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Pectobacterium and Dickeya species belonging to the Soft Rot Pectobacteriaceae (SRP) are one of the most devastating phytopathogens. They degrade plant tissues by producing an arsenal of plant cell wall degrading enzymes. However, SRP-plant interactions are not restricted to the production of these "brute force" weapons. Additionally, these bacteria apply stealth behavior related to (1) manipulation of the host plant via induction of susceptible responses and (2) formation of heterogeneous populations with functionally specialized cells. Our review aims to summarize current knowledge on SRP-induced plant susceptible responses and on the heterogeneity of SRP populations. The review shows that SRP are capable of adjusting the host's hormonal balance, inducing host-mediated plant cell wall modification, promoting iron assimilation by the host, stimulating the accumulation of reactive oxygen species and host cell death, and activating the synthesis of secondary metabolites that are ineffective in limiting disease progression. By this means, SRP facilitate host plant susceptibility. During host colonization, SRP populations produce various functionally specialized cells adapted for enhanced virulence, increased resistance, motility, vegetative growth, or colonization of the vascular system. This enables SRP to perform self-contradictory tasks, which benefits a population's overall fitness in various environments, including host plants. Such stealthy tactical actions facilitate plant-SRP interactions and disease progression. • SRP manipulate the host plants by inducing susceptible responses. • SRP populations produce physiologically and functionally specialized cells. • Susceptible responses and population behavior determine the outcome of interaction. • Induced susceptibility and population behavior are targets for disease control. [ABSTRACT FROM AUTHOR]

The impact of thermal and non-thermal treatments on the quality of amora (Spondius pinnata) juice during refrigerated storage (4 ± 1 °C) for 30 days was investigated. Freshly prepared juices from amora fruits were thermosonicated at the frequency of 44 kHz for 30, 45 and 60 min at 40 °C and also pasteurised at 90 °C for 1 min. Changes in the quality parameters, such as, pH, total soluble solids, titratable acidity, total phenolic contents, total flavonoid contents. Antioxidant activity, ascorbic acid content, browning index, cloud values and microbial populations were checked periodically. The experimental results indicated a significant increase in total phenolic contents, total flavonoid contents, antioxidant activity and the sensorial properties of thermosonicated juices during storage their period when compared to fresh and thermally treated amora juices. Maximum reduction in the microbial populations was accomplished after thermal and thermosonication for 60 min treatments. The physicochemical properties of thermosonicated juices exhibited minimal changes in contrast to other samples. The prediction of the quality changes in thermosonicated juices during storage was carried out using an artificial neural network model. From this study thermosonication at 40 °C can be recommended as a substitute to thermal processing and it may be employed to amora juice production to decrease the microbial population and improve functional and sensorial properties. • Thermosonication significantly improved the functional properties of Amora juices. • Physicochemical properties of the juices were unaffected by thermosonication. • Thermosonication extended the shelf-life of Amora juice stored at 4 °C. • Modeling of quality changes in amora juices during storage using ANN approach. • Developed ANN-PNN model was effective to predict quality changes in amora juices. [ABSTRACT FROM AUTHOR]

The Persian Gulf is a transit point for a lot of crude oil at the international level. The purpose of this research is to compare two methods of biostimulation and bioaugmentation for degradation of sediments contaminated with crude oil in the Persian Gulf. In this research, six types of microcosms were designed (Sediments from Khark Island). Some indicators such as: the quantity of marine bacteria, enzyme activity (Catalase, Polyphenol oxidase, Dehydrogenase), biodiversity indices and the percentage of crude oil degradation were analyzed during different days (0, 20, 40, 60, 80, 100 and 120). The results of this research showed that the highest quantity of heterotrophic and crude oil-degrading bacteria was found in the sixth microcosm (SB). This microcosm represents a combination of two methods: bioaugmentation and biostimulation (3.9 × 106 CFU g−1). Following crude oil pollution, the activity of catalase and polyphenol oxidase increased and the dehydrogenase enzyme decreased. The bioaugmentation microcosm exhibited the highest activity of enzymes among all the microcosms studied. Predominant bacteria in each microcosm belonged to: Cellulosimicrobium, Shewanella, Alcanivorax and Cobetia. The highest degradation of crude oil is related to the Stimulation-Bioaugmentation microcosm (SB). The statistical results of this research proved that there is a significant relationship between the type of method chosen for biodegradation with the sampling time and the quantity of marine bacteria. The results of this research confirm that crude oil pollution in the Persian Gulf sediments can be reduced by choosing the proper bioremediation method. • The effect of crude oil pollution on sediments of the Persian Gulf was studied • Stimulation of sediment in each microcosm by mineral elements cause increase in marine microbial population. • The Best microcosm for degradation of crude oil was integrated microcosm of bioaugmentation and biostimulation. [ABSTRACT FROM AUTHOR]

Driving kombucha fermentation through microbial consortia remains based on scarce scientific elements, especially regarding the consumption of nitrogenous nutrients. This study aimed at analyzing quantitatively proteins and free amino nitrogen (FAN) concentrations, and qualitatively the soluble proteins profiles during a 12-day production process. The effect of microbial interactions was evaluated by comparing the growth of previously isolated major microorganisms in monoculture and cocultures to original kombucha. Protein and FAN relative concentrations kinetics depended on microbial compositions. These parameters were associated to less variations and a positive effect on total microbial population in original kombucha, underlining a complex yet better management of the nutrients. Analysis of extracellular proteins by electrophoresis showed the presence of a microbial 15 kDa fraction common to all cultures. In contrast, a 21 kDa protein fraction was associated with the presence of Acetobacter indonesiensis. Exploratory proteomics analysis revealed the presence of characteristic extracellular moonlighting proteins, originating from this acetic bacteria. Production of extracellular vesicles was successfully confirmed with the isolation and observation of vesicles in A. indonesiensis culture, as well as in kombucha. The results characterize the central role of microbial interactions on FAN consumption and open new perspectives on the function of the bacterial vesicles observed. • Free amino nitrogen supplied by sugared tea limits protein production in kombucha. • Microbial interactions in kombucha induce better nitrogen management and growth. • Acetobacter indonesiensis ' extracellular proteins include moonlighting proteins. • Extracellular vesicles are produced in kombucha and by A. indonesiensis. • Vesicles may take part in observed proteins secretion and positive interactive effects. [ABSTRACT FROM AUTHOR]

Microbial safety of fresh produce continues to be a major concern. Novel antimicrobial methods are needed to minimize the risk of contamination. This study investigated the antimicrobial efficacy of pulsed light (PL), a novel nisin-organic acid based antimicrobial wash (AW) and the synergy thereof in inactivating E. coli O157:H7 on Romaine lettuce. Treatment effects on background microbiota and produce quality during storage at 4 °C for 7 days was also investigated. A bacterial cocktail containing three outbreak strains of E. coli O157:H7 was used as inoculum. Lettuce leaves were spot inoculated on the surface before treating with PL (1–60 s), AW (2 min) or combinations of PL with AW. PL treatment for 10 s, equivalent to fluence dose of 10.5 J/cm2, was optimal and resulted in 2.3 log CFU/g reduction of E. coli O157:H7, while a 2 min AW treatment, provided a comparable pathogen reduction of 2.2 log CFU/g. Two possible treatment sequences of PL and AW combinations were investigated. For PL-AW combination, inoculated lettuce leaves were initially exposed to optimum PL dose followed by 2 min AW treatment, whereas for AW-PL combination, inoculated lettuce were subjected to 2 min AW treatment prior to 10 s PL treatment. Both combination treatments (PL-AW and AW-PL) resulted in synergistic inactivation as E. coli cells were not detectable after treatment, indicating >5 log pathogen reductions. Combination treatments significantly (P < 0.05) reduced spoilage microbial populations on Romaine lettuce and also hindered their growth in storage for 7 days. The firmness and visual quality appearance of lettuce were not significantly (P > 0.05) influenced due to combination treatments. Overall, the results reveal that PL and AW combination treatments can be implemented as a novel approach to enhance microbial safety, quality and shelf life of Romaine lettuce. [Display omitted] • Pulsed light and antimicrobial wash individually provided about 2 log reduction of E. coli O157:H7 on Romaine lettuce. • Combinations acted synergistically providing >5 log reductions of E. coli O157:H7. • Quality of lettuce was not impacted by the combined treatments. • Combined treatment method could potentially be used as an alternative to chlorine washing. [ABSTRACT FROM AUTHOR]

Heavy metals and metalloids (HMMs) inhibit the biodegradation of organic pollutants. The degree of inhibition depends not only on the concentration and bioavailability of HMMs but also on additional factors, such as environmental variables (e.g. , inorganic components, organic matter, pH, and redox potential), the nature of the metals, and microbial species. Based on the degradation pattern and metal concentrations causing half biodegradation rate reductions (RC50s), the inhibition of biodegradation was: Hg2+, As 2 O 3 > Cu2+, Cd2+, Pb2+, Cr3+ > Ni2+, Co2+ > Mn2+, Zn2+ > Fe3+. Four patterns were observed: inhibition increases with increasing metal concentration; low concentrations stimulate, while high concentrations inhibit; high concentrations inhibit less; and mild inhibition remains constant. In addition, metal ion mixtures have more complex inhibitory effects on the degradation of organic pollutants, which may be greater than, similar to, or less than that of individual HMMs. Finally, the inhibitory mechanism of HMMs on biodegradation is reviewed. HMMs generally have little impact on the biodegradation pathway of organic pollutants for bacterial strains. However, when pollutants are biodegraded by the community, HMMs may activate microbial populations harbouring different transformation pathways. HMMs can affect the biodegradation efficiency of organic pollutants by changing the surface properties of microbes, interfering with degradative enzymes, and interacting with general metabolism. [Display omitted] [ABSTRACT FROM AUTHOR]

