Ludhiana to evaluate the effect of pyroxasulfone and pendimethalin on soil enzymatic and microbial activities when applied individually or as a tank mix combination. The experiment employed a factorial randomized complete block design in triplicate encompassing 16 treatments. Control soils exhibited a continuous increase in enzymatic and microbial activities over time. In herbicide-treated plots, a highly dose-dependent lag phase was observed in all enzymatic and microbial activities which gets shorter or disappear at higher application rates. Following the initial lag phase, inhibition in enzymatic and microbial activities was observed with higher inhibition in tank mix combination (90.7 to 99.1% up to 90days after herbicide application (DAA) followed by pendimethalin (77.3 to 92.9% up to 90 DAA) and pyroxasulfone (30.3 to 76.2% up to 45 DAA). After initial inhibition, enzymatic and microbial activities increased at harvest. Principal component analysis (PCA) revealed that dehydrogenase activity among soil enzymes and bacteria among microbial populations were more sensitive to studied herbicides. Based on the values of the Integrated Biomarker Response (IBRv2), pendimethalin had a greater impact on soil activities than pyroxasulfone, and their combined application exhibited a synergistic effect.

In vitro and In Silico Molecular Modeling Studies of Newly Synthesized Pyrrole Derivatives for their Antimicrobial and Anticancer Properties

Background: Pyrroles are biologically active scaffolds that can have a number of different effects. They also have unique pharmacophores inside their ring system that make it easier to make molecules that are more active. Significantly, in the past ten years, research has been conducted on the anti-bacterial properties, with a particular emphasis on drug-resistant Gram-positive and Gram-negative pathogens such as mycobacteria. Additionally, scaffolds based on pyrroles were utilized in the production of anti-tumor medicines that function by modulating or suppressing genes. Objective: This research aimed to create new pyrrole derivatives by chemical means and evaluate their antimicrobial and anticancer properties. Methods: By reacting diverse 1H-pyrrole-2-carbohydrazide derivatives with benzaldehyde under normal conditions, a number of pyrrole variations were created. IR, mass spectroscopy, NMR, and elemental analysis were used to characterize the synthesized compounds. The serial dilution method was used to assess antimicrobial activity, along with a molecular docking study against the enzyme α-topoisomerase II (α-Topo II), which effectively controls the topology of DNA. This enzyme is strongly expressed in rapidly dividing cells and is crucial for transcription, replication, and chromosome structure. Pyrrole and its synthetic derivatives are known to exhibit strong anticancer activity by specifically targeting α-Topo II, which has led multiple researchers to investigate α-Topo II inhibitors as potential anticancer medicines. Consequently, designing pyrroline derivatives is interesting since the succinimide portion of the joined heteroaromatic molecule can selectively engage with the ATP binding pocket via the hydrogen bond network. Newer synthesized compounds were also docked via Schrodinger 2022-4 into the active pocket of the three-dimensional crystallographic structure of the ATP site of human topoisomerase IIα (htopo IIα) (PDB ID: 1zxm). Results: Among the newly synthesized pyrrole derivatives, compounds demonstrated significant anti- microbial activity. In addition, the AutoDock Vina application was used to perform in-silico docking computations. Compounds 1a and 1h were found to have a stronger antiproliferative effect than compounds against MCF-07 breast cancer cell linen our study, ligands 1a and 1b exhibited better binding energies of -5.049 and -5.035 kcal/mol, respectively. Most of the synthesized pyrrole derivatives showed promising antiproliferative effects; however, further in vivo investigations are needed to confirm or refute these results. Conclusion: The results of this investigation show that pyrrole derivatives have the potential to be effective antimicrobial and anticancer agents. While resolving safety issues, the structural alterations carried out in this study enhanced the compounds' medicinal capabilities. To clarify the underlying mechanisms of action and enhance the pharmacological characteristics of these new pyrrole derivatives, further research is necessary.

