Main Genera Research Articles

Effects of simulated low-temperature thermal remediation on the microbial community of a tropical creosote contaminated soil.

In the search for more sustainable remediation strategies for PAH-contaminated soils, an integrated application of thermal remediation and bioremediation (TEB) may allow the use of less impacting temperatures by associating heating to biological degradation. However, the influence of heating on soil microbiota remains poorly understood, especially in soils from tropical regions. This work investigated the effects of low-temperature heating on creosote-contaminated soil bacteria. We used culture-dependent and 16S rRNA sequencing methods to compare the microbial community of soil samples heated to 60 and 100 oC for 1h in microcosms. Heating to 60°C reduced the density of cultivable heterotrophic bacteria compared to control soil (p < 0.05), and exposure to 100°C inactivated the viable heterotrophic community. Burkholderia-Caballeronia-Paraburkholderia (BCP) group and Sphingobium were the predominant genera. Temperature and incubation time affected the Bray-Curtis dissimilarity index (p < 0.05). At 60°C and 30 days incubation, the relative abundance of Sphingobium decreased and BCP increased dominance. The network of heated soil after 30 days of incubation showed fewer nodes and edges but maintained its density and complexity. Both main genera are associated with PAH degradation, suggesting functional redundancy and a likely potential of soil microbiota to maintain biodegradation ability after exposure to higher temperatures. We concluded that TEB can be considered as a potential strategy to bioremediate creosote-contaminated soils, allowing biodegradation in temperature ranges where thermal remediation does not completely remove contaminants. However, we recommend further research to determine degradation rates with this technology.

The Application of Culturomics to Explore African Skin Microbiota.

Over the past 12 years, culturomics, a high-throughput culture method, has been developed, considerably widening the repertoire of known cultured bacteria. An exhaustive database, including a list of microbes isolated by culture from human skin, was recently established by performing a review of the literature. The aim of the present study was to use the culturomics approach to explore the African skin microbiota. Skin swabs from the palms of human hands were collected between January and December 2016 from healthy subjects from the villages of Dielmo and Ndiop in rural Senegal. Three culture media were selected for the isolation of bacteria in aerobic conditions. Bacterial colonies were subjected to matrix-assisted laser desorption ionization-time of flight mass spectroscopy and the 16 S rRNA gene was sequenced for unidentified colonies. A total of 176 bacterial species were isolated. This increased the repertoire of bacterial species on the skin by 14.0%, by adding 71 bacteria, including seven new species. The culturomics approach characterizing microbial diversity has significantly changed our view of the skin microbiota, raising many important questions about the host-microorganism relationship and its relevance to skin diseases. In particular, the difference between the palm microbiota of these African populations (composed mainly of the genera Staphylococcus, Arthrobacter, Bacillus, and Microbacterium) and that of Western populations, whose main genera are Staphylococcus, Propionibacterium, Micrococcus, Corynebacterium, Enhydrobacter, and Streptococcus. This study demonstrates the need to continue to explore the skin microbiome using the culturomics approach.

Bacterial community succession and its correlation with the dynamics of flavor compound during processing of Enshi bacon

Enshi bacon, a famous specialty in Enshi Prefecture, Hu Bei, China, is renowned among customers for the nutritious content and distinct smoky flavor. This study explored the flavor and bacterial flora changes of Enshi bacon during processing and investigated the effect of bacteria on flavor formation. The results showed that the main genera in the pre-processing stage were Brochothrix, Lactococcus and Psychrobacter, which originated from raw meat. Salt-tolerant Staphylococcus and Cobetia were the dominant genera in the late stage of processing. Five free amino acids (aspartic acid, glutamic, alanine, valine, and lysine) were recognized as the flavor substances promoting taste, while aldehydes and phenols were the volatiles that contributed the most to odor. Particularly, compared to the smoking phase, phenolic content increased 2.25-fold at the end of fermentation through microbial action and tyrosine catabolism. The correlation study showed Staphylococcus and Lactococcus as fundamental functional genera that are essential for the formation of bacon flavor. This study provided reference data for the changes in flavor indicators and flora during the processing of Enshi Bacon, revealed the potential mechanism of core functional flora and characteristic flavor formation, and provided a theoretical basis for quality control of the manufacturing process.

Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease

BackgroundCoronary heart disease (CHD) is a common cardiovascular disease that is associated with altered gut microbiota. Enteroviruses, an essential component of the gut microbiome, may play an important role in disease progression. However, the relationship between enteroviruses and CHD remains unclear. The development of high-throughput sequencing technologies has facilitated research on the interconnections between viruses and disease-related metabolites.Methods and resultsMice were fed a high-fat diet (CHD group) or chow diet (Sham group) for 12 weeks, and ligation of the left anterior descending coronary artery was performed at the end of week 8. After 4 weeks, all animals were euthanised. Subsequently, the animals were evaluated for basic haemato-biochemical parameters and cardiac function, and aorta staining was performed. Based on enteroviral metagenomics and serum UPLC–MS/MS metabolomics analyses, we evaluated the association between enteroviral groups and serum metabolites of CHD mouse model. A high-fat diet and coronary ligation enabled the establishment of the CHD mouse model. Notably, the enterovirus spectrum of the sham group was significantly different from that of the CHD group, with 24 viral communities of different family and species classification, such as Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus, exhibiting significant differences. In addition, 731 Differential metabolites were detected in the serum of both groups of mice. Correlation network analysis revealed a close relationship between various metabolites related to lipid metabolism and different viruses, including Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus.ConclusionsAn animal model of CHD, characterised by lipid disturbance and myocardial ischaemia, was established using a high-fat diet and ligation of the left anterior descending branch of the coronary artery. Tsarbombavirus, Firehammervirus, Mingyongvirus, and Claudivirus were associated with metabolites in the lipid metabolism pathway. The results indicate that Tsarbombavirus may be the main genus interacting with CHD-related metabolites in mice. Conclusively, the findings of our study provide novel insights into the potential relationship enterovirus groups and metabolites associated with CHD.

Microbiomic and metabolomic dynamics in chrysanthemum waste at different fermentation stages

The microbial community and metabolite profile during the fermentation of chrysanthemum waste (CW) were studied, as well as the effect of feeding fermented chrysanthemum waste (FCW) to sows. The nutritional value of CW fermented for 30–90 days was similar to that of CW fermented for 7 days. With increasing time, the number of bacterial species, richness index, and diversity index increased. The main genera were Pediococcus. A total of 270 different metabolites were identified in FCW, among which benzenoids, amino acids, flavonoids, fatty acids, and peptides were the most significantly different metabolites. Flavone and flavonol biosynthesis, and flavonoid biosynthesis were the most important metabolic pathways in fermentation. Feeding FCW to sows was beneficial for their production performance. These provide new insights into the characteristics of microbiome and metabolome associated with CW during long-term fermentation and the feed availability of FCW.

Physicochemical characteristics and bacterial communities of meigan cai and zao cai, two home-made fermented vegetables

Meigan cai and zao cai are two important traditional fermented vegetables in Fujian Province, China. However, there is little information on the bacterial community of these two fermented vegetables. In the present work, we evaluated and compared the physicochemical characteristics and bacterial communities of meigan cai and zao cai. Results revealed that Firmicutes and Proteobacteria were the main dominant phyla, and Lactobacillus and Serratia were the main genera. Principal coordinate and significance analysis showed that the bacterial communities were similar between meigan cai and zao cai. Except for glucose, there was no significant difference in the physicochemical characteristics between meigan cai and zao cai. Our study provided information on the bacterial communities of meigan cai and zao cai, and a guide for the production of these two fermented vegetables.

Host specificity in the fungal plant parasite Anthracoidea sempervirentis (Anthracoideaceae, Ustilaginales) reveals three new species and indicates a potential split in the host plant Carex sempervirens.

