Composition Of Phyla Research Articles

Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing

BackgroundThe global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time.ResultsThe microbial diversity based on small subunit (SSU) rRNA analysis revealed the dominance of the bacterial domain representing 81.82% and 92.31% in the studied samples. Furthermore, the phylum composition result indicated the dominance of the phyla Proteobacteria (23.08%, 27.27%), Actinobacteria (11.36%, 20.51%), and Acidobacteria (10.26%, 15.91%). The study also identified unassigned bacteria which might have a unique potential for biopolymer hydrolysis. The metagenomic study revealed that 100,244 and 65,356 genes were predicted from the two distinct samples. A total number of 1806 CAZyme genes were identified, among annotated CAZymes, 758 had a known enzyme assigned to CAZymes. Glycoside hydrolases (GHs) CAZyme family contained most of the CAZyme genes with known enzymes such as β-glucosidase, endo-β-1,4-mannanase, exo-β-1,4-glucanase, α-L-arabinofuranosidase and oligoxyloglucan reducing end-specific cellobiohydrolase. On the other hand, 1048 of the identified CAZyme genes were putative CAZyme genes with unknown enzymatical activity and the majority of which belong to the GHs family.ConclusionsIn general, the identified putative CAZymes genes open up an opportunity for the discovery of new enzymes responsible for hydrolyzing biopolymers utilized for biofuel energy generation. This finding is used as a first-hand piece of evidence to serve as a benchmark for further and comprehensive studies to unveil novel classes of bio-economically valuable genes and their encoded products.

Effects of Steviol Glycosides on Growth Performance, Ruminal Fermentation and Microbial Diversity of Hu Sheep.

The experiment was conducted to investigate the potential effects of steviol glycosides on growth performance, rumen fermentation processes, and microbial diversity in Hu sheep. A single-factor design was used for the trial. Twenty healthy weaned Hu lambs, possessing comparable body weights averaging 18.31 ± 1.24 kg, were randomly allocated into two distinct groups: the control group (CON) and the experimental group (STE), with each comprising 10 lambs. The CON was fed the basal diet, and the STE was supplemented with 0.07% steviol glycosides based on the basal diet. During the experimental period, variations in body weight and feed intake were closely monitored and recorded. After feeding for 90 d, blood was collected to determine blood biochemical indices, and rumen fluid samples were gathered for an in-depth analysis of rumen fermentation parameters and microbial diversity. The outcomes revealed no statistically significant differences in growth performance or serum biochemical indices between the two groups (p > 0.05). Rumen pH in STE and CON was within the normal range. The rumen ammonia nitrogen (NH3-N) and acetic acid (AA) content of STE decreased significantly compared with CON (p < 0.05). No significant variations were observed in the levels of other volatile fatty acids (VFAs) between the two groups (p > 0.05). The rumen microbial OTUs count, as well as the Shannon, Simpson, Chao1, and Ace indices, were notably lower in the STE group compared to the CON group (p < 0.05). Additionally, at the phylum level, the relative abundance of Firmicutes, Bacteroidetes, and Proteobacteria collectively accounted for over 97% of the total phylum composition. In comparison to the CON group, the STE group exhibited an increase in the relative abundance of Proteobacteria (p < 0.05), accompanied by a significant reduction in the relative abundance of Patescibacteria and Desulfobacteria (p < 0.05). At the genus level, there was a notable increase in the relative abundance of Prevotella_7 and Succinivibrionaceae_UCG_001 in the STE group, whereas the relative abundance of Rikenellaceae_RC9_gut_group significantly decreased (p < 0.05). According to the correlation analysis between rumen microflora and VFAs, the relative abundance of Succinivibrionaceae_UCG_001 displayed a significant negative correlation with AA (p < 0.05), whereas Lactobacillus exhibited a notable positive correlation with isobutyric acid (IBA) (p < 0.05). In summary, steviol glycosides had no significant effect on the production performance and blood biochemical indexes of Hu sheep. Steviol glycosides can improve rumen fermentation parameters and rumen microflora structure of Hu sheep and have a certain effect on rumen microbial diversity and composition.

Regional Differences in Microbial Infiltration of Brain Tissue from Alzheimer's Disease Patients and Control Individuals.