Zeolite was shown to mitigate anaerobic digestion (AD) inhibition caused by several inhibitors such as long-chain fatty acids, ammonia, and phenolic compounds. In this paper, we verified the genericity of zeolite's mitigating effect against other types of inhibitors found in AD such as salts, antibiotics, and pesticides. The impacts of inhibitors and zeolite were assessed on AD performance and microbial dynamics. While sodium chloride and erythromycin reduced methane production rates by 34% and 32%, zeolite mitigated the inhibition and increased methane production rates by 72% and 75%, respectively, compared to conditions without zeolite in the presence of these two inhibitors. Noticeably, zeolite also enhanced methane production rate by 51% in the uninhibited control condition. Microbial community structure was analyzed at two representative dates corresponding to the hydrolysis/fermentation and methanogenesis stages through 16S rRNA gene sequencing. The microbial characteristics were further evidenced with common components analysis. Results revealed that sodium chloride and erythromycin inhibited AD by targeting distinct microbial populations, with more pronounced inhibitory effects during hydrolysis and VFAs degradation phases, respectively. Zeolite exhibited a generic effect on microbial populations in different degradation stages across all experimental conditions, ultimately contributing to the enhanced AD performance and mitigation of different inhibitions. Typically, hydrolytic and fermentative bacteria such as Cellulosilyticum , Sedimentibacter , and Clostridium sensu stricto 17, VFAs degraders such as Mesotoga , Syntrophomonas , and Syntrophobacter , and methanogens including Methanobacterium , Methanoculleus , and Methanosarcina were strongly favored by the presence of zeolite. These findings highlighted the promising use of zeolite in AD processes for inhibition mitigation in general. [Display omitted] • Zeolite enhanced CH 4 production rate by >70% under NaCl and erythromycin inhibitions. • Zeolite enhanced CH 4 production rate by 51% in uninhibited anaerobic digestion. • Marinilabiliaceae was resistant to NaCl inhibition and stimulated by zeolite. • Zeolite promoted Cellulosilyticum and Sedimentibacter in hydrolysis stage. • Zeolite promoted syntrophic bacteria Syntrophomonas and Syntrophobacter. [ABSTRACT FROM AUTHOR]

The efficient use of livestock and poultry manure waste has become a global challenge, with microorganisms playing an important role. To investigate the impact of novel ammonifying microorganism cultures (NAMC) on microbial community dynamics and carbon and nitrogen metabolism, five treatments [5% (v/w) sterilized distilled water, Amm-1, Amm-2, Amm-3, and Amm-4] were applied to cow manure compost. Inoculation with NAMC improved the structure of bacterial and fungal communities, enriched the populations of the functional microorganisms, enhanced the role of specific microorganisms, and promoted the formation of tight modularity within the microbial network. Further functional predictions indicated a significant increase in both carbon metabolism (CMB) and nitrogen metabolism (NMB). During the thermophilic phase, inoculated NAMC treatments boosted carbon metabolism annotation by 10.55%–33.87% and nitrogen metabolism annotation by 26.69%–63.11. Structural equation modeling supported the NAMC-mediated enhancement of NMB and CMB. In conclusion, NAMC inoculation, particularly with Amm-4, enhanced the synergistic interaction between bacteria and fungi. This collaboration promoted enzymatic catabolic and synthetic processes, resultng in positive feedback loops with the endogenous microbial community. Understanding these mechanisms not only unravels how ammonifying microorganisms influence microbial communities but also paves the way for the development of the composting industry and global waste management practices. [Display omitted] • Novel ammonifying microorganism cultures (NAMC) increased the stability of the composting • Inoculation with NAMC improved the structure of bacterial and fungal communities. • Inoculation with NAMC enhanced the complementary effects of bacteria and fungi in compost • Inoculated NAMC promoted carbon metabolism and nitrogen metabolism in composting. [ABSTRACT FROM AUTHOR]

In near-natural basins, zooplankton are key hubs for maintaining aquatic food webs and organic matter cycles. However, the spatial patterns and drivers of zooplankton in streams are poorly understood. This study registered 165 species of zooplankton from 147 sampling sites (Protozoa, Rotifers, Cladocera and Copepods), integrating multiple dimensions (i.e., taxonomic, functional, and phylogenetic) and components (i.e., total, turnover, and nestedness) of α and β diversity. This study aims to reveal spatial patterns, mechanisms, correlations, and relative contribution of abiotic factors (i.e., local environment, geo-climatic, land use, and spatial factors) through spatial interpolation (ordinary kriging), mantel test, and variance partitioning analysis (VPA). The study found that α diversity is concentrated in the north, while β diversity is more in the west, which may be affected by typical habitat, hydrological dynamics and underlying mechanisms. Taxonomic and phylogenetic β diversity is dominated by turnover, and metacommunity heterogeneity is the result of substitution of species and phylogeny along environmental spatial gradients. Taxonomic and phylogenetic β diversity were strongly correlated (r from 0.91 to 0.95), mainly explained by historical/spatial isolation processes, community composition, generation time, and reproductive characteristics, and this correlation provides surrogate information for freshwater conservation priorities. In addition, spatial factors affect functional and phylogenetic α diversity (26%, 28%), and environmental filtering and spatial processes combine to drive taxonomic α diversity (10%) and phylogenetic β diversity (11%). Studies suggest that spatial factors are key to controlling the community structure of zooplankton assemblages in near-natural streams, and that the relative role of local environments may depend on the dispersal capacity of species. In terms of diversity conservation, sites with high variation in uniqueness should be protected (i) with a focus on the western part of the thousand islands lake catchment and (ii) increasing effective dispersal between communities to facilitate genetic and food chain transmission. [Display omitted] • Unravelling the relative roles of abiotic factors on zooplankton α and β diversity. • Phylogenetic and taxonomic β diversity are highly correlated. • Spatial factors strongly affect phylogenetic and functional α diversity. • Environmental filtering and spatial processes co-drive phylogenetic β diversity. • Zooplankton diversity protection should focus on the western TIL catchment. [ABSTRACT FROM AUTHOR]

The anaerobic digestion (AD) process has become significant for its capability to convert organic wastewater into biogas, a valuable energy source. Excessive acetic acid accumulation in the anaerobic digester can inhibit methanogens, ultimately leading to the deterioration of process performance. Herein, the effect of magnetite particles (MP) as an enhancer on the methanogenic degradation of highly-concentrated acetate (6 g COD/L) was examined through long-term sequential AD batch tests. Bioreactors with (AM) and without (AO) MP were compared. AO experienced inhibition and its methane production rate (q m) converged to 0.45 L CH 4 /g VSS/d after 10 sequential batches (AO10, the 10th batch in a series of the sequential batch tests conducted using bioreactors without MP addition). In contrast, AM achieved 3–425% higher q m through the sequential batches, indicating that MP could counteract the inhibition caused by the highly-concentrated acetate. MP addition to inhibited bioreactors (AO10) successfully restored them, achieving q m of 1.53 L CH 4 /g VSS/d, 3.4 times increase from AO10 after 8 days lag time, validating its potential as a recovery strategy for inhibited digesters with acetate accumulation. AM exhibited higher microbial populations (1.8–3.8 times) and intracellular activity (9.3 times) compared to AO. MP enriched Methanosaeta , Peptoclostridium , Paraclostridium , OPB41, and genes related to direct interspecies electron transfer and acetate oxidation, potentially driving the improvement of q m through MP-mediated methanogenesis. These findings demonstrated the potential of MP supplementation as an effective strategy to accelerate acetate-utilizing methanogenesis and restore an inhibited anaerobic digester with high acetate accumulation. [Display omitted] • Magnetite particles MP accelerated CH 4 production from highly concentrated acetate. • MP promoted methanogenic degradation of the concentrated acetate by 3–425% in rate. • Inhibited bioreactor was successfully recovered by MP addition with 8d of lag time. • MP stimulated growth and intracellular activity of methanogenic consortia. • Methanosaeta , Paraclostridium and OPB41 contributed to MP -mediated methanogenesis. [ABSTRACT FROM AUTHOR]

The biofilm sequencing batch reactor (BSBR) technique has been deployed in the laboratory to enrich phosphorus from simulated wastewater, but it is still not clear what its performance will be when real world sewage is used. In this work, the effluent from the multi-stage anoxic-oxic (AO) activated sludge process at a sewage plant was used as the feed water for a BSBR pilot system, which had three reactors operating at different levels of dissolved oxygen (DO). The phosphorus adsorption and release, the biofilm growth, and the extracellular polymeric substances (EPS) components and contents were examined. The microbial communities and the signaling molecules N -acyl- l -homoserine lactones (AHLs) were also analyzed. Gratifyingly, the BSBR process successfully processed the treated sewage, and the biofilm developed phosphorus accumulation capability within 40 days. After entering stable operation, the system concentrated phosphate from 2.59 ± 0.77 mg/L in the influent to as much as 81.64 mg/L in the recovery liquid. Sludge discharge had profound impacts on all aspects of BSBR, and it was carried out successfully when the phosphorus absorption capacity of the biofilm alone was comparable to that of the reactor containing the activated sludge. Shortly after the sludge discharge, the phosphate concentration of the recovery liquid surged from 50 to 140 mg/L, the biofilm thickness grew from 20.56 to 67.32 μm, and the diversity of the microbial population plunged. Sludge discharge stimulated Candidatus competibacter to produce a large amount of AHLs, which was key in culturing the biofilm. Among the AHLs, both C10-HSL and 3OC12-HSL were significantly positively correlated with EPS and the abundance of Candidatus competibacter. The current results demonstrated BSBR as a viable option to enrich phosphorus from real world sewage with low phosphorus content and fluctuating chemistry. The mechanistic explorations also provided theoretical guidance for cultivating phosphorus-accumulating biofilms. [Display omitted] • BSBR was launched successfully using real world sewage with low and fluctuating P. • Phosphate enrichment from 2.59 ± 0.77 to as much as 81.64 mg/L was realized. • DO had opposite impacts on P metabolism before and after sludge discharge. • The P removal capacity of the biofilm can determine the timing of sludge discharge. • Sludge discharge stimulated Candidatus competibacter to produce AHLs. [ABSTRACT FROM AUTHOR]