The smut fungal genus Anthracoidea contains more than 100 species that parasitize hosts predominantly in the sedge genus Carex. Anthracoidea species are mainly found in the boreal zones of the Northern Hemisphere and many species have an arctic-alpine distribution. Recent re-organization of the taxonomy of the main host genus Carex questions current understanding of host associations in Anthracoidea. Host specificity for many of the species in this genus is considered to be quite broad and a host spectrum of over 10 host species is common. One aim of the study is to understand the potential influence that host taxonomy has on the evolutionary patterns of Anthracoidea. Additionally, by including more specimens, we clarify host specificity and species delimitation in Anthracoidea sempervirentis, a prevalent species occurring on different host species in different Carex subgroups using molecular data. Host colonization patterns within Anthracoidea are complex, and different subclades of Carex have been colonized several times independently, whereas clades of related Anthracoidea species often occur on Carex species from the same host clade. Parasites previously thought to be Anthracoidea sempervirentis occurring on the different Carex host are shown to be at least four distinct species that are restricted to individual host species. Three new species, Anthracoidea ferrugineae on Carex ferruginea from the Alps and the Carpathians, A. firmae on Carex firma from the Alps, and A. kitaibelianae on Carex kitaibeliana from mountains in the Balkan Peninsula, are described and illustrated. An emended description of Anthracoidea sempervirentis is also provided. Anthracoidea sempervirentis in its emended circumscription consists of two clades that correspond to respective clades within Carex sempervirens. The study shows that host colonization in Anthracoidea is more complex than current host taxonomy suggests. Further, including several specimens per host species results in a much higher diversity within Anthracoidea than previously assumed. Citation: Kemler M, Denchev TT, Feige A, Denchev CM, Begerow D (2024). Host specificity in the fungal plant parasite Anthracoidea sempervirentis (Anthracoideaceae, Ustilaginales) reveals three new species and indicates a potential split in the host plant Carex sempervirens. Fungal Systematics and Evolution 13: 91-110. doi: 10.3114/fuse.2024.13.04.

Composition and distribution of bacterial communities and potential radiation-resistant bacteria at different elevations in the eastern Pamirs.

Altitude and ultraviolet (UV) radiation may affect the community composition and distribution of microorganisms in soil ecosystems. In this study, 49 soil samples from 10 locations were collected from different elevations on the eastern Pamir Plateau and analyzed for soil microbial community structure and function using high-throughput sequencing. The results showed that soil samples from different elevations of the eastern Pamir Plateau contained 6834 OTUs in 26 phyla and 399 genera. The dominant phyla common to different elevations were Actinobacteria, Proteobacteria, Bacteroidota, Acidobacteriota, and Gemmatimonadota. The dominant genera were Rubrobacter, Sphingomonas, Nocardioides, and Solirubrobacter. Species richness increased slightly with elevation, and there were significant differences in community composition between the elevations. Elevation and UV exposure are important factors that drive changes in bacterial communities. The results of the KEGG pathway showed that drug resistance, antineoplastic, aging, replication, and repair were enhanced and then slightly decreased with increasing elevation. Bacterial communities at different elevations were rich in radiation-resistant microorganisms, and the main genera were Rubrobacter, Sphingomonas, Nocardioides, Pontibacter, and Streptomyces. The findings have shown the composition and distribution of bacterial communities at different elevations on the Eastern Pamir Plateau. Potentially radiation tolerant microbial species were also examined. The results are of considerable importance for the succession of bacterial microorganisms in the plateau region, the study of radiation tolerant bacterial germplasm resources, and the application of biofunctionality.

Comparative analysis of commercial cleaning and disinfection formulations and protocols for effective eradication of biofilms formed by a Pseudomonas fluorescens strain isolated from a poultry meat plant

Pseudomonas spp. is the main genus of spoilage bacteria for meat stored under aerobic chilling conditions. Given their ability to adapt to various environmental conditions and to form biofilms, they are common among residential microbiota in the food industry. Biofilms are complex, structured microbial communities encased in a self-produced exopolysaccharide matrix. Resident biofilm bacteria show increased resistance against disinfectants and dynamic or hostile environments, and are therefore a persistent source of food contamination. Hence, there is a need to design and implement control strategies that are effective against biofilms in the food industry. In this study, we tested a series of commercial cleaning and disinfection agents applied by immersion or aerosolization against robust biofilms of a Pseudomonas fluorescens strain isolated from a poultry meat plant by comparing the sessile cell counts before and after the procedure. The single application of a) an alkaline or an enzymatic detergent, b) a disinfectant based on peracetic acid and hydrogen peroxide, or c) a detergent-disinfectant based on tertiary alkylamines or sodium hypochlorite, failed to completely eradicate the biofilm. However, two-step cleaning and disinfection procedures involving the application of a detergent (either alkaline or enzymatic at 50 °C) followed by the application of the disinfectant based on peracetic acid and hydrogen peroxide at the manufacturer's recommended concentrations did result in the complete eradication (p ≤ 0.05) of the robust biofilm. In addition, cleaning and disinfection procedures applied by aerosolization showed a notable efficacy (p ≤ 0.05) against surface-dried cells and sessile cells of P. fluorescens. Therefore, this approach could be regarded as a potentially viable alternative to commonly applied immersion techniques.

