Composition Of Microorganisms Research Articles

Enhanced nitrogen and phosphorus removal from mariculture water using immobilized bacteria and macroalgae

With the vigorous development of the mariculture industry, the untreated wastewater from mariculture has exerted significant pressure on the water environment. The untreated N and P in the wastewater from mariculture can deteriorate the quality of the mariculture. In this study, a composite in situ treatment system involving macroalgae (Caulerpa lentillifera/Caulerpa sertularoides f. Longipes) and immobilized degrading bacteria was established to handle wastewater from shrimp culture. The changes in nutrients in aquaculture wastewater were studied by chemical analysis, and the microbial community structure was analyzed using molecular biology technology and high-throughput sequencing technology. The removal efficacy of nutrients in aquaculture wastewater and the composition of microorganisms in the wastewater were examined, and the primary causes for the alteration of the microbial community were analyzed. The results demonstrated that when the macroalgae in the system were Caulerpa lentillifera (CL), the removal efficiencies of TN, PO43--P, and COD from shrimp culture were 59.04%, 34.26%, and 68.61% respectively. When the macroalgae was Caulerpa sertularoides f. Longipes (CSF), the removal efficiencies of TN, PO43--P, and COD generated by experimental shrimp culture were 51.50%, 33.69%, and 50.88% respectively. The biomass (wet weight) of both macroalgae species also increased, facilitating the removal of nutrients from the wastewater. Additionally, both Proteobacteria and Bacteroidetes were the dominant bacteria in the three samples, and the addition of the composite in-situ treatment system had no impact on the dominant bacteria in the water. The results of FAPROTAX analysis indicated that compared with the untreated samples, the abundances of methyl-functional bacteria and amino acid-functional bacteria in the samples increased due to organic matter such as COD produced during shrimp culture and the addition of feed, suggesting that shrimp culture can influence the abundances of functional bacteria in the water. In conclusion, the combined in situ treatment system can effectively eliminate nutrients from aquaculture wastewater, and the combined effect of macroalgae and immobilized degrading bacteria plays a vital role in this process.

Environmental Heat Stress Decreases Sperm Motility by Disrupting the Diurnal Rhythms of Rumen Microbes and Metabolites in Hu Rams.

Heat stress (HS) has become a common stressor, owing to the increasing frequency of extreme high-temperature weather triggered by global warming, which has seriously affected the reproductive capacity of important livestock such as sheep. However, little is known about whether HS reduces sperm motility by inducing circadian rhythm disorders in rumen microorganisms and metabolites in sheep. In this study, the year-round reproduction of two-year-old Hu rams was selected, and the samples were collected in May and July 2022 at average environmental temperatures between 18.71 °C and 33.58 °C, respectively. The experiment revealed that the mean temperature-humidity index was 86.34 in July, indicating that Hu rams suffered from HS. Our research revealed that HS significantly decreased sperm motility in Hu rams. Microbiome analysis further revealed that HS reshaped the composition and circadian rhythm of rumen microorganisms, leading to the circadian disruption of microorganisms that drive cortisol and testosterone synthesis. Serum indicators further confirmed that HS significantly increased the concentrations of cortisol during the daytime and decreased the testosterone concentration at the highest body temperature. Untargeted metabolomics analysis revealed that the circadian rhythm of rumen fluid metabolites in the HS group was enriched by the cortisol and steroid synthesis pathways. Moreover, HS downregulated metabolites, such as kaempferol and L-tryptophan in rumen fluid and seminal plasma, which are associated with promotion of spermatogenesis and sperm motility; furthermore, these metabolites were found to be strongly positively correlated with Veillonellaceae_UCG_001. Overall, this study revealed the relationship between the HS-induced circadian rhythm disruption of rumen microorganisms and metabolites and sperm motility decline. Our findings provide a new perspective for further interventions in enhancing sheep sperm motility with regard to the circadian time scale.

Three-Year Monitoring of Microorganisms' Composition and Concentration in Atmospheric Aerosols of Novosibirsk City and Suburbs.