Improvement of the safety of artisanal Spanish fermented sausages: Spotlight on the role of bacteriocinogenic Lactiplantibacillus paraplantarum against a Companilactobacillus alimentarius histaminogenic strain

Biogenic amines (BA) in fermented sausages result from amino acid decarboxylation by microbial activity, either from technological or spoilage bacteria. Certain lactic acid bacteria typically found in fermented sausages are characterised for their ability to produce BA, especially histamine and tyramine. On the other hand, the bacteriocinogenic strain Lactiplantibacillus paraplantarum BPF2, isolated from a Spanish spontaneously dry-fermented sausages, has been characterized by good technological properties, production of leucocin K with antimicrobial activity against Listeria monocytogenes and ability to reduce the accumulation of BA in the final products. The antagonistic activity of leucocin K bacteriocin was tested in vitro against Companilactobacillus alimentarius SE14 (histamine producer), Enterococcus faecalis EF37 (tyramine producer), and L. monocytogenes Scott A. The inhibition of Comp. alimentarius SE14 by Lpl. paraplantarum BPF2 was assessed in traditional Spanish fermented sausages obtained in pilot plant, and chemico-physical parameters, microbial counts, and BA accumulation were monitored during fermentation and ripening. Leucocin K produced by Lpl. paraplantarum BPF2 was active in vitro against Comp. alimentarius SE14 and L. monocytogenes but was ineffective against E. faecalis EF37. The inoculation of the strain BPF2 as starter culture did not affect the expected chemico-physical (pH and colour) and microbial characteristics of the dry-fermented sausages. On the other hand, this strain was effective to significantly reduce the accumulation of histamine produced by the strain SE14, as well as putrescine and cadaverine. These findings demonstrated the relevant role of bacteriocin-producing strains as bio-protective starter cultures in improving the safety and quality of fermented meat products.

Mechanisms of Irrigation Water Levels on Nitrogen Transformation and Microbial Activity in Paddy Fields

Nitrogen is a vital nutrient for rice growth; however, its inefficient use often results in nutrient loss, environmental degradation, and the emission of greenhouse gases. In this study, a rice paddy simulation was conducted under different water levels (1–4 cm), incorporating a comprehensive analysis of nitrogen dynamics, environmental factors, and microbial communities to evaluate the impact of water levels on nitrogen concentrations and microbial composition. The results indicated that the water level had a greater impact on nitrogen concentrations in surface water than in soil water. Compared to low water level conditions (1 cm), the average concentrations of ammonium nitrogen, nitrate nitrogen, and nitrite nitrogen in surface water under 2–4 cm water levels decreased by approximately 53.8%, 36.7%, and 78.9%, respectively. Water levels also influenced the microbial composition and nitrogen cycling in paddy soil, with lower water levels promoting aerobic processes such as nitrification, while higher water levels facilitated anaerobic processes such as denitrification and dissimilatory nitrate reduction to ammonium. Correspondingly, microbial composition shifted, with aerobic bacteria predominating in shallow water conditions and anaerobic bacteria flourishing under deeper water. These findings suggest that optimized water management, particularly through shallow irrigation, may mitigate nitrogen loss and improve nitrogen use efficiency. Nevertheless, additional field studies are necessary to validate these results and explore their interaction with other agricultural practices.

Differences in microbial communities among different types of zaopei and their effects on quality and flavor of baijiu