Effects of denitrification on speciation and redistribution of arsenic in estuarine sediments

Microbially-mediated redox processes involving arsenic (As) and its host minerals significantly contribute to the mobilization of As in estuarine sediments. Despite its significance, the coupling between As dynamics and denitrification processes in these sediments is not well understood. This study employed sequential sediment extractions and simultaneous monitoring of dissolved iron (Fe), nitrogen (N), and sulfur (S) to investigate the impact of nitrate (NO3−) on the speciation and redistribution of As, alongside changes in microbial community composition. Our results indicated that NO3− additions significantly enhance anaerobic arsenite (As(III)) oxidation, facilitating its immobilization by increased adsorption onto sediment matrices in As-contaminated estuarine settings. Furthermore, NO3− promoted the conversion of As bound to troilite (FeS) and pyrite (FeS2) into forms associated with Fe oxides, challenging the previously assumed stability of FeS/FeS2-bound As in such environments. Continuous NO3− additions ensured As and Fe oxidation, thereby preventing their reductive dissolution and stabilizing the process that reduces As mobility. Changes in the abundance of bacterial communities and correlation analyses revealed that uncultured Anaerolineaceae and Thioalkalispira may be the main genus involved in these transformations. This study underscores the critical role of NO3− availability in modulating the biogeochemical cycle of As in estuarine sediments, offering profound insights for enhancing As immobilization techniques and informing environmental management and remediation strategies in As-contaminated coastal regions.

Effects of sludge retention time on sludge reduction by ultrasound treatment: Sludge characteristics, microbial community, and metabolism

Both ultrasound and sludge retention time (SRT) enable the in-situ sludge reduction during wastewater treatment, but the influence of SRT on ultrasonic lysis – cryptic growth is unclear. This paper researched the influence of different SRTs on sludge lysis - cryptic growth using a sequential bio-reactor (SBR), then explained in details the changes of microorganisms in the SBR. The best SRT for sludge reduction was 30 d, and 47.29% reduction in sludge was achieved. The different SRTs changed the organic matter removal in the wastewater, and the removal rate decreased when SRT exceeded 60 d. The size of the sludge particles varied depending on the SRT, with the smallest size at SRT of 10d being 45.6 μm and the largest size at SRT of 90d being 110.0 μm. SEM showed that the sludge surface changed rough at longer SRT. FTIR and XPS showed notable effect in sludge functional group strength at SRT of 30 d. Extracellular polymeric substance (EPS) reduced the most at SRT of 30 d. The microbial communities of sludge varied with the SRT, and the unique main genus at SRT of 5, 15, 30 and 90 d were C10-SB1A, Lactococcus, Propioniciclava, Lactococcus, respectively. Furthermore, the SRT changed relative abundance of enzymes concerned with metabolism of carbon, nitrogen, and phosphorus. Similarly, SRT changed the metabolic rate, and the metabolic rate of carbon, nitrogen and phosphorus was best at SRT of 30 d.

Shelf life extended: Focus on microbiota identification, nutrition value, color difference and lipid oxidation of puffed bean products

Puffed bean products(PBP)contain a large amount of protein, and are susceptible to microbial contamination or harmful substances during storage and processing. In this study, the migration rule of microbial quantity and basic index during storage of the same batch and taste PBP was analyzed, and the spoilage bacteria in different periods of PBP were identified and analyzed by high-throughput DNA sequencing (HTS) The results showed that the peroxide value, acid value and mold count of PBP did not exceed the Chinese national standard, and the peak heights of the functional group characteristic peaks in different periods did not change significantly, further indicating that the degree of oxidation of fats and oils in the PBP was relatively light. During storage, the total colony count of PBP increased rapidly in the first two weeks, and controlling the microbial count of the products is the key to extend the shelf life of PBP. Bacterial colonisation affected the alkaline nitrogen and free amino acid content, resulting in a small increase in content. There was no significant change in the content of water activity this may be related to the choice of vacuum packaging for PBP. The brightness value in the colour difference value increased and the redness value decreased this may be related to the high temperature during the high temperature refining process of the chilli seasoning, the high temperature destroys the pigment in the chilli. The dominant bacterial genera of puffed soya products within shelf life were Pantoea, Streptococcus, Kocuria and the dominant fungal genera were Altemaria, Aspergillus. The dominant bacterial genera of expired samples were Bacillus, Rhodococcus. The main dominant fungal genus was Aspergillus. Results of the study will help to better control the growth of microorganisms in the future, as well as to improve the shelf-life and taste of the products.