The atmospheric environment is formed under the influence of local and distant sources as a result of horizontal and vertical transport. In the present work, microbiological analysis of 604 samples of atmospheric aerosol collected in the period from September 2020 to September 2023 at four sites differing in anthropogenic load, located in Novosibirsk and the region, was carried out. Day and night aerosol samples were collected during 12 h every two weeks by filtration using Sartorius reinforced Teflon membranes, then sown on a set of nutrient media. The taxonomic affiliation of the isolated microbial isolates was determined based on phenotypic characteristics and analysis of 16S rRNA gene nucleotide sequences. Changes in the composition and concentration of culturable microorganisms depending on the season, time of day, and site of aerosol sampling were observed. In winter, lower fungi and bacteria of the genera Bacillus, Staphylococcus, Micrococcus dominated with an average concentration from zero to 12.5 CFU/m3 of aerosol. In the warm period, the concentration and diversity of cocci, spore-forming and non-spore-forming bacteria, actinomycetes, and fungi (up to 1970 CFU/m3), among which pathogenic microorganisms were found, increased sharply in aerosols. The use of 16S metabarcoding techniques has greatly expanded the range of aerosols' microbial diversity detectable.

Are you filtering enough? Unveiling the impact of water sample volumes on eukaryotic microbial community in freshwater lakes

The appropriate volume of filtered water samples is crucial for accurately reflecting microbial community characteristics. Previous research has shown that changes in water sample volumes significantly affect bacterial diversity and the relative abundance of dominant taxa in marine environments. However, the specific impact on freshwater microbial diversity and community structure, particularly for eukaryotic microorganisms, remains unclear. To address this gap, we collected water samples from eutrophic Lake Taihu and mesotrophic Lake Bosten. We filtered the samples through 0.2 μm filters using volumes ranging from 0.1 to 2 L for Lake Taihu and 0.1 to 3.2 L for Lake Bosten. Analysis of 18S rRNA gene amplicons revealed that variations in filtered water sample volume significantly affected the diversity, community structure, and composition of eukaryotic microorganisms. In light of these findings, we recommend using a filtered water sample volume of approximately 0.2 L for eutrophic aquatic ecosystems and 0.8 L for mesotrophic aquatic ecosystems in microbial analyses. These recommendations underscore the importance of selecting the appropriate filtered water sample volume to ensure representative and reliable results in the study of eukaryotic microorganisms in freshwater ecosystems.

Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.

Rhizosphere microbial community assembly as influenced by reductive soil disinfestation to resist successive cropping obstacle.

Reductive soil disinfestation (RSD), which involves creating anaerobic conditions and incorporating large amounts of organic materials into the soil, has been identified as a reliable strategy for reducing soilborne diseases in successive cropping systems. However, limited research exists on the connections between soil microorganism composition and plant diseases under various types of organic material applications. This study aimed to evaluate the effects of distinct RSD strategies (control without soil amendment; RSD with 1500 kg ha-1 molasses powder; RSD with 3000 kg ha-1 molasses powder; RSD with 3000 kg ha-1 molasses powder and 37.5-41.3 kg ha-1 microbial agent) on the plant disease index, bacterial community composition and network structure in rhizosphere soil. RSD treatments significantly reduced the occurrence of black shank disease in tobacco and increased soil bacterial diversity. High amounts of molasses powder in RSD treatments further enhanced disease inhibition and reduced fungal abundance and Shannon index. RSD also increased the relative abundance of bacterial phylum Firmicutes and fungal phylum Ascomycota, while decreasing the relative abundance of bacterial phyla Chloroflexi and Acidobacteriota and fungal phylum Basidiomycota in rhizosphere soil. A multiple regression model identified bacterial positive cohesion as the primary factor influencing the plant disease index, with a greater impact than bacterial negative cohesion and community stability. The competition among beneficial bacteria for creating a healthy rhizosphere environment is likely a key factor in the success of RSD in reducing plant disease risk. RSD, especially with higher rates of molasses powder, is a viable strategy for controlling black shank disease in tobacco and promoting soil health by fostering beneficial microbial communities. This study provides guidelines for soil management and plant disease prevention. © 2024 Society of Chemical Industry.