Three types of zaopei (fermented grain) of xiaoqu light-flavor baijiu (XQZP), daqu light-flavor baijiu (DQZP), and strong-flavor baijiu (SFZP) at the end of fermentation and their dominant lactic acid bacteria were systematically compared and analyzed in this study. The results showed that these three types of zaopei differed significantly in acidity, reducing sugar content, and ethanol content, and that the main factors influencing their microbial community were acidity and lactic acid. The diversity and contents of flavor substances were significantly higher in SFZP than in DQZP and XQZP. Additionally, there was a strong correlation between dominant lactic acid bacteria and flavor substances in all three zaopei, but the correlation between fungi and flavor substances was higher than that between bacteria and flavor substances. Differential gene analysis revealed that the microbial activities followed the order of SFZP > DQZP > XQZP. The KEGG enrichment analysis indicated that the differential genes from different zaopei were enriched in different metabolic pathways. Furthermore, various microorganisms in 3 types of zaopei contained different functional genes, of which fungi mainly contained genes responsible for the synthesis of ethanol and acetic acid, while lactic acid bacteria mainly contained genes responsible for the synthesis of lactic acid. In XQZP, L. helveticus was dominant lactic acid bacteria prominent in acetic acid tolerance and lactic acid production; in DQZP, L. acetotolerans was remarkable in its tolerance to lactic acid, acetic acid, ethanol and lactic acid production; and in SFZP, A. jinshanensis was superior in acetic acid tolerance and production. Taken together, this study reveals the mechanism underlying flavor differences among three types of baijiu and provides valuable references for the development and utilization of baijiu microbial resources.

Jivamrit as a Sustainable Approach: A Review of Natural Farming and Future Agriculture.

Green Revolution aims to boost food production and feed millions of Indians, but it also has negative effects on agriculture and society's health. Natural manures like cow dung and cow urine can counteract the adverse effects of inorganic fertilizer on soil along with improving physicochemical qualities, maintaining the soil quality, and increasing crop output. Zero Budget Natural Farming (ZBNF) formulations like Jivamrit promote soil health and microbial activities and are an excellent source of macronutrients, other micronutrients needed for plant growth, plus adds beneficial microbes, nitrogen (N2), phosphorus (P), potassium (K), and natural carbon (C). Further, conventional agricultural methods, like monocropping and heavy tillage, can damage soil bacteria which contributes to sustainable agriculture through nitrogen fixation, siderophore synthesis and nutrient absorption. A sustainable agricultural system is resource-efficient, socially and commercially competitive, ecologically sound, and supportive of society. Jivamrit, a natural organic manure, is gaining interest due to concerns about the sustainability of input-intensive agriculture systems. It promotes crop growth, quality, and yield, enhances soil pH, population, and activity of beneficial microorganisms, and helps with nitrogen fixation, phosphate solubili-zation, and easy decomposition. Long-term use of Jivamrit, may disrupt soil microbial balance, may leading to overpopulation of certain species. The current review on the Jivamrit emphasizes on the biological and chemical characterization and its significance to the agriculture.

Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems.

Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)-cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.

Fabrication of Bio-Based Composite Materials forAntimicrobial Cotton Fabric With Microbial Anti-Adhesive Activity.

The development of multifunctional cotton fabrics that are stain-resistant, antimicrobial, and easy to clean has sparked scientific interest as well as practical usefulness, owing to its medical and healthcare applications. The purpose of this study was to fabricate self-cleaning and antimicrobial cotton for final use by soaking the cotton fabric in nonfluorinated hybrid formulations based on quaternary chitosan-silane using the sol-gel process. The fluorine-free cotton fabric demonstrated high self-cleaning behavior and outstanding bacterial killing efficacy against E. coli and S. aureus bacteria, without altering the desired textile properties of cotton fabric. Remarkably, cotton textiles using the hybrid formulations HTACC-VTES (N-(2-hydroxy)propyl-3-trimethylammonium chitosan chloride-vinyltriethoxy silane) and TMCC-VTES (N, N, N-trimethyl chitosan chloride-vinyltriethoxy silane) demonstrated promising water contact angles of 147° and 142° respectively, indicating a move toward superhydrophobicity. In FTIR spectra, both treated cotton textiles had an absorption peak at 1208 cm-1 (SiOC bending), indicating a stronger interaction between silane binding agents and the cotton substrate. The treated cotton fabric with desirable features retains its stability and endurance after 12 cycles of washing for antibacterial tests and 15 cycles for wettability tests. The manufactured cotton fabric has several potential applications, such as in personal hygiene items and medical applications.