Analysis of fecal microbiota and related clinical indicators in ICU patients with sepsis

BackgroundTo analyze the characteristics of fecal microbiota disturbance in the intensive care unit (ICU) patients with sepsis and the correlation with related clinical indicators. MethodsThis study included 31 patients with sepsis admitted to the emergency ICU ward between September 2019 and December 2021. They were divided into Group without septic shock (ND_NS group, 7 cases) and Group with septic shock (ND_S group, 24 cases) according to the presence or absence of septic shock. Furthermore, we divided these 31 sepsis patients into Clinical Improvement group (21 cases) and Death or DAMA group (10 cases) based on clinical outcome, 15 cases of Physical Examiner recruited in the same period were included as control group: ND_HC group (15 cases). The fecal samples of the patients with sepsis within 24 h of admission and random fecal samples of the control group were collected and analyzed by 16S rDNA gene sequencing used for the analysis of fecal microbiota. At the same time, the relevant clinical data of these patients with sepsis were also collected for analysis. ResultsThere were 15 cases with drug-resistant bacteria in the ND_S group and only 2 cases in the ND_NS group (P = 0.015). There were significant differences in APACHE II score, length of ICU stay, lactate level, and oxygenation index of patients between the Death or DAMA group and Clinical Improvement group (all P < 0.05). For phylum level, the abundance of Firmicutes, Actinobacteria, and Bacteroidetes decreased in the ND group compared with the ND_HC group, while the abundance of Proteobacteria increased (P < 0.05). For genus level, the relative abundance of Escherichia-Shigella and Klebsiella were significantly increased in the ND group compared with the ND_HC group (P < 0.05). The top six genera in relative abundance in the ND_S group were Escherichia-Shigella, Enterococcus, Bifidobacterium, Lactobacillus, Akkermansia, and Klebsiella. Compared with the Clinical Improvement group, the relative abundance of Escherichia-Shigella and Klebsiella in the Death or DAMA group showed an increasing trend with no significant significance, while the relative abundance of Enterococcus and Faecalibacterium decreased in the Death or DAMA group (P < 0.05). Alpha diversity analysis showed that compared with the ND_HC group, the alpha diversity of the fecal microbiota in the ND group decreased. There were significant differences in the Observed_species index, Chao1 index, and ACE index of patients between the ND_HC group and ND group (all P < 0.05). Moreover, compared with the ND_NS group, the Alpha diversity of the ND_S group was more abundant. PCoA analysis showed significant differences in microbial community structure between the ND group and ND_HC group (P = 0.001). There also were significant differences in microbial community structure between the ND_S group and ND_NS group (P = 0.008). LEfSe analysis showed that compared with the ND_HC group, there were significant differences in the species of the ND group, including Enterobacteriaceae, Escherichia-Shigella, Enterococcus, Elizabethkingia, and Family_XIII_AD3011_group. ConclusionsICU patients with sepsis suffered intestinal microecological disturbances with significantly decreased abundance of fecal microbiota, diversity, and beneficial symbiotic bacteria. For these patients, the ratio of pathogenic bacteria, including Escherichia-Shigella and Klebsiella increased and became the main bacterial genus in some samples. Moreover, the increasing trend of these two pathogenic bacteria may be correlated with the development of septic shock and the risk of death in patients with sepsis.