Fungal Biostarter and Bacterial Occurrence of Dry-Aged Beef: The Sensory Quality and Volatile Aroma Compounds after 21 Days of Aging

In this study, we decided to test the hypothesis that the fungal biostarter M. flavus used during a 21-day beef dry-aging process significantly impacts the composition of other microorganisms, the profile of volatile compounds, meat hardness characteristics, and, consequently, the sensory quality. The experiments were performed on samples derived from animals crossbred between Holstein–Fresian cows and meat breed bulls. Two groups of samples were studied, including the control group, without biostarter, and a group inoculated with the M. flavus biostarter. Both sample groups were seasoned for 21 days in the dry-aging fridge. The physicochemical parameters (pH, color parameters), the chemical composition of muscle, the determination of the shear force, the profile of volatile compounds (VOCs), and the sensory quality were evaluated after aging. During this study, classical microbiological methods were used to investigate the influence of fungal biostarters on the growth and survival of bacteria and other fungi (e.g., yeasts) during the dry-aging process of beef (DAB). The M. flavus biostarter improved the sensory quality of DAB, allowing high sensory quality to be achieved after just 21 days. This is likely due to the diverse VOCs produced by the fungus, including 1-tetradecanol, 2-nonenal, trans-2-undecenoic acid, and the following esters: formic acid hexyl ester, 10-undecenoic acid methyl ester, and 4-methylpentanoic acid methyl ester. The presence of the biostarter had no significant effect on the number of the bacteria or the survivability of the L. monocytogenes on the meat’s surface in laboratory conditions.

Aeration treatment promotes transformation of soil phosphorus fractions to plant-available phosphorus by modulating rice rhizosphere microbiota

Microorganisms play an important role in affecting the content of available phosphorus (P) in plant rhizosphere soil. However, the effect of aeration on available P in rice rhizosphere soil and its microbial mechanism remain unclear. This study aimed to elucidate the effects of aeration strategies on available P and P-solubilizing microorganisms in rhizosphere soil, employing three different aeration methods (continuous flooding (CF), continuous flooding and aeration (CFA), and alternate wetting and drying (AWD)). We analyzed the bacterial and fungal community structures in rice rhizosphere soil via Illumina sequencing techniques and quantified the abundance of P transformation functional genes related to inorganic P solubilization (pqqC) and organic P mineralization (phoC, phoD, and appA) through quantitative PCR. Our findings revealed that the AWD treatment significantly increased soil pH and Eh; Both AWD and CFA treatments markedly increased soil Olsen-P content at the tillering and heading stages, as well as the microbial carbon-to-phosphorus ratio (MBC/MBP) at the heading and maturity stages. Cluster analysis showed distinct bacterial communities at the heading and maturity stages under AWD, which differed from those in other treatments. Fungal communities at the tillering and heading stages under CFA and AWD grouped together. AWD and CFA treatments consistently enhanced labile-P in the rhizosphere soil throughout the entire growth stages, while reducing moderately labile-P during the tillering and heading stages. Compared to CF, at the heading and maturity stages, the copy numbers of pqqC, phoD, phoC, and appA were higher under AWD compared to other treatments. In conclusion, this study posits that the increase in Olsen-P in paddy fields due to aeration results from improved oxygen conditions in the rhizosphere, alterations in pH and Eh, effects on microbial stoichiometry, and adjustments in the abundance and composition of P-solubilizing microorganisms, thereby promoting P transformation. This conclusion provides new insights into the conversion of soil P Fractions into plant-available forms.