Modification of Portland cement matrix with diethyldithiocarbamate for technetium immobilization

The paper considers the effect of sodium diethyldithiocarbamate (SDDC) addition on the immobilization of technetium in a Portland cement matrix. The leaching process was evaluated in a model solution that simulated the conditions of the future radioactive waste (RW) storage site at the Yeniseisky site. The results demonstrated that the addition of 1.0 wt % SDDC to the cement composite increased the incorporation of immobilized technetium into the cement matrix by 35% in comparison to the blank sample. Furthermore, the retention of technetium in the cement matrix was observed to be enhanced, with a retention of up to 90% observed on the 200th day of the experiment. Resulting materials fulfill the necessary technical characteristics for use as a matrix and engineered safety barrier in the concept of deep RW disposal. The addition of SDDC into cement results in microbial respiratory activity decreasing. In order to evaluate the mechanisms of technetium immobilization, the structure of the technetium compound with diethyldithiocarbamate (DDC) [Tc(C5H10NS2)4]TcO4 is described for the first time. This compound contains a Tc(V) atom which coordinates four diethyldithiocarbamate C5H10NS2 moieties through eight sulfur atoms to form a complex cation. The addition of SDDC in cement is presumed to result in a cascade of disproportionation reactions and the formation of stable Tc(IV) compounds, as it was evidenced by XANES spectroscopy.

Exploring the Relationship Between Biochar Pore Structure and Microbial Community Composition in Promoting Tobacco Growth.

The potential benefits of biochar, a carbon-rich substance derived from biomass, for enhancing agricultural yield and soil health have drawn increasing interest. Nevertheless, owing to the lack of specialized studies, the role of its poly-spatial structure in the success of fostering plant growth remains unclear. This study aimed to assess the effects of various biochar pore shapes on tobacco growth and the underlying microbiological processes. Three pyrolysis temperatures (250 °C, 400 °C, and 550 °C) were used to produce biochar from tobacco stems, resulting in different pore structures (T3 > T2 > T1). We then used BET-specific surface area (BET), t.Plot micropore specific surface area (t.Plot), mesopore specific surface area (MSSA), specific pore volume (SPV), average pore size (AP), and mesopore pore volume (MPV) measurements to evaluate the effects of these biochars on tobacco growth and biomass accumulation, and microbial analyses were performed to investigate the underlying mechanisms. When applied to plants, biochar increased their growth compared to untreated controls. The most notable improvement in tobacco growth was observed in the biochar produced at 400 °C (T3), which possessed the largest and most advantageous pore structure among all treatments. Further studies demonstrated that biochars with greater specific surface areas (BET, t.Plot, and MSSA) positively altered the abundance of key microbial taxa (e.g., Stenotrophobacter, Ensifer, Claroideoglomus) and community composition, thereby encouraging plant development and biomass accumulation. Conversely, greater pore volumes (SPV, AP, and MPV) inhibited microbial activity and significantly affected growth and biomass accumulation. Structural equation modeling further demonstrated that the pore structure of biochar greatly affected plant growth by changing the relative abundance and community composition of soil microbes. Maximizing the benefits of biochar in stimulating plant growth and improving soil microbial communities depends on optimizing the material's pore structure, particularly by increasing the specific surface area. These findings will help expand the use of biochar in sustainable agriculture.

When are you measuring soil β‐glucosidase activities in cropping systems?

AbstractIn situ soil respiration is driven by annual patterns of temperature and soil moisture, but what about extracellular enzyme activities responsible for depolymerizing soil organic matter? We conducted biweekly measurements of potential soil β‐glucosidase activities during a 4‐month period from March soil thawing through July in annually cropped field plots in eastern South Dakota. Our objective was to determine the best sampling time to resolve the effects of crop rotational diversity on soil microbial activities. Potential β‐glucosidase activities were elevated immediately following soil thaw, peaked in May, and declined to their lowest value in mid‐summer. Temperature and precipitation had no value in predicting enzyme activities; however, enzyme activities were affected by crop rotational diversity and responded to current crop and previous crop. These findings are pertinent to the use of soil extracellular enzymes in soil health assessments and as indicators of microbial substrate preference with implications for soil carbon stabilization.