A novel microbial community restructuring strategy for enhanced hydrogen production using multiple pretreatments and CSTR operation

To achieve rapid enrichment of the targeted hydrogen-producing bacterial population and reconstruction of the microbial community in the biological hydrogen-producing reactor, the activated sludge underwent multiple pretreatments using micro-aeration, alkaline treatment, and heat treatment. The activated sludge obtained from the multiple pretreatments was inoculated into the continuous stirred tank reactor (CSTR) for continuous operations. The community structure alteration and hydrogen-producing capability of the activated sludge were analyzed throughout the operation of the reactor. We found that the primary phyla in the activated sludge population shifted to Proteobacteria, Firmicutes, and Bacteroidetes, which collectively accounted for 96.69% after undergoing several pretreatments. This suggests that the multiple pretreatments facilitated in achieving the selective enrichment of the fermentation hydrogen-producing microorganisms in the activated sludge. The CSTR start-up and continuous operation of the biological hydrogen production reactor resulted in the reactor entering a highly efficient hydrogen production stage at influent COD concentrations of 4000 mg/L and 5000 mg/L, with the highest hydrogen production rate reaching 8.19 L/d and 9.33 L/d, respectively. The main genus present during the efficient hydrogen production stage in the reactor was Ethanoligenens, accounting for up to 33% of the total population. Ethanoligenens exhibited autoaggregation capabilities and a superior capacity for hydrogen production, leading to its prevalence in the reactor and contribution to efficient hydrogen production. During high-efficiency hydrogen production, flora associated with hydrogen production exhibited up to 46.95% total relative abundance. In addition, redundancy analysis (RDA) indicated that effluent pH and COD influenced the distribution of the primary hydrogen-producing bacteria, including Ethanoligenens, Raoultella, and Pectinatus, as well as other low abundant hydrogen-producing bacteria in the activated sludge. The data indicates that the multiple pretreatments and reactor's operation has successfully enriched the hydrogen-producing genera and changed the community structure of microbial hydrogen production.

Characteristics of bacterial community structure in the sediment of Chishui River (China) and the response to environmental factors

Sediment microorganisms performed an essential function in the biogeochemical cycle of aquatic ecosystems, and their structural composition was closely related to environmental carrying capacity and water quality. In this study, the Chishui River (Renhuai section) was selected as the research area, and the concentrations of environmental factors in the water and sediment were detected. High⁃throughput sequencing was adopted to reveal the characteristics of bacterial community structures in the sediment. In addition, the response of bacteria to environmental factors was explored statistically. Meanwhile, the functional characteristics of bacterial were also analyzed based on the KEGG database. The results showed that the concentration of environmental factors in the water and sediment displayed spatial differences, with the overall trend of midstream > downstream > upstream, which was related to the wastewater discharge from the Moutai town in the midstream directly. Proteobacteria was the most dominant phylum in the sediment, with the relative abundance ranged from 52.06% to 70.53%. The distribution of genus-level bacteria with different metabolic activities varied in the sediment. Upstream was dominated by Massilia, Acinetobacter, and Thermomonas. In the midstream, Acinetobacter, Cloacibacterium and Comamonas were the main genus. Nevertheless, the abundance of Lysobacter, Arenimonas and Thermomonas was higher in the downstream. Redundancy analysis (RDA) showed that total nitrogen (TN) and total phosphorus (TP) were the main environmental factors which affected the structure of bacterial communities in sediment, while total organic carbon (TOC) was the secondary. The bacterial community was primarily associated with six biological pathway categories such as metabolism. Carbohydrate metabolism and amino acid metabolism were the most active functions in the 31 subfunctions. This study could contribute to the understanding of the structural composition and driving forces of bacteria in the sediment, which might benefit for the ecological protection of Chishui River.

The accumulation of active ingredients of Polygonatum cyrtonema Hua is associated with soil characteristics and bacterial community.