Atractylodes macrocephala polysaccharides shield a D-galactose-induced aging model via gut microbiota modulation

This study explored the effect of a heteropolysaccharide (RAMP) on aging model mice and the importance of changes in the gut microbiota mediated by RAMP for the first time. The findings revealed that RAMP exerted protective effects on cognitive decline and oxidative stress in mice subjected to D-gal-induced aging, potentially by regulating the intestinal flora, according to the results of the Morris water maze test; brain and immune organ indices; hematoxylin and eosin-stained cerebral cortex images; transmission electron microscopy analysis of cortical neurons; and biochemical index measurements. In addition, 16S rRNA sequencing revealed notable changes in the abundance of Acidobacteriota, Anaerovoracaceae, and GCA-900066575 in the mouse model, all of which were abrogated by RAMP. These findings confirm that RAMP regulates the composition of mouse intestinal microorganisms. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional analyses linked these changes to 27 metabolic pathways, including those of the nervous system. Furthermore, metabolomics analysis revealed four RAMP-regulated metabolites related to lipid metabolism (2-dodecylbenzenesulfonic acid, N-undecylbenzenesulfonic acid, aspartyl-isoleucine, and 1-palmitoyl-2-(5-oxo-valeroyl)-sn-glycero-3-phosphate), suggesting that the mechanism potentially associated with lipid metabolism regulation. This study provides novel insights into the antiaging mechanisms of RAMP, suggesting its potential use in antiaging treatments.

Effects of water immersion on immune, intestinal flora and metabolome of Chinese mitten crab (Eriocheir sinensis) after air exposure

Air exposure stress can induce stress response of Eriocheir sinensis and affect its normal life activities. The goal of this study was to investigate the effects of water immersion on the recovery of hepatopancreas immune-related enzyme activity, intestinal microbial diversity and metabolic level of Chinese mitten crabs after exposure to air. The results show that immersion can effectively alleviate the adverse effects of air exposure on the antioxidant capacity and immune capacity of Chinese mitten crabs, and the longer the time of immersion, the more obvious the recovery effect. Among them, the levels of aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase and acid phosphatase significantly increased after exposure to air (P < 0.05), reached a peak at 3 h, began to decline after immersion, and returned to a level close to the initial value at 24 h (P < 0.05). In addition, after exposure to air, the glucose and total cholesterol in haemolymph of Eriocheir sinensis were significantly different from the initial values (P < 0.05), gradually recovered to the initial level after re-immersion. However, changes in intestinal flora and hepatopancreas metabolism caused by air exposure did not fully recover after water exposure, and its negative effects did not completely disappear. The sequencing results showed that the species composition and diversity of intestinal microorganisms of Chinese mitten crab changed after air exposure and immersion treatment. The relative abundance of Actinomycetes increased significantly, while that of Proteobacteria and Firmicutes decreased significantly. Metabolomics analysis showed that air exposure and immersion destroyed the metabolic balance of amino acids and carnitine, reduced the level of carnitine metabolism, hindered the absorption of nutrients, and led to the accumulation of harmful substances.

Effect of Rice–Carp Coculture on Phytoplankton and Microzooplankton Community Composition in Paddy Water during Different Rice Growth Stages

Integrated rice–fish farming, an agricultural practice that combines cultivating rice and breeding fish in the same field, has attracted widespread attention. However, there is limited research on how the rice–carp coculture impacts the community structure of phytoplankton and microzooplankton in paddy water. This study employed eDNA metabarcoding sequencing to analyze the composition of phytoplankton and microzooplankton in a rice monoculture system (RM) and a rice–carp coculture system (RF). Following annotation, we identified 9 phyla, 89 families, 275 genera, and 249 species of phytoplankton, along with 20 phyla (or subphyla and classes), 85 families, 222 genera, and 179 species of microzooplankton. The alpha diversity indices revealed significantly higher richness, diversity, and evenness in the RF group compared to the RM group during grain-filling stage. Principal coordinates analysis (PCoA) demonstrated notable differences in the phytoplankton and microzooplankton compositions between the two groups across various rice growth stages. Composition analysis showed that rice–carp coculture increased the relative abundance of dominant phytoplankton phyla such as Bacillariophyta, Chrysophyta, and Euglenophyta while decreasing that of Cryptophyta. In microzooplankton, the coculture resulted in an increased abundance of Intramacronucleata (subphylum) and a decrease in Conoidasida (class). In conclusion, the rice–carp coculture enhances the diversity of plankton, particularly during the grain-filling stage, and simultaneously alters the composition and abundance of dominant plankton species in the paddy water. These findings enhance understanding of the broader impacts of integrated rice–carp farming on agricultural ecosystems, emphasizing alterations in the diversity and composition of aquatic microorganisms