Effect of integrated microbial fuel cell in a two-stage vertical flow constructed wetland for piggery wastewater treatment and resource recovery by photobioreactor

ABSTRACT This study developed a nature-based pilot-scale technology for simultaneous piggery WW treatment and resource recovery potential. The technology comprised a two-stage vertical flow constructed wetland (2-VFCW) integrated with a microbial fuel cell (MFC) and microalgal photobioreactor. The first and second stage was an unsaturated and saturated type, respectively. The bioelectricity generation was optimised by investigating the suitable electrode zonation, hydraulic retention time (HRT) and WW loading rate. The 2-VFCW-MFC-treated effluent was studied to grow microalgae for biomass production. The 2-VFCW-MFC showed better treatment efficiency than the 2-VFCW, possibly due to enhanced microbial activity on the electrode surface, leading to improved organic matter degradation and electron transfer to the cathode, enhancing NO3− and PO43− reduction. The 2-VFCW-MFC with electrode zonation of 20 cm (cathode) and 60 cm (anode) and HRT of 76 h, 48 min showed the highest open-circuit voltage of 291.83+13.53 mV and WW treatment efficiency. The highest algal biomass of 21,323.34+8,316.26 mg/L (wet weight) was produced at HRT of 96 h, then entered the death phase. Comparatively, the 2-VFCW-MFC showed higher WW treatment efficiency than 2-VFCW at 2 L/day by 23.24% COD, 27.43% TOC, 33.05% PO43−, 13.51% NO3−, 8.14% TN, except TAN (22.71%).

Plant and Microbial Carbon Are Important Drivers of Free‐Living Nitrogen Fixation in Tropical Forest Soils: A New Discovery of Carbon‐Driven Nitrogen Input

AbstractNitrogen (N) availability limits plant growth and soil carbon (C) sequestration in N‐limited ecosystems, however, plant and soil C feedback on the free‐living nitrogen fixation (FLNF) process is poorly understood. Moreover, whether this feedback is influenced by initial N availability in leguminous and non‐leguminous forest soils has not been clarified. Here, we found that the addition of plant‐ and microbial‐derived C significantly enhanced soil nitrogenase activity (13∼28%) and that microbial‐derived C had a more positive impact. These positive effects were attributed to the direct C‐energy supply (0.49∼0.84) rather than variations in soil microbial activity (−0.01∼0.21) and substrate resources (−0.45∼0.27). Long‐term N addition did not inhibit FLNF. C addition promoted FLNF in soils of the two forests, but the response rate was higher in the leguminous forest soils. Our study reveals that increased soil C availability can drive FLNF in tropical forests, enhancing our understanding of the soil C‐N coupling mechanism.

Microbial Activity of TiO2 NPs via Two Phases Synthesized by The Sol-Gel Method

TiO2 titanium dioxide nano phases of anatase and rutile were controlled only by temperature control of the calcination process, which is a cheap technical technique, and were organized using a sol-gel process, which involved mixing titanium tetrachloride (TiCl4) with ethanol as starting materials, as well as heating at various temperatures (650, 850 ℃ ). The fundamental properties of the as-prepared nanomaterials were investigated using Fourier transform infrared spectra (FTIR). The antibacterial activity of TiO2 was next investigated using two strains of E. coli, Staphylococcus aureus, and Streptococcus bacteria. The TiO2 structure has a dominating phase of 650 °C in addition to rutile at 850 °C, with an average volume of crystalline (D) of 21.9 nm for the anatase phase and 30.41 nm for the rutile phase. According to XRD data, the spherical shape of the rutile phase is clearly evident in the TEM of TiO2 NPs, the tetragonal shape is clearly seen in the anatase, and the calcination process had a major effect on the crystal size. According to FTIR analysis, the majority of peaks are seen between 400 and 700 cm-1 as a result of bending and oscillation lengthening. The studies demonstrated that TiO2, in both protease and rutile forms, is a highly efficient antibacterial that can be used as a self-cleaning exterior to exterior surfaces (windows) as well as in bio-penetration places like hospitals and medical clinics.