Alzheimer's disease (AD) is characterized by cognitive decline and neuropathology including amyloid beta (Aβ) plaques and neurofibrillary tangles (tau). Factors initiating or driving these pathologies remain unclear, though microbes have been increasingly implicated. Our data and others' findings indicate that microbes may be common constituents of the brain. It is notable that Aβ and tau have antimicrobial properties, suggesting a response to microbes in the brain. We used 16S rRNA sequencing to compare major bacterial phyla in post-mortem tissues from individuals exhibiting a range of neuropathology and cognitive status in two brain regions variably affected in AD. Our data indicate that strong regional differences exist, driven in part by the varied presence of Proteobacteria and Firmicutes. We confirmed our data using ELISA of bacterial lipopolysaccharide (LPS) and lipoteichoic acid in the same brain tissue. We identified a potential association between the composition of phyla and the presence of neuropathology but not cognitive status. Declining cognition and increasing pathology correlated closely with serum LPS, but not brain levels of LPS, although brain LPS showed a strong negative correlation with cerebral amyloid angiopathy. Collectively, our data suggest a region-specific heterogeneity of microbial populations in brain tissue potentially associated with neurodegenerative pathology.

Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil

Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the “biosynthesis process”. Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.

Impact of biocrust on soil nitrogen maintenance and microbial composition in citrus orchards under varying urea application rates

Biocrust communities and their effects on soil nitrogen (N) content in natural drylands have been extensively studied. However, their significance in citrus orchards, which are typically managed with N fertilizer, remains unclear. To address this, an investigation was conducted in a citrus orchard subjected to varying levels of urea application (0 %, 70 %, and 100 % of the local N fertilizer application) over three years. The study focused on biocrust communities dominated by bryophytes, examining their community and individual characteristics, and comparing the properties and microbial communities of soils with and without biocrust cover. The results showed that biocrust had the highest percent coverage (56.1 %) in the plot with 70 % local N fertilizer application. Dicranella heteromalla was the dominant biocrust species across all treatments, exhibiting greener and longer leaves with 70 % local N fertilizer application. Biocrust cover significantly (P < 0.01) influenced soil total nitrogen content, soil water content, soil total carbon content, and soil dissolved organic carbon content. In contrast, fertilizer application had non-significant effects on the physicochemical properties of soils, regardless of biocrust cover. A notable difference in bacterial phyla composition was observed between soils with and without biocrust cover (PERMANOVA, P = 0.001), although fertilization did not significantly affect the bacterial diversity index. Additionally, biocrust cover significantly (P < 0.01) influenced predicted soil bacterial functional groups, including ureolysis and nitrogen fixation, while fertilizer application had a weaker impact on these bacterial functional groups. In conclusion, nitrogen application altered the community and dominant species characteristics of biocrust but did not overshadow the effects of biocrust on soil N dynamics. In the citrus orchard with varying levels of urea application, biocrust played a crucial role in soil water retention, N maintenance, and predicted microbial ecological functions related to N cycling.

Ability of Hypocaloric Diets to Change Nutrient–Phyla Associations after 8 Weeks of Intervention

Background: Previous studies have suggested that changes in the composition of intestinal microbiota may be influenced by dietary quality. Objective: This study aimed to assess the impact of a hypocaloric diet on the relationship between microbiota and clinical/dietary variables. Methods: This was a longitudinal study. Ten women with obesity (Obese Group, ObG) participated in an 8-week home-based hypocaloric diet intervention. Anthropometric, dietary intake, biochemical, and gut microbiota assessments were conducted before and after the intervention. Microbiota relative abundance was determined using real-time PCR in triplicate. Results: In the ObG, the hypocaloric diet intervention led to significant weight loss (before: 119.5 ± 10.3 kg; after: 114.9 ± 10.2 kg; p = 0.003). Following the intervention, positive correlations were observed between nutrient intake and phyla composition: Actinobacteria phylum with fibers (r = 0.787; p = 0.012), Firmicutes phylum with proteins (r = 0.736; p = 0.024), and Proteobacteria phylum with lipids (r = 0.669; p = 0.049). Conclusions: The hypocaloric diet intervention improved health parameters associated with obesity and its comorbidities, demonstrating associations between nutrient intake and specific phyla.

Diversity of bacterial communities in the Sundarbans mangrove, Bangladesh, with special focus on pathogens affecting aquatic organisms