Plant-based meat analogues have gained significant popularity in recent years. Different from ground beef, plant-based meat analogues are derived from a broader range of raw ingredients and undergo more complex manufacturing processes. In this study, 16S rRNA and internal transcribed spacer sequencing techniques were employed to profile and compare the microbial populations present in ground beef (GB), soy-, and pea-based meat analogues (SBM and PBM), and their changes during refrigeration (4 °C) and ambient temperature storage (22 °C). The sequencing results illustrated remarkable microbial differences among GB, PBM, and SBM. Pseudomonas , Brochothrix , and Lactobacillus were the top dominate bacterial genera, Cladosporium, Candida, and Komagataella were the top dominant fungal genera present in GB, PBM, and SBM respectively. At the end of storage, dominant microorganisms present in meat samples, in general, were determined by meat types and storage temperatures, except for SBM. For example, in PBM, refrigeration favored the proliferation of Leuconostoc , while Lactococcus emerged as the primary genus at ambient temperature. For SBM, Lactobacillus and Komagataella were dominate bacterial and fungal species regardless of the storage temperatures. These findings provide crucial information for the development of preventive measures to ensure the microbial safety and quality of plant-based meat analogues. • Ground beef has the highest initial microbial diversity than plant-based meat. • Dominant spoilage microbes are determined by meat types and storage conditions. • Soy-based meat analogues have lower microbial diversity than pea-based meat. • Lactic acid bacteria are the main spoilage bacteria of plant-based meat analogues. • Komagetaella was one major fungal taxa in plant-based meat analogues. [ABSTRACT FROM AUTHOR]

Postharvest management strategies like cutting height and anaerobic fermentation may affect the microbial risk of vegetables. This study evaluated the effects of cutting height and storage length on the fermentation characteristics, microbial diversity, co-occurrence networks, potential functionality and pathogenic risk of sweet sorghum stem (SSS). Fresh SSS harvested at two cutting heights (15 cm, F 15 ; 45 cm, F 45) was spontaneously fermented (S 15 and S 45) for 2, 4, 8, 16, 32 and 64 days. Decreasing the cutting height of SSS increased the dry matter, water-soluble carbohydrate content as well as Acinetobacter (23.0% vs. 44.9%) and Klebsiella (1.84% vs. 6.58%) proportion but decreased the crude protein content (P < 0.05). After fermentation, both cutting heights presented desirable fermentation. Anaerobic fermentation promoted the Glycolysis pathway (0.009 vs. 0.018) and related enzymes (l -lactate dehydrogenase, etc.) associated with lactate synthesis, but suppressed the degradation pathways of valine, leucine, isoleucine (0.011 vs. 0.003) and lysine (0.008 vs. 0.002). In microbial phenotype analysis, although F 15 had higher proportions of 'Potentially Pathogenic' than F 45 , this undesirable phenotype declined to negligible levels via fermentation. These results concluded that, for SSS, concerns about the risk of microbial contamination and pathogens from low cutting height can be dispelled by well fermentation. • Microbial succession was studied from fresh to fermented sweet stalk. • Low cutting height increased the risk of pathogenic contamination. • Sequencing showed potential probiotics were dominant in all fermented materials. • Spontaneous fermentation dispelled microbial risk from low mowing heights. [ABSTRACT FROM AUTHOR]

The uterine endometrial surface of bovines is in constant exposureconstantly exposed with to a multitude ofmany microbial populations that changes throughout the post-partum phase in terms of complexity and dynamics. These microbes contribute to the host pathology, leading to severe economic losses along withnd reproductive capabilities. The basic primary interface that occurs between the internal tissues of the body of the hostbetween the host body's internal tissues and the microbes is the endometrial surface of the uterus. As a result of the infinite pathogenic population, there is always a danger for the opportunistic organisms to attack. Therefore, it is paramount that any interactions, especially microbial microbes with the endometrial surface, are regulated by the host cells. However, the inflammatory response as the defense mechanism contributes a pivotal roleis pivotal in host immunity and pathology. The inflammatory cascade and pathways are important essential to eliminate this clinical problem. In this review, we will discuss and explain how the inflammation and the various components of the immune system play their role in host pathology and therapeutic strategies, taking into account the interface between the host and the microbes on the surface of the endometrium. This review is also instrumental in further explanation of inflammatory uterine disease by discussing the response of inflammation to external insult. • Potential targets of immune cells for the treatment of endometritis. • Therapeutic targeting of EM for endometritis treatment. • Function of neutrophils (PMC) in endometritis. • The role of microRNA in inflammation of uterus. • Targeting uterine pathogens for endometritis treatment. [ABSTRACT FROM AUTHOR]

The study aimed to determine the optimal ratio for the mixture of forage cactus and corn stover silage, emphasizing the evaluation of fermentative profile, microbial populations, dry matter losses, chemical composition, and aerobic stability. A completely randomized design with four treatments and five replications was employed in this study. Treatments included varying proportions of forage cactus in corn stover at ensiling (0%, 10%, 20%, and 40% of fresh matter). After a 100-day fermentation period, the assayed variables underwent regression analysis. Forage cactus inclusion led to linear dry matter and ether extract reductions, with crude protein showing a negative quadratic effect (p < 0.05). The pH and water-soluble carbohydrates exhibited negative quadratic effects with the increasing proportion of forage cactus (p < 0.05). Lactic and acetic acids exhibited quadratic effects, reaching their peaks at approximately 20% forage cactus (p < 0.05). Lactic acid bacteria demonstrated a linear decrease, while yeasts/molds displayed a negative quadratic effect (p < 0.05). Dry matter losses followed a quadratic pattern, with the minimum values observed at 20% forage cactus (p < 0.05). Additionally, the inclusion of forage cactus significantly enhanced aerobic stability (p < 0.05). The incorporation of 20% forage cactus into corn stover silage markedly improved its quality. • Forage cactus is suitable to produce mixed silages with corn stover. • The forage cactus is a sustainable source of water to be supplied via feeding. • The fermentative profile is improved, resulting in reduced dry matter losses. • The aerobic stability is improved according to the inclusion of forage cactus. • Incorporating 20% forage cactus improved silage quality. [ABSTRACT FROM AUTHOR]

Enterococcus faecalis , a conditional pathogenic bacterium, is prevalent in the intestinal, oral, and reproductive tracts of humans and animals, causing a variety of infectious diseases. E. faecalis is the main species detected in secondary persistent infection from root canal therapy failure. Due to the abuse of antibacterial agents, E. faecalis has evolved its resistant ability. Therefore, it is difficult to treat clinical diseases infected by E. faecalis. Exploring new alternative drugs for treating E. faecalis infection is urgent. We cloned and expressed the gene of phage holin, purified the recombinant protein, and analyzed the antibacterial activity, lysis profile, and ability to remove bacterial biofilm. It showed that the crude enzyme of phage holin pEF191 exhibited superior bacterial inhibiting activity and a broader lysis host range compared to the parent phage PEf771. In addition, pEF191 demonstrated high efficacy in eliminating E. faecalis biofilm. The therapeutic results of the Sprague-Dawley (SD) rats model infected showed that pEf191 did not affect SD rats, indicating that pEF191 provided greater protection against E. faecalis infection in SD rats. Based on the 16 S rDNA data of SD rats intestinal microorganism population, holin pEF191 exhibited no impact on the diversity of intestinal microorganisms at the phylum and genus levels and improved the relative abundance of favorable bacteria. Thus, pEF191 may serve as a promising alternative to antibiotics in the management of E. faecalis infection. • A new holin gene from phage, infecting Enterococcus faecalis YN771, was cloned and expressed. • The crude enzyme of phage holin pEF191 exhibited superior bacterial inhibiting activity. • The pEF191 provided greater protection against E. faecalis infection in SD rats. [ABSTRACT FROM AUTHOR]

Microbial communities first respond to changes of external environmental conditions. Observing the microbial responses to environmental changes in terms of taxonomic and functional biodiversity is therefore of great interest, particularly in extreme environments, where the already extreme conditions can become even harsher. In this study, sediment samples from three different shallow hydrothermal vents in Levante Bay (Vulcano Island, Aeolian Islands, Italy) were used to set up microcosm experiments with the aim to explore the microbial dynamics under changing conditions of pH and redox potential over a 90-days period. The leading hypothesis was to establish under microcosm conditions whether the starting microbial communities of the sediments evolved differently depending on their origin. To profile the dynamics of microbial populations over time, biodiversity, enzymatic profile, total cell abundance estimations, total/respiring cell ratio were estimated by using different approaches. An evident change in the microbial community structure was observed, mainly in the microcosm containing the sediment from the most acidified site, which was characterized by a highly diversified microbial community (in prevalence composed of Thermotoga , Desulfobacterota , Planctomycetota , Synergistota and Deferribacterota). An increase in microbial resistant forms (e.g., spore-forming species) with anaerobic metabolism was detected in all experimental conditions. Differential physiological responses characterized the sedimentary microbial communities. Proteolytic activity appeared to be stimulated under microcosm conditions, whereas the alkaline phosphatase activity was significantly depressed at low pH values, like those that were measured at the station showing intermediate pH-conditions. The results confirmed a differential response of microbial communities depending on the starting environmental conditions. • Marine hydrothermal vents are study model of climate change and ocean acidification. • Microcosms were used to study microbial community's responses to extreme conditions. • Strongest changes of the microbial diversity observed under more acidified conditions. • An increase in microbial resistant forms was detected in all experimental conditions. • A starting more specialized community is more responsive to exacerbated conditions. [ABSTRACT FROM AUTHOR]

In this paper we investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution, namely dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial communities, affecting their dynamics in important ways. Recently, they have each moved (separately) into the focus of stochastic individual-based modelling (Billiard et al. 2016, 2018; Champagnat, Méléard and Tran, 2021; Blath and Tóbiás 2020). Here, we investigate their combined effects in a unified model. Indeed, we consider the (idealized) scenario of two sub-populations, respectively carrying 'trait 1' and 'trait 2', where trait 1 individuals are able to switch (under competitive pressure) into a dormant state, and trait 2 individuals are able to execute horizontal gene transfer, which in our case means that they can turn trait 1 individuals into trait 2 ones, at a rate depending on the density of individuals. In the large-population limit, we examine the fate of (i) a single trait 2 individual (called 'mutant') arriving in a trait 1 resident population living in equilibrium, and (ii) a trait 1 individual ('mutant') arriving in a trait 2 resident population. We analyse the invasion dynamics in all cases where the resident population is individually fit and the behaviour of the mutant population is initially non-critical. This leads to the identification of parameter regimes for the invasion and fixation of the new trait, stable coexistence of the two traits, and 'founder control' (where the initial resident always dominates, irrespective of its trait). One of our key findings is that horizontal transfer can lead to stable coexistence even if trait 2 is unfit on its own. In the case of founder control, the limiting dynamical system also exhibits a coexistence equilibrium, which, however, is unstable, and with overwhelming probability none of the mutant sub-populations is able to invade. In all cases, we observe the classical (up to three) phases of invasion dynamics à la Champagnat (2006). [ABSTRACT FROM AUTHOR]