Enhanced removal of chiral emerging contaminants by an electroactive biofilter

50% of pharmaceuticals and 25% of herbicides used worldwide are chiral. Each enantiomer has a unique toxicity and biodegradation profile, affecting differently to organisms. Chirality plays a key role in the behavior of these emerging contaminants (ECs) in terms of their pharmacological or herbicidal activity, but this peculiarity is often overlooked in environmental research. The complexity of chiral ECs is underestimated, as the varying sensitivity of biological systems to enantiomers is rarely considered. Biofilters can promote the activity of specific microbial communities, facilitating the degradation of ECs, due to the greater interaction between water and microorganisms and their compact design. Here, we show that an electroactive biofilter can alter the chirality of drugs and herbicides in wastewater treatment, impacting their removal and toxicity. The electrochemical biofilter (BioeF) removed 80% of pharmaceuticals and 50–75% of herbicides, outperforming the conventional filter (ConF). BioeF also showed greater chiral alterations and lower ecotoxicity. This work provides the first evidence of a relationship between changes in contaminant chirality and detoxification capacity, enhanced by electroactive systems. The increased microbial activity observed in the BioeF suggests that bioelectrochemical systems offer a valuable advance for ECs removal and ecotoxicity reduction, addressing the environmental challenge posed by ECs.

Examining the effect of post-depositional processes on the preservation and identification of stone tool residues from temperate environments: An experimental approach.

Studying taphonomy is crucial for understanding how post-depositional processes impact archaeological remains. This knowledge is pivotal for accurately interpreting the archaeological record. Although taphonomy has a long tradition in archaeology, it is less developed in the analysis of stone tool residues compared to other subdisciplines. To address this gap, our study aims to further develop our understanding of the preservation potential of stone tool residues in temperate environments through actualist experiments. To achieve this, we develop a multidimensional experimental program that features the first biweekly monitoring of weathering processes on residues over a one-year cycle, aiming to understand the short-term effects of weathering immediately after tool discard. Additionally, the program involves the study of longer-term burial and weathering visual effects on different residue types within various previously unexplored depositional environments. This approach allows us to observe the visual effects of both weathering and burial processes and to improve our understanding of the different mechanisms involved in the diagenesis of stone tool residues. While known factors such as microbial activity and soil acidity play a primary role in residue decay, specific stone tool-related factors also prove important, underscoring the need to develop further a specific branch of taphonomy related to stone tool residues. Moreover, our results show that certain residue types may survive within these environments that are often considered as being hostile. A residue analysis of stone tools from temperate contexts may thus contribute unique data that can improve our understanding of past human behaviour. Future research with more diverse residue types and depositional conditions will permit further refinement of our understanding of how taphonomy affects residue preservation and enhance the reliability of residue identifications. As such, stone tool residue analysis will become firmly rooted within broader functional approaches to address how humans use stone tools and how this affects stone tool variability.

Lymphocystis viral disease impacts the diversity and functional profiles of the skin microbiome in gilthead seabream.

Lymphocystis viral disease (LVD) is a highly transmissible disease known to affect multiple fishes worldwide. Although this disease is usually benign, mortalities can occur in cases where infection is severe or secondary infection with bacterial pathogens and parasites occur. However, little is known about the bacterial dynamics of fish with LVD or what bacterial pathogens may be responsible for secondary infections. Here we assessed the effects of LVD on the skin microbiome of gilthead seabream by comparing 30 symptomatic, asymptomatic and recovered (three weeks after infection) fish using 16S rRNA high-throughput sequencing. Our results show that LVD is associated with significant changes in microbiome structure and function. Importantly, fish pathogens like Tenacibaculum maritimum and some Vibrio species increased their abundance. Moreover, microbial metabolic activities of the commensal microbiota that may confer some protection to fish were suppressed in diseased fish. After reducing fish cage density to treat symptoms and three weeks of recovery, the abundance of pathogens was significantly reduced and microbiome functionality was recovered, although community structure remained significantly different. These results show that LVD can severely disrupt the bacterial communities of the skin of the gilthead seabream, leading to an increase in bacterial pathogens responsible for relevant diseases in gilthead seabream farms.