With the increasing demand for health products derived from Polygonati rhizoma (PR), people begin to artificially plant Polygonatum cyrtonema Hua (P. cyrtonema) in the middle and lower reaches of the Yangtze River. To promote P. cyrtonema cultivation and increase farmers' income, efforts are needed to understand the ways to obtain high-quality PR under artificial cultivation conditions. Rhizomes of artificial planting P. cyrtonema and rhizosphere soils were collected across five regions in Zhejiang Province, China. Subsequently, the contents of the main active ingredients of P. cyrtonema and soil properties were analyzed, and both rhizosphere and endophytic bacteria of P. cyrtonema were detected by 16S rDNA sequencing. The relationship between the active ingredients and soil properties, and the dominant bacteria were investigated by correlation analysis. The content of active ingredients of P. cyrtonema from the five regions varied significantly, especially polysaccharides and saponins. High-throughput sequencing demonstrated that Proteobacteria was the dominant bacterial phylum in all samples, and Burkholderia-Caballeronia-Paraburkholderia was the main endophytic bacterial genus in rhizome. In addition, the bacterial diversity and richness of rhizosphere soil samples were higher than those of rhizome samples. Soil physicochemical properties and enzyme activities were significantly different across regions, leading to notable variations in the community structures of rhizosphere and endophytic bacteria. Redundancy analysis (RDA) displayed that pH and urease (UE) were the major factors altering shifting rhizosphere bacteria community structure. Moreover, the composition and diversity of rhizome endophytic bacteria were principally affected by both soil physicochemical properties and soil enzyme activities. Soil properties and bacteria from rhizosphere soil and rhizome had a considerable impact on certain active ingredients in P. cyrtonema under artificial cultivation conditions after Pearson correlation analysis. Polysaccharides were significantly correlated with nutrient-rich soil and endophytic bacteria, such as Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Ralstonia, and Bacillus. However, flavonoids were associated with nutrient-poor soil. Saponins were positively correlated with OM and available phosphorous (AP) and were significantly negatively affected by rhizosphere bacterial communities. The study demonstrated that bacterial microorganisms were involved in the accumulation of active ingredients of P. cyrtonema together with soil physicochemical properties and enzyme activities, which provided a theoretical basis for the scientific and effective artificial cultivation of high-quality P. cyrtonema.

Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves

BackgroundLong-distance transportation, a frequent practice in the cattle industry, stresses calves and results in morbidity, mortality, and growth suppression, leading to welfare concerns and economic losses. Alkaline mineral water (AMW) is an electrolyte additive containing multiple mineral elements and shows stress-mitigating effects on humans and bovines.ResultsHere, we monitored the respiratory health status and growth performance of 60 Simmental calves subjected to 30 hours of road transportation using a clinical scoring system. Within the three days of commingling before the transportation and 30 days after the transportation, calves in the AMW group (n = 30) were supplied with AMW, while calves in the Control group (n = 29) were not. On three specific days, namely the day before transportation (day -3), the 30th day (day 30), and the 60th day (day 60) after transportation, sets of venous blood, serum, and nasopharyngeal swab samples were collected from 20 calves (10 from each group) for routine blood testing, whole blood transcriptomic sequencing, serology detection, serum untargeted metabolic sequencing, and 16S rRNA gene sequencing. The field data showed that calves in the AMW group displayed lower rectal temperatures (38.967 ℃ vs. 39.022 ℃; p = 0.004), respiratory scores (0.079 vs. 0.144; p < 0.001), appetite scores (0.024 vs. 0.055; p < 0.001), ocular and ear scores (0.185 vs. 0.338; p < 0.001), nasal discharge scores (0.143 vs. 0.241; p < 0.001), and higher body weight gains (30.870 kg vs. 7.552 kg; p < 0.001). The outcomes of laboratory and high throughput sequencing data revealed that the calves in the AMW group demonstrated higher cellular and humoral immunities, antioxidant capacities, lower inflammatory levels, and intestinal absorption and lipogenesis on days -3 and 60. The nasopharynx 16S rRNA gene microbiome analysis revealed the different composition and structure of the nasopharyngeal microflora in the two groups of calves on day 30. Joint analysis of multi-omics revealed that on days -3 and 30, bile secretion was a shared pathway enriched by differentially expressed genes and metabolites, and there were strong correlations between the differentially expressed metabolites and the main genera in the nasopharynx.ConclusionsThese results suggest that AMW supplementation enhances peripheral immunity, nutrition absorption, and metabolic processes, subsequently affecting the nasopharyngeal microbiota and improving the respiratory health and growth performance of transported calves. This investigation provided a practical approach to mitigate transportation stress and explored its underlying mechanisms, which are beneficial for the development of the livestock industry.9KT6u9sWWs8ZH5U7yZx1qCVideo

Partial nitrification response to dissolved oxygen variation and aerobic starvation: Kinetics and microbial community analyses