The gut microbiota composition and dietary factors in our food along with the use of prebiotics and probiotics play an important role in the maintenance of human health. A well-balanced gut microbial population is necessary for the host and the microbiota to coexist in a mutually beneficial relationship maintaining homeostasis. Considering the potential of modern technological tools, it is possible nowadays to engineer prebiotic bacteria having a positive influence on the microbiome on one hand while on the other one may have the ease to get rid of the pathogenic proinflammatory microbes or elements causing dysbiosis. Past studies have seen that in cancer there is a loss of inter-microbial relationship cum interactions within microbiota members, the metabolic products produced by them and the host immune system in a microbial ecosystem, leading to dysbiosis. Current review highlights the importance of probiotics in the management of cancer by bringing together majority of the studies together at a single platform and moreover, stresses upon the need to maintain eubiosis in order to evade and inhibit the progression of cancer. Continuous expansion in knowledge about probiotics, their effect on various cancers and the underlying mechanism of action has raised the global scientific interest towards their possible use against different cancers. Furthermore, the article emphasizes upon the need to explore newer therapeutic targets comprising of the microbiome which could further pave the way to the concept of personalized medicines for various kinds of malignancies so as to derive maximum benefits of a treatment modality and to preserve the microbial homeostasis. [ABSTRACT FROM AUTHOR]

• Metaproteomics enables exploration into active microbial populations in the rumen. • Key methods include protein sampling, extraction, identification and quantification. • Metagenome-integrated metaproteomics improves protein identification. • Future metaproteomic studies will connect rumen microbiome function to phenotypic traits in the host animal. The rumen microbiome constitutes a dense and complex mixture of anaerobic bacteria, archaea, protozoa, virus and fungi. Collectively, rumen microbial populations interact closely in order to degrade and ferment complex plant material into nutrients for host metabolism, a process which also produces other by-products, such as methane gas. Our understanding of the rumen microbiome and its functions are of both scientific and industrial interest, as the metabolic functions are connected to animal health and nutrition, but at the same time contribute significantly to global greenhouse gas emissions. While many of the major microbial members of the rumen microbiome are acknowledged, advances in modern culture-independent meta-omic techniques, such as metaproteomics, enable deep exploration into active microbial populations involved in essential rumen metabolic functions. Meaningful and accurate metaproteomic analyses are highly dependent on representative samples, precise protein extraction and fractionation, as well as a comprehensive and high-quality protein sequence database that enables precise protein identification and quantification. This review focuses on the application of rumen metaproteomics, and its potential towards understanding the complex rumen microbiome and its metabolic functions. We present and discuss current methods in sample handling, protein extraction and data analysis for rumen metaproteomics, and finally emphasize the potential of (meta)genome-integrated metaproteomics for accurate reconstruction of active microbial populations in the rumen. [ABSTRACT FROM AUTHOR]

Chronodisruption, commonly displayed by people living with obesity (PLO), is linked to colonic microbiota dysbiosis, and may increase the risk of many chronic non-communicable diseases, whereas dietary interventions–called chrononutrition may mitigate it. We evaluated the in vitro effects of spent coffee grounds (SCG), and their antioxidant dietary fiber (SCG-DF) on the colonic microbiota of an obese donor displaying dysbiosis and chronodisruption. Basal microbiota pattern was associated with an increased risk of non-communicable chronic diseases. Both samples decrease species richness and increase microbiota diversity (p < 0.05; Chao and Shannon index, respectively), positively enhancing Firmicutes/Bacteroidetes index (SCG, p < 0.04; SCG-DF, p < 0.02). SCG and SCG-DF modulated the microbiota, but SCG-DF induced greater changes, significantly increasing. p_Actonobacterias (SCG p < 0.04; SCG-DF, p < 0.02), and reducing g_ Alistipes ; s_ putredinis , g_ Prevotella ;s_ copri. The highest increase was displayed by p_Proteobacteria (f_Desulfovibrionaceae and f_Alcanigenaceae, p < 0.05), while g_ Haemophilus ; s_ parainfluenzae decreased (p < 0.05). However, neither SCG nor SCG-DF modulated g_ Alistipes (evening-type colonic microbial marker) beneficially. SCG and SCG-DF reduced (p < 0.05) g_ Lachnospira , a microbial evening-type marker, among other microbial populations, of an obese donor displaying chronodisruption and dysbiosis. SCG and SCG-DF displayed a prebiotic effect with the potential to mitigate diseases linked to chronodisruption. [Display omitted] • SCG and SCG-DF decrease species richness and increase microbiota diversity. • SCG and SCG-DF positively enhancing Firmicutes/Bacteroidetes index. • SCG and SCG-DF can selectively modulate g_ Lachnospira. • SCG and SCG-DF may contributing to alleviate chronodisruption. [ABSTRACT FROM AUTHOR]

Alkaline fermentation for volatile fatty acids (VFAs) production has shown potential as a viable approach to treat sewage sludge. The hydrolysis and acidogenesis of sludge are greatly influenced by mixing. However, the effects of mixing intensity on VFAs production in sludge alkaline fermentation (SAF) remain poorly understood. This study investigated the impacts of mixing intensity (30, 90 and 150 rpm continuous mixing, and 150 rpm intermittent mixing) on VFAs production, dissolved organic matter (DOM) characteristics, phospholipid fatty acid profiles and microbial population distribution in SAF. Results showed that 150 rpm continuous and intermittent mixing enhanced the hydrolysis of sludge, while 150 rpm intermittent mixing resulted in the highest VFAs production (3886 ± 266.1 mg COD/L). Analysis of fluorescent and molecular characteristics of DOM revealed that 150 rpm intermittent mixing facilitated the conversion of released DOM, especially proteins-like substances, into VFAs. The abundance of unsaturated and branched fatty acids of microbes increased under 150 rpm intermittent mixing, which could aid in DOM degradation and VFAs production. Firmicutes and Tissierella were enriched at 150 rpm intermittent mixing, which favored the maximum VFAs yield. Moreover, Firmicutes were found to be the key functional microorganisms influencing the yield of VFAs during SAF. This study provides an understanding about the mixing intensity effects on VFAs production during SAF, which could be helpful to improve the yield of VFAs. [Display omitted] • 150 rpm continuous mixing led to the highest hydrolysis of sludge. • 150 rpm intermittent mixing resulted in the maximum VFAs production. • The enhanced degradation of DOM molecules contributed to VFAs production. • Firmicutes were the key functional microorganisms influencing VFAs yield. [ABSTRACT FROM AUTHOR]

Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria. [Display omitted] • Bacteria from giant pandas and environment have similar trend resistance. • Disinfection decreased the abundance of some pathogens in feces and environment. • Disinfection shapes microbial populations of the giant panda gut and habitat. • Disinfection results in increased antibiotic resistance genes. [ABSTRACT FROM AUTHOR]

The use of beneficial microbes, i.e., probiotics, to reduce pathogens and promote the performance of the target species is an important management strategy in mariculture. This study aimed to investigate the potential of four microbes, Debaryomyces hansenii , Ruegeria mobilis , Lactobacillus plantarum , and Bacillus subtilis , to suppress Vibrio and increase survival, population growth and digestive enzyme activity (protease, lipase, and amylase) in the harpacticoid copepod, Tigriopus japonicus. Copepod, T. japonicus stock culture with an initial mean density of 50 individual/mL (25 adult male and 25 adult female) was distributed into five treatments (i.e., four experimental and a control, each with four replicates; repeated twice) using 20 beakers (100 mL capacity each). The copepods were fed a mixture of the dinoflagellate Alexandrium tamarense and the diatom Phyaeodactylum tricornutum (3 × 104 cells/mL−1). Each microbe's concentration was adjusted at 108 CFU/mL−1 and applied to the culture condition. D. hansenii , L. plantarum , and B. subtilis all improved the copepods' survival and population growth, likely by including a higher lipase activity (P < 0.05). In contrast, using R. mobilis did not improve the copepod's culture performance compared to control. B. subtilis was the most effective in decreasing the copepod's external and internal Vibrio loading. The probiotic concentrations in the copepod decreased within days during starvation, suggesting that routine re-application of the probiotics would be needed to sustain the microbial populations and the benefits they provide. Our results demonstrated that D. hansenii and B. subtilis are promising probiotics for mass copepod culture as live food for mariculture purposes. • B. subtilis was the most effective for suppressing Vibrio in Tigriopus japonicus. • D. hansenii improved population growth and increased the survival of T. japonicus. • The probiotic concentrations in T. japonicus declined over time during starvation. • Routine re-applications of the probiotics would be needed to sustain the microbial populations in T. japonicus. [ABSTRACT FROM AUTHOR]

The microbiome is recognized as a quasi-organ in the human body. When dysbiosis of the microbiome occurs, this variation may contribute to alterations in the microenvironment, potentially inducing an inflammatory immune response and providing a niche for neoplastic growth. However, there is limited evidence regarding the correlation and interaction between the microbiome and tumorigenesis. By utilizing microRNA sequencing data of patients with colon and rectal cancer from The Cancer Genome Atlas, we designed a novel analytical process to extract non-human small RNA sequences and align them with the microbial genome to obtain a comprehensive view of the cancer-associated microbiome. In the present study, we identified >1000 genera among 630 colorectal samples and clustered these samples into three distinctive colorectal enterotypes. Furthermore, we found 12 genera from these clusters that are associated with cancer stages and revealed their putative functions. Our results indicate that the proposed analytical approach can effectively determine the cancer-associated microbiome. It may be readily applied to explore other types of cancer, in which specimens of the microbiome are difficult to collect. • Devising a novel analysis method for detecting microbiome using miRNA-Seq data. • The proposed method generates compelling results for colorectal cancer and can be applied to different types of cancer. • Integrating related high-throughput data and clinical data to reveal the influence of microbial populations. [ABSTRACT FROM AUTHOR]

Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where ensembles of local communities (subpopulations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. As a specific but generic biological example, we consider populations of Pseudomonas putida and its regulation and use of pyoverdines, iron scavenging molecules, as public goods. The review closes with an overview on cooperation in spatially extended systems and also provides a critical assessment of the insights gained from the experimental and theoretical studies discussed. Current challenges and important new research opportunities are discussed, including the biochemical regulation of public goods, more realistic ecological scenarios resembling native environments, cell-to-cell signaling, and multispecies communities. Image 1 • Cooperation and public good production of microbial communities. • Evolutionary stability of cooperation in structured microbial population. • Theoretical concepts and models to analyze evolutionary dynamics in structured populations. • Pyoverdine – a public good of Pseudomonas populations: regulation and benefits. • The public good dilemma in spatially extended systems. [ABSTRACT FROM AUTHOR]

Recent studies revealed an amazing phenotypic heterogeneity between genetically identical individual cells within populations of microbial pathogens. During the course of an infection, subpopulations occur, which differ in certain virulence-relevant factors, stress adaptation functions or physiological and metabolic abilities. The mechanisms driving this heterogeneity are divergent reactions of the pathogens to differences in host tissue microenvironments. In addition, certain genetic regulatory circuits with positive feedback loops and stochastic differences in gene expression can generate endogenous fluctuations in regulatory components leading to bistable expression of virulence-associated functions. Here, we focus on the occurrence of phenotypic heterogeneity in populations of well-studied examples of pathogens, which enables cooperative, social behavior where a subpopulation of producers shares fitness- and/or virulence-relevant goods and traits with non-producers. We further highlight that this strategy allows preadaptation of a subgroup of cells to recurrent and thus predictable changes of the environment that they encounter during the different stages of the infection. The diversity within bacterial communities has a significant influence on the survival of the pathogens within their hosts and the progression of the disease. Unlabelled Image • Phenotypic diversification between genetically identical individual cells is frequently observed in populations of microbial pathogens during the infection and is crucial for virulence. • Phenotypic heterogeneity promotes division of labor and bet-hedging and allows preadaptation of a subgroup of pathogen to recurrent stresses and growth conditions. • Occurrence of phenotypic heterogeneity is initiated by divergent reactions of patho¬gens to en¬vironmental cues, genetic regulatory circuits including positive feedback control and stochastic differences in transcription processes. • Diversity in pathogen communities has a strong impact on the development of the disease and must be considered for treatments and the design of antimicrobials. [ABSTRACT FROM AUTHOR]

In response to environmental changes, cells often adapt by up-regulating genes to synthesize proteins that generate a benefit in the new environment. Several such cases of gene induction have been reported where the timing was heterogeneous, with some cells responding early and others responding late, although the microbial population was genetically homogeneous and the environment was well mixed. Here, we explore under which conditions heterogeneous timing of gene induction could be advantageous for the population as a whole. We base our study on a mathematical model that accounts for the cost of protein synthesis in terms of resources, which cells must provide immediately, whereas the associated benefit accumulates only slowly over the protein lifetime. Due to this delayed benefit, gene induction can be a risky investment, if resources are scarce and the environment fluctuates rapidly and unpredictably. Unprofitable gene induction then depletes the remaining limiting resource needed for maintenance of cell viability. We show that whenever gene induction is associated with a transient risk but beneficial in the long run, the stochastic timing of gene induction maximizes the reproductive success of a population. In particular, in an environment of stochastic periods of famine and feast, an optimum emerges from a trade-off between short-term growth, favoring rapid and homogeneous responses, and long-term survival, favoring a broadly heterogeneous response. Our analysis suggests that the optimal variability of induction times is just as large as the time required for the amortization of the initial investment into protein synthesis. Unlabelled Image • Unprofitable gene induction poses a risk in unpredictably fluctuating environments • Cells often respond with different time delays to an environmental change • Such heterogeneous timing can be advantageous as a bet-hedging strategy • It mitigates the risk of energy deficits from gene expression • Optimal strategy is a trade-off between short-term growth and long-term survival [ABSTRACT FROM AUTHOR]

For several decades, laboratory evolution has served as a powerful method to manipulate microorganisms and to explore long-term dynamics in microbial populations. Next to canonical Escherichia coli planktonic cultures, experimental evolution has expanded into alternative cultivation methods and species, opening the doors to new research questions. Bacillus subtilis , the spore-forming and root-colonizing bacterium, can easily develop in the laboratory as a liquid–air interface colonizing pellicle biofilm. Here, we summarize recent findings derived from this tractable experimental model. Clonal pellicle biofilms of B. subtilis can rapidly undergo morphological and genetic diversification creating new ecological interactions, for example, exploitation by biofilm non-producers. Moreover, long-term exposure to such matrix non-producers can modulate cooperation in biofilms, leading to different phenotypic heterogeneity pattern of matrix production with larger subpopulation of "ON" cells. Alternatively, complementary variants of biofilm non-producers, each lacking a distinct matrix component, can engage in a genetic division of labor, resulting in superior biofilm productivity compared to the "generalist" wild type. Nevertheless, inter-genetic cooperation appears to be evanescent and rapidly vanquished by individual biofilm formation strategies altering the amount or the properties of the remaining matrix component. Finally, fast-evolving mobile genetic elements can unpredictably shift intra-species interactions in B. subtilis biofilms. Understanding evolution in clonal biofilm populations will facilitate future studies in complex multispecies biofilms that are more representative of nature. Unlabelled Image • B. subtilis pellicle serves as a tractable and realistic model in laboratory evolution. • Biofilm diversification creates new competitive or cooperative interactions. • Division of labor in biofilms is vulnerable to evolution of individual traits. • Evolution with non-producers alters phenotypic heterogeneity of matrix expression. • Understanding complexity evolution in clonal population aids multispecies systems. [ABSTRACT FROM AUTHOR]

The existence of sulfate-reducing bacteria (SRB) is a major concern in oil industry due to the detrimental effects of SRB in oil technology. SRB are co-habited with diverse microbial populations in oil fields. The presence of other bacterial groups in oil fields may alter SRB activity in different ways. Therefore, understanding this coexistence may provide insights into problems induced by SRB activity and possible solutions to these problems. To investigate this aspect, not only the presence and abundance of SRB but also bacterial population that coexists with SRB in sulfate-reducing enrichment cultures obtained from the Diyarbakır oil fields in southeast of Turkey was determined by using cultivation- and molecular-based approaches. The most probable number technique (MPN) was used to determine the number of sulfidogenic bacteria in the enrichments. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction-amplified 16S rRNA gene fragments was performed to examine the bacterial diversity of the enrichments. The results demonstrated that the number of sulfidogenic bacteria in the enrichments was low (<103 cells/mL). The DGGE analysis indicated that community members belonging to the Firmicutes were more abundant than those of other phyla. Members belonging to SRB mainly consisted of the genera Desulfosporosinus , Desulfovibrio , Thermodesulfovibrio , and Desulfotomaculum. Fermentative bacteria, acetogens, nitrate reducers, and sulfur reducers were also detected in the enrichments. The results of this study not only provide information regarding the diversity of the cultivable portion of the bacterial community that coexists with cultivable SRB, but they also offer insights into the interactions of bacteria in complex microbial communities that inhabit natural environments. • The number of sulfidogenic bacteria in the enrichments was low. • Firmicutes were more abundant than those of other phyla detected in the cultures. • SRB were detected in the enrichment cultures of eight oil wells. • Bacteria with different metabolic capabilities were detected in the enrichments. • The presence of coexisting bacteria can be used as a proxy for the presence of SRB. [ABSTRACT FROM AUTHOR]

Genetic exchange in microbes and other facultative sexuals can be rare enough that evolution is almost entirely asexual and populations almost clonal. But the benefits of genetic exchange depend crucially on the diversity of genotypes in a population. How very rare recombination together with the accumulation of new mutations shapes the diversity of large populations and gives rise to faster adaptation is still poorly understood. This paper analyzes a particularly simple model: organisms with two asexual chromosomes that can reassort during rare matings that occur at a rate r. The speed of adaptation for large population sizes, N , is found to depend on the ratio ∼ log (N r) ∕ log (N). For larger populations, the r needed to yield the same speed decreases as a power of N. Remarkably, the population undergoes spontaneous oscillations alternating between phases when the fittest individuals are created by mutation and when they are created by reassortment, which – in contrast to conventional regimes – decreases the diversity. Between the two phases, the mean fitness jumps rapidly. The oscillatory dynamics and the strong fluctuations this induces have implications for the diversity and coalescent statistics. The results are potentially applicable to large microbial populations, especially viruses that have a small number of chromosomes. Some of the key features may be more broadly applicable for large populations with other types of rare genetic exchange. • Evolution with rare sex between individuals with two asexual chromosomes is studied. • Fit chromosomes produced by process of asymmetric mutation and clonal growth. • Oscillations alternate between phases with and without sex creating fittest genomes. • Transition from asexual to sexual described by logarithmic dependence on mating rate. [ABSTRACT FROM AUTHOR]

A novel composite biochar (NCB) was produced from the pyrolysis of co-fermentation products of sewage sludge, food wastes and rice straw, and exhibited higher nitrogen and phosphorus adsorption capacity due to the larger surface area (14.7 m2 g−1) and higher Ca content (51753.7 mg kg−1) than single rice straw biochar. The addition of NCB was then investigated in a non-aerated vertical baffled flow constructed wetland (VBFCW) for contaminated water treatment. The VBFCW with NCB addition significantly improved COD Mn , NH 4 +-N, TN and TP removal efficiencies of 83.3 ± 5.3%, 95.9 ± 3.4%, 28.0 ± 4.0% and 59.5 ± 11.8%, respectively, at a hydraulic retention time (HRT) of 3 d. In addition, the TN and TP removal rates at a decreased HRT of 2 d were much higher than those at an HRT of 3 d without NCB addition. The presence of NCB in the VBFCW system enhanced nutrient adsorption and improved the enrichment of bacteria for organic and nitrogen removal mainly including the genera Bacillus and Lactococcus. • Novel composite biochar (NCB), pyrolysis from fermented sludge-food wastes-rice straw. • NCB had good adsorption for N and P due to large surface and high Ca content. • NCB addition improved the removal of organics, N and P in CWs. • NCB addition favored to achieve efficient nutrients removal in CWs at short HRT. • NCB improved enrichment of nitrogen and organics removal related bacteria in media. [ABSTRACT FROM AUTHOR]