Microbiomes-Plant Interactions and K-Humate Application for Salinity Stress Mitigation and Yield Enhancement in Wheat and Faba Bean in Egypt’s Northeastern Delta

Salinity, resulting from climate change and excessive mineral fertilization, burdens farmers and negatively impacts soil and water ecosystems in the Northeastern Nile Delta. Organic and biological approaches are crucial for addressing these issues. This study examined the effects of individual and combined inoculations with cyanobacteria, yeast, and Arbuscular Mycorrhizal Fungi (AMF), with or without K-Humate and reducing Nitrogen, phosphorus and potassium (NPK) mineral fertilizers application rates to crop quality of wheat and faba bean. In preliminary laboratory experiments, the interactive effects of these microbiomes on plant antioxidant and soil enzyme production were examined under salinity stress. Results showed that co-inoculation, especially with K-Humate, yielded superior outcomes compared to individual inoculations. These findings were validated by a field trial conducted in saline-alkaline soil in the Northeastern Nile Delta region. All biological treatments 25% of recommended doses, and enhancing salinity tolerance, increasing yield, and improving enhanced rhizosphere microbial activity, including soil enzyme activity, AMF colonization, spore density, and the total numbers of bacteria, cyanobacteria, and yeast. These effects were further amplified by K-Humate and were more pronounced with combined inoculations than with individual ones, leading to improved soil fertility and significant increases in both crop quantity and quality compared to control treatments. The triple treatment, combining cyanobacteria, yeast, and mycorrhizae in the presence of K-Humate while reducing the mineral NPK rate by 75%, achieved superior increases in the productivity of wheat grains and faba bean seeds, reaching 54.72% and 128.92%, respectively, compared to the 100% NPK mineral control. This treatment also significantly improved crop quality, with notable increases in nitrogen, potassium, phosphorus, and protein percentages in wheat grains and faba bean seeds. Microbiomes-interaction increased potassium uptake over sodium, enhancing the plant’s potassium/sodium ratio and improving salt stress tolerance. This approach reduces reliance on costly mineral fertilizers, enabling bio-organic farming in marginal lands, optimizing resource utilization, and preserving natural resources.

Mechanisms of heavy metal-induced rhizosphere changes and crop metabolic evolution: The role of carbon materials

To investigate the effects of modified carbon-based materials on soil environmental remediation and crop physiological regulation, this research relied on rice pots with lead (Pb) and cadmium (Cd) composite contamination. Dolomite, montmorillonite, attapulgite and sepiolite modified biochar with different doses have been developed to explore the mechanisms on heavy metal passivation, nutrient improvement, microbial activation, and crop growth. The results indicated that the modified materials effectively reduced heavy metal bioavailability and accumulation in plant tissues through adsorption complexation. Specifically, under montmorillonite and sepiolite modified treatments, the Grains-Pb content significantly decreased by 29.23–30.31% and 27.49–30.58%, compared to the control group (CK). Meantime, carbon-based materials increased available nutrient levels, providing a biological substrate for soil microorganisms metabolism. The content of ammonium nitrogen (NH4+-N) and available phosphorus (AP) in different proportions of montmorillonite modified biochar increased by 10.99–13.98% and 55.76–77.86%, respectively, compared to CK. Furthermore, sepiolite modified biochar enhanced bacterial community diversity, significantly improving the tolerance and resistance of bacterial communities such as Proteobacteria and Acidobacteria to heavy metals. Meanwhile, carbon-based materials enhanced community stability and network complexity, improving microbial stress resistance to adverse environments. In summary, montmorillonite and sepiolite modified biochar regulated microbial community interaction mechanisms by mitigating the physiological toxicity of heavy metals. This process enhanced soil available nutrients and ecological function stability, which had significant implications for improving crop growth and quality.