ZiBu PiYin recipe regulates central and peripheral Aβ metabolism and improves diabetes-associated cognitive decline in ZDF rats

Ethnopharmacological relevanceCognitive impairment caused by central neuropathy in type 2 diabetes mellitus (T2DM), namely diabetes-associated cognitive decline (DACD), is one of the common complications in patients with T2DM. Studies have shown that brain β-amyloid (Aβ) deposition is a typical pathological change in patients with DACD, and that there is a close relationship between intestinal microorganisms and cognitive impairment. However, the specific mechanism(s) of alteration in Aβ metabolism in DACD, and of the correlation between Aβ metabolism and intestinal microorganisms remain unknown. Aim of the studyRevealing the mechanism of ZBPYR regulating Aβ metabolism and providing theoretical basis for clinical evaluation and diagnosis of DACD. Materials and methodsWe characterized Aβ metabolism in the central and peripheral tissues of Zucker diabetic fatty (ZDF) rats with DACD, and then explored the preventive and therapeutic effects of ZiBu PiYin Recipe (ZBPYR). Specifically, we assessed these animals for the formation, transport, and clearance of Aβ; the morphological structure of the blood-brain barrier (BBB); and the potential correlation between Aβ metabolism and intestinal microorganisms. ResultsZBPYR provided improvements in the structure of the BBB, attenuation of Aβ deposition in the central and peripheral tissues, and a delay in the development of DACD by improving the expression of Aβ production, transport, and clearance related protein in ZDF rats. In addition, ZBPYR improved the diversity and composition of intestinal microorganisms, decreased the abundance of Coprococcus, a bacterium closely related to Aβ production, and up regulate the abundance of Streptococcus, a bacterium closely related to Aβ clearance. ConclusionThe mechanism of ZBPYR ability to ameliorate DACD may be closely related to changes in the intestinal microbiome.

Microbial diversity and cellulase activity of forest soils and litters

The quantity, composition and cellulase activity of forest soils and litters with deciduous and coniferous tree vegetation on the territory of Natural Park "Vitosha" were investigated. Biogenicity, the rate of decomposition of organic matter and specifically of cellulose decomposition were higher in Fagus sylvatica litters than in Pinus sylvestris. In most soil profiles, the total microflora has higher values in the mixed fermentative and humic layer of the litter compared to the fresh litter. The quantity of microorganisms and cellulase activity decrease in the depth of the soil profiles. In general, non-spore-forming bacteria, followed by mold fungi and bacilli, occupy a major share in the composition of the total microflora in litters and soils, and actinomycetes are less represented. The cellulase activity depends to the highest degree on the non-sporulating bacteria, and the values of the mineralization coefficient on the bacteria assimilating mineral nitrogen. The humidity of the litters and soils has a stronger influence on the development, composition, mineralization and cellulase activity of microorganisms, compared to the altitude.

Combined analysis of cecal microbiota and metabolomics reveals the intervention mechanism of Dayuan Yin in acute lung injury.