Composting is a biological process in which the organic matter is degraded by the mixed population of microorganisms in a moist aerobic environment to more stable and humidified end products. The composting process involves an interaction between the organic waste, microorganisms, moisture and oxygen. The molasses-based biomethanated distillery wastewater is presently effectively utilized with sugarcane pressmud through the composting process. The aim of present work was to evaluate the effect of ozone pretreatment on the rate of composting process and the quality of compost obtained. The GC-MS & FTIR analysis of ozone pretreated wastewater indicated the degradation and/or transformation of the organic compounds to simpler compounds present in the wastewater. Composting was performed by mixing fixed weight ratios of pressmud and different ratios of ozone pretreated wastewater (1:3, 1:4 and 1:5). The composting process was found to occur faster in the ozone pretreated wastewater for all the ratios as compared to the untreated wastewater. The final compost characteristics were found to be optimum for the 1:3 and 1:4 ratios of pressmud and wastewater. The bio-oxidative phase duration of composting has been reduced for the ozone pretreated wastewater. • Ozone pretreatment for Biodegradability enhancement of BMDWW. • Composting period has been reduced for the ozone pretreated BMDWW. • Improved quality of compost for ozone pretreated BMDWW. • GC-MS analysis confirms the cleavage of recalcitrant organic compounds. • 96% germination index for ozone pretreated BMDWW compost. [ABSTRACT FROM AUTHOR]

The purpose of this study was to investigate the efficacy of pulsed light (PL), a new formula of sanitizer (HEN) consisting of hydrogen peroxide, EDTA and Nisin, as well as synergy of PL and HEN sanitizer (PL-HEN) wash in inactivating E. coli O157:H7 on spinach. The treatment effect on microbial loads and apparent quality during 13 days storage at 4 °C was also determined. A bacterial cocktail containing three strains of E. coli O157:H7 was used as inoculum based on their association with produce-related outbreaks. Spinach leaves were spot inoculated on surface before treating with PL (1–63J/cm2), HEN sanitizer wash (2 min) or their combinations. PL inactivation was influenced significantly at low doses. Treatment dose of 15.75 J/cm2, equivalent to 15 s intense PL treatment, was found optimal above which adverse quality effect was evident. The optimal PL dose resulted 2.7 log CFU/g reduction of E. coli O157:H7 while a rapid 2 min wash in sanitizer formulation HEN, provided comparatively low, 1.8 log CFU/g, reduction of the pathogen. Two different sequences of PL and HEN treatment combinations were tested. In PL-HEN treatment, inoculated leaves were first treated at optimal PL dose (15.75 J/cm2) followed by 2 min immersion in HEN whereas in HEN-PL treatment, leaves were first washed in HEN before PL exposure. HEN-PL treatment indicated a compound inactivation activity (4.6 logs reduction) while PL-HEN treatment indicated a strong synergistic inactivation as E. coli cells were not detectable after treatment indicating >5 log reduction. The PL-HEN treatment not only significantly reduced spoilage microbial populations on spinach but also slowed their growth during storage. Furthermore, the visual and firmness quality of spinach were not significantly affected by the PL-HEN treatment. Overall, our results demonstrate that integrated PL-HEN technology can be used to enhance microbial safety of spinach. • Pulsed light (PL) is effective for surface decontamination of E. coli O157:H7 on spinach. • Combinations of PL and sanitizer formula showed additive or synergistic effects. • PL-sanitizer combination inactivated >5 log10 CFU/g of spot inoculated E. coli. • Spinach quality is not significantly impacted by the combined treatment. • PL-sanitizer technology could potentially be used as an alternative to chlorine washing. [ABSTRACT FROM AUTHOR]

The aim of this study was to analyze the microbiology of buckwheat honey fermentation inoculated with different starter cultures by culturing and PCR-DGGE, taking as a model for comparison a spontaneously fermented batch. The inoculants tested were (i) cider lees (from a cider factory), (ii) sourdough (from a bakery), and (iii) a commercial Saccharomyces cerevisiae strain. The results of the culturing and culture-independent techniques agreed well and detected the same dominant species along the fermentations. Our results suggest that S. cerevisiae strains, which constituted a majority population in all batches including the uninoculated one, carried out the fermentations. The highest microbial diversity was found at the beginning of the fermentation in the uninoculated batch; this contained in addition to S. cerevisiae bacteria (Paracoccus sp., Staphylococcus sp., and Bacillus sp.) and yeast (Candida sp.) species. Candida sp. was also common in batches inoculated with sourdough and cider lees cultures. Lactobacillus species were found throughout the fermentation of the sourdough-inoculated batch. Basic chemical analysis and testing trials demonstrated that the overall sensory acceptance of the four meads were highly similar. Yeast and bacteria isolated in this study could serve as a source of technologically relevant microorganisms for mead production. • The composition and succession of the microbial populations during fermentation of buckwheat honey was assessed. • The eukaryotic microorganisms during mead fermentation were investigated by the culture-independent PCR-DGGE technique. • The sensory analysis by the acceptance test of meads was performed. • Saccharomyces cerevisiae and Candida sp. Are the most competitive species during fermentation. • The strong aroma and flavor of buckwheat honey masks the organoleptic factors produced by lactic acid bacteria. [ABSTRACT FROM AUTHOR]

Table olives harbour a variable microbial population, dominated by lactic acid bacteria and yeasts. Clarifying the effect of the yeast population during table olive fermentation requires methods for yeast species identification. Until now, the most used molecular methods (culture-dependent and -independent) are limited to species level identification, whereas RAPD-PCR is primarily chosen when strain typing is required. In this work, species identification by sequencing of the ITS1–5.8S rDNA–ITS4 region, was followed by inter-simple-sequence-repeat-anchored PCR (ISSR-PCR) using the (CAG)4 primer, to evaluate its suitability for species clustering and strain typing of the yeast population from table olives. Yeast were isolated from ten table olive samples: seven samples were purchased from local markets (sliced, naturally fermented, crushed and Spanish-style fermented), and three samples were from pilot fermentations (Spanish-style fermented). Ten yeast species were identified by sequencing that were correctly clustered by ISSR-PCR, but without a clear association with the type of olive processing. ISSR-PCR revealed 57 different profiles into 254 total isolates. Citeromyces nyonsensis (39.4%) and Yarrowia deformans (22.2%), which have not previously been associated to table olives, showed high intraspecific variability. ISSR-PCR using (CAG)4 primer is a valuable method for identification and strain typing of yeast from table olives. • Ten yeast species identified without a clear association with the four types of table olives. • W. anomalus (23.2%), K. lactis (16.5%), and Y. lipolytica (16.5%) were predominating species. • ISSR-PCR using (CAG)4 correctly clustered 254 isolates into 57 yeasts strains. • High intraspecific variability in most species, e.g., C. nyonsensis (39.4%). • ISSR-PCR using (CAG)4 is accurate for typing of yeast strains from table olives. [ABSTRACT FROM AUTHOR]

Abstract The systematic application of slightly acidic electrolyzed water (SAEW) for natural microbial reduction of buckwheat sprouts were investigated including seed-dipping, germination and sprouts-washing in the present study. The results show that all the three SAEW treatments with similar pH value (approximately 6.0) used in the study resulted in the reduction of the natural moulds and yeasts and total bacteria counts in buckwheat seeds and harvested sprouts in spite of their different available chlorine concentration (ACC, approximately 10, 28 and 92 mg/L respectively), which was equivalent or high disinfectant efficacy for buckwheat seeds and sprouts compared to NaClO solutions and acidic electrolyzed water (AEW). Moreover, SAEW treatments could control the growth of natural microbial populations during germination and decrease the E. coli O78 and L. monocytogenes counts on 8-day-old sprouts by 1.10–2.74 and 1.85–2.46 log 10 CFU/g, respectively. However, too high ACC (91.96 mg/L) in SAEW had adverse effect on the sprouts length. SAEW with appropriate ACC (10–28 mg/L) could be considered in the whole process of sprouts industry because of its strong disinfection efficacy and less adverse effect on the sprouts growth than NaClO solutions and AEW. Highlights • SAEW treatment can reduce the natural microorganisms in buckwheat seeds. • SAEW treatment could reduce the microbial populations during buckwheat germination. • SAEW treatment could reduced the natural microorganisms in buckwheat sprouts. • SAEW treatment with appropriate ACC had no adverse impact on the sprouts growth. • SAEW could be applied in the whole process of sprouts industry. [ABSTRACT FROM AUTHOR]

Roasted seaweed snacks are getting popular worldwide. To reveal the main origins of microorganisms present in the roasted seaweed snacks, samples of raw materials, finished products, and environment (both food-contact and nonfood-contact surfaces) were collected from four plants. The total aerobic plate (APC), coliform, and mold counts of these samples were analyzed and the selected samples were also used for 16S rRNA sequencing. Results showed that dried laver contained the highest levels of APC among all raw ingredients, ranging from 2.72 to 6.95 Log CFU/g. Crushed pumpkin seeds and almond flakes had the highest coliform (up to 5.57 Log CFU/g) and mold counts (up to 2.16 Log CFU/g). The addition of seasoning to seaweed sandwich snacks increased the total microbial loads. The roasting process decreased the APC, coliforms, and mold counts of seaweed snacks by 0.22–1.73 Log CFU/g, >0.18- >2.46 Log CFU/g, and >0.18- >0.88 Log CFU/g respectively. The 16S rRNA sequencing analysis showed that the microbiota of roasted seaweed snacks was closely correlated with that of dried laver and the microbial load of roasted sandwich seaweed was primarily from the dried laver while less from microorganisms present in the processing plant environment and line workers. • Dried laver (DL) had the highest microbial loads among all raw ingredients. • Almonds and crushed pumpkin seeds contained highest coliform counts. • Far infrared heating and roasting reduced the APC by only 0.22–1.73 Log CFU/g. • DL contributed the most significantly to microbial populations in seaweed snacks. [ABSTRACT FROM AUTHOR]