Partial nitrification (PN) has great significance in promoting both anaerobic ammonium oxidation (anammox) and advanced nitrogen removal. However, the kinetics of PN have not been sufficiently studied. Deterioration of PN often occurs due to nitrite-oxidizing bacteria (NOB) outgrowth, for which the dissolved oxygen (DO) is a critical factor. This study investigated the kinetic parameters of ammonia-oxidizing bacteria (AOB) and NOB by varying the DO concentration. The partial nitrification-anammox (PNA) process was operated under sequentially low (0.3–0.8 mg/L) and high (4.0–5.0 mg/L) DO. The results show that AOB could not adapt to low DO, resulting in a significant decrease in the maximum AOB activity (Vmax,AOB) and a slightly altered oxygen half-saturation constant of AOB (KO,AOB). Conversely, KO,NOB decreased and Vmax,NOB maintained, indicating that the main NOB genus, Nitrospira, was more adaptable to DO changes. Under high DO, AOB growth was weaker than NOB, leading to a low Vmax,AOB – Vmax,NOB value; KO,AOB increased and was larger than KO,NOB and PNA was eventually destroyed. The aerobic starvation was then adopted to restore PN. AOB recovered faster and dominated, with Vmax,AOB greatly exceeding Vmax,NOB. Finally, NOB were inhibited and PN was recovered. During this process, KO,NOB increased and was higher than KO,AOB. Changes in the kinetic parameters, especially the Vmax,AOB -Vmax,NOB value, have specific guiding significance for DO regulation during PNA. This work helps better understand the effect of DO variations on the nitrifying microbial community, which influences oxygen affinity and maximum activity.

Using algae to treat wastewater from vegetables cooking: screeningScreening algal strains and assessing bacterial communities

Algae have the advantages of a fast growth rate, strong adaptability to various wastewater environments, and low biomass production costs. A total of seven algal species used in the current study, including two cyanobacterial species and five green algal strains belonging to three species were used to treat the wastewater from vegetable cooking (WWVC), and the algal species that could adapt to the wastewater with a high concentration of organic matter and had good purification ability for the WWVC were screened out. Among them, Desmodesmus sp. HXY3, Desmodesmus sp. HXY7, and Chlorella vulgaris FACHB 8 have good adaptability in the environment of WWVC. After 30 days of culture, the Chl-a content was basically stable at about 3 mg m–3. Flow cytometry and 16 S high-throughput results showed that there were bacteria in the Desmodesmus sp. HXY3 and Desmodesmus sp. HXY7 systems, accounting for 14.5% and 8.46%, respectively. The main phyla was Proteobacteria, and the main genus was Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, accounting for 20.56% and 45.26%, respectively. Desmodesmus sp. HXY3, Desmodesmus sp. HXY7, and Chlorella vulgaris FACHB 8 have strong abilities to purify WWVC, and the removal efficiency of TDN, TDP, and TOC is 97.16%, 95.71%, and 95.09%, respectively. This experiment proves that Desmodesmus sp. HXY3, Desmodesmus sp. HXY7, and Chlorella vulgaris FACHB 8 have strong tolerance and an obvious treatment effect on WWVC.

Comparison of microbial diversity and metabolites on household and commercial doenjang

In this study, the microbial diversity, free amino acid (FAA), and biological activities of household doenjang (HDJ) from four different regions and commercial doenjang (CDJ) four manufacturers were analyzed. And volatile flavor compound (VFC) and isoflavone profiles were analyzed using gas chromatograph-mass spectrometer (GC-MS) and high performance liquid chromatography (HPLC), respectively. The major bacterial genus in 1HDJ and 2HDJ was Bacillus (97.5%), while in 3HDJ and 4HDJ, it was Enterobacter (47.5%) and Pseudomonas (80%), respectively. Tetragenococcus was the main bacterial genus of CDJ. The Zygosaccharomyces genus among yeast was comparatively high in all samples. In all samples, glutamic acid predominated among the FAAs, and the 3-methyl butanal, benzeneacetaldehyde, and diallyl disulphide were major VFCs. CDJ contained higher levels of isoflavone-glycoside and total phenolics. Except for 3HDJ and 4CDJ, the isoflavone-aglycone and total flavonoid contents were higher in HDJ. The correlation between bacterial genus and metabolited of doenjang showed that Tetragenococcus was closely related to glutamic acid, Bacillus was related to aglycones and ammonia, and Pseudomonas was highly related to isovaleric acid. While, correlation between yeast genus and metabolited of doenjang confirmed that Candida, Hanseniaspora, and Saccharomyces were related with furfural, benzeneacetaldehyde, and 3-methyl butanal, respectively. The results of this study can be utilized as basic data for the industrialization and development of doenjang.