The ancient Chinese medicinal formula, Dayuan Yin (DYY), has a long history of use in treating respiratory ailments and is shown to be effective in treating acute infectious diseases. This study aims to explore how DYY may impact intestinal flora and metabolites induced by acute lung injury (ALI). ALI rats were induced with lipopolysaccharide (LPS) to serve as models for assessing the anti-ALI efficacy of DYY through multiple lung injury indices. Changes in intestinal microflora were assessed via 16SrRNA gene sequencing, while cecum contents were analyzed using non-targeted metabonomics. Differential metabolites were identified through data analysis, and correlations between metabolites, microbiota, and inflammatory markers were examined using Pearson's correlation analysis. DYY demonstrated a significant improvement in LPS-induced lung injury and altered the composition of intestinal microorganisms, and especially reduced the potential harmful bacteria and enriched the beneficial bacteria. At the gate level, DYY exhibited a significant impact on the abundance of Bacteroidota and Firmicutes in ALI rats, as well as on the regulation of genera such as Ruminococcus, Lactobacillus, and Romboutsia. Additionally, cecal metabonomics analysis revealed that DYY effectively modulated the abnormal expression of 12 key metabolic biomarkers in ALI rats, thereby promoting intestinal homeostasis through pathways such as purine metabolism. Furthermore, Pearson's analysis indicated a strong correlation between the dysregulation of intestinal microbiota, differential metabolites, and inflammation. These findings preliminarily confirm that ALI is closely related to cecal microbial and metabolic disorders, and DYY can play a protective role by regulating this imbalance, which provides a new understanding of the multi-system linkage mechanism of DYY improving ALI.

Insights into Women's health: Exploring the vaginal microbiome, quorum sensing dynamics, and therapeutic potential of quorum sensing quenchers

The vaginal microbiome is an important aspect of women's health that changes dynamically with various stages of the woman's life. Just like the gut microbiome, the vaginal microbiome can also be affected by pathologies that dramatically change the typical composition of native vaginal microorganisms. However, the mechanism as to how both vaginal endemic and gut endemic opportunistic microbes can express pathogenicity in vaginal polymicrobial biofilms is poorly understood. Quorum sensing is the cellular density-dependent bacterial and fungal communication process in which chemical signaling molecules, known as autoinducers, activate expression for genes responsible for virulence and pathogenicity, such as biofilm formation and virulence factor production. Quorum sensing inhibition, or quorum quenching, has been explored as a potential therapeutic route for both bacterial and fungal infections. By applying these quorum quenchers, one can reduce biofilm formation of opportunistic vaginal microbes and combine them with antibiotics for a synergistic effect. This review aims to display the relationship between the vaginal and gut microbiome, the role of quorum sensing in polymicrobial biofilm formation which cause pathology in the vaginal microbiome, and how quorum quenchers can be utilized to attenuate the severity of bacterial and fungal infections.

Soil Microbial Properties of Durum Grown after Camelina, Carinata, Cover Crops, and Fallow

Novel crop rotation is an important factor influencing the composition of soil microorganisms. However, the effect of introducing oilseed and cover crops (CCs) into monoculture durum rotations on soil microbial communities is not clear in the Northern Great Plains. The objective of this study was to evaluate the effects of 2-year durum (Triticum durum D.) rotations with Ethiopian mustard (Brassica carinata A.) or camelina (Camelina sativa L.) or a 10-species forage/CC mix planted to replace fallow rotations with wheat on soil microorganisms. This study was designed as a randomized complete block with three replications in a no-tillage system. The results showed that total bacterial proportion was significantly higher in durum following fallow and camelina compared to durum following CC and carinata. Total fungal proportion was significantly higher in durum following CC compared to durum following oilseed crops and fallow. The fungal-to-bacterial ratio was significantly higher in durum following CC compared to durum following camelina and fallow. The crop species, soil pH and highly variable rainfall influenced the microbial community dynamics. The abundance of specific microbial groups due to crop-related changes might play a key role in the yield of subsequent crops and soil biological health. This study provides valuable insights into the use of CC mix and oilseeds as an alternative crop for fallow in a wheat–fallow system under dryland farming conditions. Future work is required to elucidate the biological mechanisms and functions of the soil microbial communities in the preceding and subsequent crop relative to soil health and crop productivity.

Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba.

Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.