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria , Bacteroidetes , Planctomycetes , Chloroflexi , and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35–77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota , Ascomycota , Aphelidiomycota , Basidiomycota , and Mortierellomycota , constituted 24.26–32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum , Woeseia , Sulfurimonas , Desulfosarcina , and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10−2 to 1.90 × 10−1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management. [Display omitted] • This study explored the antibiotic resistance profiles in various aquaculture ponds. • Bacterial communities demonstrated greater sensitivity than fungal communities. • Newly reclaimed aquaculture ponds exhibited emerging antibiotic-resistant profiles. • Antibiotic resistances were linked to the suppressive effects of nitrogen metabolism. [ABSTRACT FROM AUTHOR]

Abstract Oxic-settling-anoxic (OSA) process is one of the promising variants that produces lower amounts of sludge and has been applied to aerobic and nutrient removal systems. The only consequence on this modification is that supplementary research is advisable to fully understand the mechanism, which eventually leads to the development of a more realistic model. This study evaluated the characteristics of an OSA process as a sludge reduction system by calibration of kinetic coefficients of ASM1 model with some modifications. A series of respirometric tests were designed for the assessment of microbial kinetics and for further clarification of sludge reduction mechanism. The calibration results depicted that the decay rate is the most variable kinetic parameter depending on the system configuration. It was determined that this kinetic coefficient increased significantly after the system was modified into OSA configuration while other model parameters were almost kept constant. This may be referred to a change either in the microbial population or in the metabolism of the community. The active biomass ratio in the CAS reactor was found to be around 75%, while it was almost 2 times lower in the side-stream reactor. All results led to a conclusion that OSA process is encouraging endogenous decay and consequently lowers biomass viability in the reactor and achieves excess sludge reduction in the system. All experimental results confirmed that side-stream reactor accelerates decay rate of the community and causes the introduction of sludge with low viability to the main reactor. Graphical abstract Image 108597 Highlights • Calibration of coefficients of ASM1 for the development of a more realistic model. • Respirometry testing designed for the assessment of microbial kinetics. • Increased decay rate after the system was modified into OSA configuration. • Two times lower active biomass ratio in the side-stream reactor compared to CAS. • SR accelerates decay rate of the community and lowers viability to the main reactor. [ABSTRACT FROM AUTHOR]

Free-living amoebae belong to the genus Acanthamoeba; can feed on microbial population by phagocytosis, and with the capability to act as a reservoir and a vehicle of microorganisms to susceptible host. Therefore, the role of endosymbiosis in the pathogenesis of Acanthamoeba is complex and not fully understood. The aim of the present study was to identify bacterial, fungal, and human adenovirus (HADV) endosymbionts as well as evaluating the endosymbionts role of such organisms in the pathogenesis of Acanthamoeba in keratitis patients living in Iran. Fifteen Acanthamoeba (T4 genotype) isolates were recovered from corneal scrapes and contact lenses of patients with keratitis. Cloning and purification was performed for all isolate. Gram staining was performed to identify bacterial endosymbionts. DNA extraction, PCR, and nested PCR was set up to identify endosymbiont of amoeba. Evaluation of pathogenicity was conducted by osmo-tolerance and thermo-tolerance assays and cell culture, and then CPE (cytopathic effect) was survey. Statistical analysis was used between Acanthamoeba associated endosymbionts and Acanthamoeba without endosymbiont at 24, 48, 72, and 96 h. A p value < 0.05 was considered as significant, statistically. A total of 9 (60%) Acanthamoeba (T4 genotypes) isolates were successfully cloned for detecting microorganism endosymbionts. The only isolate negative for the presence of endosymbiont was ICS9. ICS7 (Pseudomonas aeruginosa , Aspergillus sp., and human adenovirus endosymbionts) and ICS2 (Escherichia coli endosymbiont) isolates were considered as Acanthamoeba associated endosymbionts. ICS7 and ICS2 isolates were highly pathogen whereas ICS9 isolate showed low pathogenicity in pathogenicity evaluated. Positive CPE for ICS7 and ICS2 isolates and negative CPE for ICS9 isolate were observed in cell culture. The average number of cells, trophozoites, and cysts among ICS7, ICS2, and ICS9 isolates at 24, 48, 72, and 96 h was significant. This is the first survey on microbial endosymbionts of Acanthamoeba in keratitis patients of Iran, and also the first report of Aspergillus sp, Achromobacter sp. , Microbacterium sp., Brevibacillus sp , Brevundimonas sp and Mastadenovirus sp in Acanthamoeba as endosymbionts. Our study demonstrated that microbial endosymbionts can affect the pathogenicity of Acanthamoeba ; however, further research is required to clarify the exact pattern of symbiosis, in order to modify treatment protocol. Image 1 • Our study demonstrated that microbial endosymbionts can affect the pathogenicity of Acanthamoeba. • This is the first report of some microbial endosymbionts in Acanthamoeba. • Further research is required to clarify the exact pattern of symbiosis, in order to modify treatment protocol. [ABSTRACT FROM AUTHOR]

Highlight • We modeled microbial population growth based on low-energy redox reactions. • More energy is extracted when the reactants are abundant and the products are rare. • This "abundant resource premium" has been neglected in ecological models. • Incorporating this effect leads to qualitatively new dynamics. • An intermediate rate of resource acquisition maximizes the steady-state population. Abstract We present a new model of microbial population growth that focuses on the acquisition of metabolic energy through chemosynthesis and how this depends on the concentration of resources and byproducts. Due to entropy effects, organisms extract the greater energy (i.e., they produce the greater amount of adenosine triphosphate) when they use resources that are abundant and generates byproducts that are rare. This effect, which we call the "abundant resource premium," has been neglected in traditional models of microbial growth because the total metabolic energy acquisition is generally far greater than this premium. This term, however, cannot be neglected for many microbes, such as sulfate reducers, iron oxidizers, and methanogens, which live under conditions of low-energy availability. Our model showed qualitatively different behaviors from those observed in traditional microbial population growth models, such as the Monod model. For example, the steady-state population density was maximum at an intermediate resource-utilizing ability, suggesting that high substrate acquisition is not always advantageous for a microbial population when the availability of metabolic energy is low. We discuss possible implications for evolutionary and ecosystem sciences. [ABSTRACT FROM AUTHOR]

Abstract Effective treatment of food waste is inherently difficult due to several factors, including its heterogeneous composition, high moisture content, and low heating value. To address these issues, this study aims to convert food waste into an energy resource using naturally occurring fermentative microorganisms embedded in wooden biochips (bio-catalysis), utilizing a "Smart Food Waste Recycling Bin" (S-FRB) system. High-throughput 16S rRNA gene sequencing analysis identified the major aerobic and facultatively anaerobic bacteria with alpha-diversity in terms of the Phylogenetic Diversity index ranging from 40.8 (initial stage) to 24.5 (mature stage), which indicates the microbial communities are relatively homogeneous and effective for use in the S-FBR. Operational results indicated that the organic content of food waste traded in the system increased from 53% up to 72% in the final end-product and achieved a mass reduction rate of approximately 80%. The heating value of the end-product, which was 3300 kcal/kg waste when measured by the differential scanning calorimeter (DSC) method, confirmed its high potential as a biofuel. Overall, the S-FRB system presents a practical approach for food waste treatment that solves the putrescible waste problem and maximizes utility through resource circulation. Graphical abstract Image 102 Highlights • Stability of S-FRB suggests the on-site waste treatment could be practical in Hong Kong. • S-FRB system performed sufficient biodegradation procedure with the assistance of microbial activity. • Calorific value of the end product proves the applicability of food waste conversion to energy resources. • The species and abundance of microbial population are integral to the effectiveness of S-FRB processes. [ABSTRACT FROM AUTHOR]

Abstract The effects of E-beam radiation on microbiota, colour, texture and sensorial properties of hard annatto-coloured cheese during storage at 4 and 14 °C were studied. Doses of up to 2 kGy provoked a decrease in the total bacterial number, although microbiota recovery to initial levels during storage, even under refrigeration temperature, was observed. However, a higher temperature (14 °C) was required to detect bacterial growth in cheese treated at 3 kGy. Moreover, the effects of the dose on the hardness, springiness, cohesiveness and colour parameters were interdependent of the storage conditions. According to the combined effects of E-beam treatment and storage conditions, multivariate cluster analysis allowed treated cheeses irradiated at 0–1 kGy (cluster 1) to be distinguished from those irradiated at 2–3 kGy (cluster 2), which were stored at 4 °C for 28 days. Cluster 3 included irradiated cheeses (1–3 kGy) stored at a higher temperature (14 °C). Although off-odour and off-flavours arose immediately after treatment, they disappeared progressively during storage at doses lower than 2 kGy. Nevertheless, consumers could detect changes in the colour derived from the radiation at 2 kGy, however, those changes may be unimportant because of the wide colour ranges of commercial annatto-coloured cheeses. Highlights • Microbiota of cheese treated up to 2 kGy reach initial levels during storage at 4 °C. • Orange cheese discolouration due to air exposure is attenuated by E-beam radiation. • Colour and texture changes depend on both, dose and storage conditions. • E-beam treatment does not compromise the sensory quality of hard cheeses. [ABSTRACT FROM AUTHOR]

Abstract Background A reciprocal relationship between oral health and systemic disease, such as type 2 diabetes, has been suggested, whereby a systemic disease is a predisposing factor for oral infection. If the infection occurs, it in turn aggravates the progression of the systemic disease. According to several studies, certain constituents of the oral microbiota are linked to diabetes, metabolic syndrome, and obesity. In the current study, we aimed to compare the microbial diversity and population structure of the oral microbiota of normoglycemic, impaired glucose tolerance (IGT), and diabetes patients. Methodology The study followed a case-control design, with 15 type 2 diabetes patients, 10 IGT subjects, and 19 control subjects. All subjects underwent assessment of periodontitis and oral health. Saliva samples were collected, and DNA was isolated from these samples. Hypervariable regions of the 16Sr RNA gene were amplified and sequenced, and the generated sequences underwent bioinformatics analysis. Statistical analysis and diversity index calculations were made using the statistical software R, vegan R-package, and Past3.20 software. Results Overall, 551 operational taxonomic units (OTUs) were identified. Based on OTU analysis, a clear reduction of the number of species was observed in both IGT (412) and diabetes groups (372) compared with that in the normoglycemic group (502). This was associated with a similar pattern of reduction of biological diversity among the three groups. The phylogenetic diversity (PD-SBL) value in the normoglycemic group was higher than that in the diabetes group. The diabetes group exhibited the highest evenness value and the highest microbiota bacterial pathogenic content. Conclusion A clear reduction of the biological and phylogenetic diversity was apparent in the diabetes and pre-diabetes oral microbiota in comparison with that in the normoglycemic oral microbiota. However, this was associated with an increase in the pathogenic content of the hyperglycemic microbiota. The results of this study may aid to better understanding of the directionality of the mysterious reciprocal relationship. Highlights • The reciprocal relationship between diabetes and oral health has been supported by multiple lines of evidence. • We compared the oral microbiomes, to the species level, in normoglycemic, glucose intolerant, and diabetes patients. • A clear reduction of the biological and phylogenetic diversity was apparent in diabetes and pre-diabetes oral microbiomes. • This was associated with an increase in the pathogenic content of the hyperglycemic microbiome. • The results of this study may aid to better understanding of the directionality of the mysterious reciprocal relationship. [ABSTRACT FROM AUTHOR]

Highlights • Viruses of microbes can influence the fate of individual microbes and entire populations. • In this paper, we present a model of chronic infections as well as a model of interactions between lytic and chronic viruses competing for the same microbial population. • In the chronic only model, we identify conditions underlying complex bifurcations such as saddle-node, backward and Hopf bifurcations, leading to parameter regions with multiple at-tractors and/or oscillatory behavior. • We conduct invasion analysis of the multi-strain model, and find a parameter regime where the chronic virus requires the lytic virus for persistence and invasion. Abstract Viral infections of microbial cells often culminate in lysis and the release of new virus particles. However, viruses of microbes can also initiate chronic infections, in which new viruses particles are released via budding and without cell lysis. In chronic infections, viral genomes may also be passed on from mother to daughter cells during division. The consequences of chronic infections for the population dynamics of viruses and microbes remains under-explored. In this paper we present a model of chronic infections as well as a model of interactions between lytic and chronic viruses competing for the same microbial population. In the chronic only model, we identify conditions underlying complex bifurcations such as saddle-node, backward and Hopf bifurcations, leading to parameter regions with multiple attractors and/or oscillatory behavior. We then utilize invasion analysis to examine the coupled nonlinear system of microbes, lytic viruses, and chronic viruses. In so doing we find unexpected results, including a regime in which the chronic virus requires the lytic virus for survival, invasion, and persistence. In this regime, lytic viruses decrease total cell densities, so that a subpopulation of chronically infected cells experience decreased niche competition. As such, even when chronically infected cells have a growth disadvantage, lytic viruses can, paradoxically, enable the proliferation of both chronically infected cells and chronic viruses. We discuss the implications of our results for understanding the ecology and long-term evolution of heterogeneous viral strategies. [ABSTRACT FROM AUTHOR]

Dithianon is a broad-spectrum anthraquinone fungicide used to control several diseases of grapes, apples, and other fruits and vegetables. Its mode of action is described as multi-site and associated to thiol-reactivity. As other fungicides can affect non-phytopathogenic organisms as yeasts and bacteria, with impact on microbial population, diversity, and fermentation processes. In this context, we study the effect of dithianon on the model organism and fermentative yeast Saccharomyces cerevisiae in order to elucidate the mechanisms involved in yeast cell death., and explain its interference on wine fermentation kinetics. Thus for, we analyzed cellular protein and non-protein thiols, membrane and cell wall integrity, reactive oxygen species accumulation, mitochondrial membrane potential, and phosphatidylserine externalization. The results showed that when exponentially aerobic growing cells of S. cerevisiae are submitted to acute dithianon treatment they loss cell wall and membrane integrity, dying by necrosis, and this behavior is associated to a depletion of reduced proteic and non-proteic thiol groups. We also detected an important increase of cellular reactive oxygen species (ROS) associated to mitochondrial membrane potential modifications on dithianon treated cells. ROS accumulation was not associated to apoptotic cell death, but can be responsible for intracellular damages. Moreover, necrotic cell death induced by dithianon explains its effect on the kinetics of wine fermentations. [ABSTRACT FROM AUTHOR]

With the increase of global demand for cash crops, a large of cash crop waste was produced and caused severe environmental issues. To produce Agricultural Jiaosu (AJ) using these wastes is a sustainable waste disposal method. However, the fermentation mechanism, metabolites, and microbial characteristics of AJ fermented with different substrates remain unclear. In this study, the effects of different substrates (fruit and vegetable waste and Chinese herbal medicine waste) on the fermentation characteristics of AJ, including metabolites and microbial community properties, were investigated. The results revealed that AJ fermentation was a process of converting organic matter into organic acids and other metabolites, mainly including hydrolysis, acidogenesis, and maturation stages. At the genus level, Lactobacillus , Acetobacter , Hydrogenibacillus , Halomonas , and Prevotella_1 were the dominant bacteria in the fermentation system. The bacterial diversity of composite substrate AJ was higher than that of single substrate AJ. The organic acids and secondary metabolites concentration and the composition of key microorganisms depended on the substrate type. Furthermore, AJ's potential functional genes were mainly concentrated in cofactors and vitamin, carbohydrate, and amino acid metabolism. The findings of this study indicated that AJ is an innovative eco-friendly technology that can convert cash crop wastes into sustainable eco-products, and that its characteristics depend on the substrate type. Therefore, the substrate used to produce AJ should be carefully selected according to the application field. [Display omitted] • Cash crop wastes were treated by an eco-friendly method (Agricultural Jiaosu (AJ)). • The three stages of AJ fermentation process were summarized. • Microorganisms and metabolites characteristics of different AJ were analyzed. • AJ's main metabolic pathways were amino acid, carbohydrate, cofactors and vitamin. [ABSTRACT FROM AUTHOR]

The quality of gray sufu has been significantly influenced by microbes, but little is known about the spatiotemporal changes in microbes during fermentation and how they relate to quality. This study showed that after 28 days of fermentation, the texture and physicochemical indexes of gray sufu reached the best, and the taste was better on the 21st day. On the surface of gray sufu, the abundance of Bacillus and Trichosporon increased over time, while Lactobacillus , Pediococcus , and Pseudomonas decreased. In the middle and central parts, the abundance of Lactobacillus and Sarocladium increased over time, while Pediococcus , Pseudomonas , and Apiotrichum decreased. Physicochemical index (pH, amino acid nitrogen, TCA-soluble peptide), biogenic amines and benzoic acid were negatively correlated with the genera Pediococcus , Pseudomonas and Apiotrichum , while positively correlated with Sarocladium and Trichosporon. Propionic acid was positively correlated with Pediococcus and Pseudomonas but negatively with Apiotrichum. This demonstrated that the microflora in gray sufu has a spatiotemporal distribution and is associated with the product quality. Tracker analysis demonstrated that yellow serofluids, salt brine, and tofu pehtze provided microflora for fermentation. This study would be useful in understanding the production mechanism of gray sufu and strengthening its quality control by developing microbial regulation strategies. [Display omitted] • The microorganisms in gray sufu showed spatial and temporal distribution. • The values of all safety indices were below the limit. • The microorganisms of gray sufu were mainly originate from the three raw materials. • The dominant microorganisms were closely related to the quality characteristics. [ABSTRACT FROM AUTHOR]

The Gulf of La Spezia (northern Tyrrhenian Sea, Italy) is a commercially important area both as a shipping port and for mussel farming. Recently, there has been increased concern over environmental disturbances caused by anthropogenic activities such as ship traffic and dredging and the effects they have on the health of farmed mussels. This paper reports the results of microbiological and histological analyses, as well as of measurement of several biomarkers which were performed to assess the health status of mussels ( Mytilus galloprovincialis ) from four rearing sites in the Gulf of La Spezia. Mussels were collected between October 2015 and September 2016 and histological analyses (including gonadal maturation stage), as well as the presence of pathogenic bacteria ( Vibrio splendidus clade, V. aestuarianus and V. harveyi ), viruses (Herpes virus and ostreid Herpes virus 1) and protozoa ( Marteilia spp., in the summer season only) were carried out on a monthly basis. Conversely, biomarker responses in haemocyte/haemolymph (total haemocyte count, haemocyte diameter and volume, lysozyme and lactate dehydrogenase activities in cell-free haemolymph, and micronuclei frequency) and in gills and digestive gland (cortisol-like steroids and lipid peroxidation levels), were evaluated bimonthly. Microbiological data indicated that mussels contain a reservoir of potentially pathogenic bacteria, viruses and protozoa that in certain environmental conditions may cause a weakening of the immune system of animals leading to mortality episodes. The percentage of parasites detected in the mussels was generally low (9.6% for Steinhausia mytilovum , that is 17 samples out of 177 examined females; 3.4% for Proctoeces maculatus ; 0.9% for Mytilicola intestinalis and 2% for ciliated protozoa), while symbiont loads were higher (31% for Eugymnanthea inquilina and Urastoma cyprinae ). Interestingly, a previously undescribed haplosporidian was detected in a single mussel sample (0.2%) and was confirmed by in situ hybridization. Cells morphologically similar to Perkinsus sp. trophozoites were observed in 0.7% of the mussels analysed; however, infection with Perkinsus spp. could neither be confirmed by ISH nor by PCR. Different pathological aspects, such as host defence responses and regressive/progressive changes were detected in the gills, digestive glands, gonads and mantle. Only one single case of disseminated neoplasia (0.2%) was observed. As for the biomarker evaluation, the MANOVA analysis revealed the statistically significant effect that the variable “sampling site” had on the biological parameter measured, thus suggesting that the multibiomarker approach was able to differentiate the rearing sites. [ABSTRACT FROM AUTHOR]