Diversity in gut microbiota among colorectal cancer patients: findings from a case–control study conducted at a Tunisian University Hospital

PurposeGlobally, colorectal cancer (CRC) is among the most prevalent cancers. One distinctive feature of colorectal cancer is its close relationship to the gut microbiota, which is a crucial component of the tumor microenvironment. Over the last ten years, research has demonstrated that colorectal cancer is accompanied with dysbiosis of gut bacteria, fungi, viruses, and Archaea, and that these alterations may be causal. Objectives: This study aimed to evaluate the disruption of the microorganism composition in the intestine, especially bacteria and to determine their relationship with colorectal cancer.MethodsAn evaluation system for determining colorectal cancer (CRC) risk and prognosis can be established more easily with the help of accurate gut microbiota profiling. Stool samples from 14 CRC patients and 13 controls were collected and the flora relative abundance was measured using targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers: Streptococcus gallolyticus and Enterococcus faecalis. Culture and MALDI-TOF mass spectrometry were coupled to identify the gut microbiota in both colorectal cancer and control groups.ResultsCompared with controls, the gut microbiota of CRC patients showed an increase in the abundance of Enterococcus, Fusobacterium and Streptococcus. At the species level, the CRC enriched bacterium including Escherichia coli, Enterococcus faecalis, Fusobacterium nucleatum, Streptococcus gallolyticus, Flavoni fractorplautii and Eggerthella lenta acted as promising biomarkers for early detection of CRC.ConclusionThis study highlights the potential of gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with CRC.

The sewer advances: How to select eco-friendly pipe materials for environmental protection

Sewer pipe materials exhibit diverse inner-surface features, which can affect the attachment of biofilm and influence microbial metabolic processes. To investigate the role of the type of pipe material on the composition and metabolic capabilities of the adhering microorganisms, three sets of urban sewers (High-Density Polyethylene Pipe (HDPE), Ductile Iron Pipe (DIP), and Concrete Pipe (CP)) were constructed. Measurements of biofilm thickness and environmental factors revealed that the thickest biofilm in CP pipes reached 2000 μm, with ORP values as low as −325 mV, indicating a more suitable anaerobic microbial habitat. High-throughput sequencing showed similar relative abundances of genera related to carbon and sulfur metabolism in the DIP and CP pipes, whereas HDPE exhibited only half the relative abundance compared to that found in the other pipes. To explore the impact of pipe materials on the mechanisms of microbial response, a metagenomic approach was used to investigate the biological transformation of carbon and sulfur in wastewater. The annotations of the crucial enzyme-encoding genes related to methyl coenzyme M and sulfite reductase in DIP and CP were 50 and 110, respectively, whereas HDPE exhibited lower counts (25 and 70, respectively). This resulted in significantly lower carbon and sulfur metabolism capabilities in the HDPE biofilm than in the other two pipes. The stability of wastewater quality during the transmission process in HDPE pipes reduces the metabolic generation of toxic and harmful gases within the pipes, favoring the preservation of carbon sources for sewer systems. This study reveals the variations in carbon and sulfur metabolism in wastewater pipe systems influenced by pipe materials and provides insights for designing future sewers.

Effects of low temperature air exposure and immersion on antioxidant, immune, intestinal flora and metabolome of Chinese mitten crab (Eriocheir sinensis)

The aim of this study was to investigate the effects of immersion on immune enzyme activity, haemolymph index, intestinal microbiome and metabolome of E. sinensis after low temperature air exposure. The results showed that low temperature air exposure induced stress response, which led to hepatopancreas injury and increased membrane permeability, but this situation was reversible and alleviated after immersion. In addition, after exposure to low temperature air, haemolymph metabolism-related substances such as glucose and total cholesterol were significantly different from the initial value (P < 0.05), and gradually returned to the initial level after immersion. The changes of intestinal flora and hepatopancreas metabolism caused by low temperature air exposure did not fully recover after immersion, and its negative effects did not completely disappear. The sequencing results showed that the species composition and diversity of intestinal microorganisms of Chinese mitten crabs were changed after low temperature air exposure and immersion treatment. The relative abundance of Bacteroidetes and Proteobacteria were increased, while the relative abundance of Firmicutes was decreased (P < 0.05). Metabolomics analysis showed that lysine levels increased significantly, taurocholic acid levels decreased significantly, and amino acid metabolism and lipid metabolism balance were disturbed in hepatopancreas of E. sinensis after exposure to low temperature air and immersion (P < 0.05). This study will provide new insights into the recovery mechanism of water immersion on Chinese mitten crabs after exposure to air.