The Sundarbans, located in Bangladesh, is the world's largest mangrove forest with a rich and diverse microbial community. The main objective of this study was to use 16S rRNA sequencing to identify the bacterial community in the Sundarban mangrove forest, particularly pathogenic bacteria to aquatic organisms. This study conducted in Bangladesh collected 225 samples of soil, water, fish, and shellfish from five locations with a typical mangrove environment. All samples underwent genomic DNA extraction, quantification, gel documentation, and subsequent sequencing. Sanger sequencing was then carried out, followed by sequencing 11 concentrated samples using the universal bacterial primer 16S rRNA. The study found 872 bacterial species, 94 genera, 38 families, and 6 phyla. Pseudomonades or proteobacteria accounted for 92% of the phylum composition, with firmicutes, bactericides, cyanobacteria, Verrucomicrobia, and actinobacteria also present at smaller percentages. Chromatiaceae had the highest species count (20.3%), followed by Ectothiorhodospiraceae (15.5%), Methylococcaceae (12.3%), Moraxellaceae (10.7%), Thiotrichaceae (8.7%), Idiomarinaceae (5.4%), and smaller groups. All the species that were identified were gram-negative bacteria and were found in different environments, mainly halophilic ones. Based on 16 s rRNA sequencing, additional experimental and clinical data, as well as NCBI (BLAST), approximately 49.3% of the 872 bacterial species are typically harmless and not classified as pathogenic. The pathogenic characteristics of 24.9% of the species are still unidentified. 13.4% showed either pathogenic or non-pathogenic characteristics (a bacterium as having the potential to exhibit pathogenic or non-pathogenic characteristics in certain circumstances), while 8.4% were exclusively pathogenic, potentially capable of causing disease. Also, the bacterial species are categorized as 2.6% non-highly pathogenic (a bacterium can still have a significant impact on health, especially in weakened immune systems or other underlying health conditions), 1.3% sometimes pathogenic and 0.1% potentially pathogenic (a bacterium don't always cause disease). Sequence analysis, combination of phylogenetic, biochemical characterization (data were not shown), and other experimental validation conclude a genetic baseline of bacterial community, this research may serve as a valuable reference for future ecological and taxonomical studies as well as addressing further research scope on bacterial diversity found in the Sundarbans mangrove of Bangladesh.

Taxonomic profiling of Nasutitermes takasagoensis microbiota to investigate the role of termites as vectors of bacteria linked to ironwood tree decline in Guam.

The ironwood tree (Casuarina equisetifolia, family Casuarinaceae), an indigenous agroforestry species in Guam, has been threatened by ironwood tree decline (IWTD) since 2002. Formation of bacterial ooze by the wilt pathogen from the Ralstonia solanacearum species complex and wetwood bacteria (primarily Klebsiella species) has been linked to IWTD. In addition, termite infestation of trees was statistically associated with IWTD. Termites are known carriers of a diverse microbiome. Therefore, we hypothesized that termites could be vectors of bacteria linked to IWTD. To investigate the potential role of termites as pathogen vectors, we employed next-generation 16S rRNA gene sequencing to describe the bacteria diversity of Nasutitermes takasagoensis (Family Termitidae) workers collected from 42 ironwood trees of different disease stages in Guam in association with tree-, plot-, and location-related factors. Nasutitermes takasagoensis workers account for the majority of termite infestations of ironwood trees. The bacterial phyla composition of N. takasagoensis workers was typical for wood-feeding higher termites consisting mainly of Spirochaetes and Fibrobacteres. However, Ralstonia species were not detected and Klebsiella species were rare even in termites collected from trees infected with Ralstonia and wetwood bacteria. Feeding experiments suggested that termites prefer to consume wood with low pathogen content over wood with high pathogen load. Termites were able to ingest Ralstonia but Ralstonia could not establish itself in healthy termite bodies. We concluded that N. takasagoensis workers are not vectors for Ralstonia spp. or the bacterial endophytes associated with wetwood (Klebsiella, Pantoea, Enterobacter, Citrobacter, and Erwinia) that were previously observed in IWTD-infested trees. The bacterial diversity in termite samples was significantly influenced by various factors, including Tree Health, Site Management, Plot Average Decline Severity, Proportion of Dead Trees in the Plot, Proportion of Trees with Termite Damage in the Plot, Presence of Ralstonia, and Altitude.

Effect of long-term conservation tillage management on microbial diversity under Mediterranean rainfed conditions

Conservation Agriculture has been the subject of numerous studies for decades. However, its impact on the soil microbial community has often been overlooked. Recent studies have shed light on the changes in soil bacterial composition resulting from modifications in tillage practices, particularly when compared to conventional tillage methods. However, there is a lack of soil microbial community analysis conducted under conservation tillage and rainfed conditions in the Mediterranean basin. A metataxonomic approach was employed to assess the influence of 19 years (2004–2022) of minimum tillage (MT) and no-till (NT) practices, along with crop rotation, on the soil bacterial community at upper layers (15 cm depth). This field study involved three different seasonal moments throughout the year. Results revealed that both sampling time and tillage management significantly influenced the structure of the bacterial community, whereas no effect was observed due to the crop. May showed a higher taxonomic diversity than July and December, showing differences in some o fthe most abundant phyla, such as Actinobacteria, Firmicutes and Proteobacteria. On the other hand, the long-term application of NT was found to lead to a significant decrease in bacterial diversity, with lower abundances of the phyla Chloroflexi, Gemmatimonadetes, and Armatimonadota, as well as an increase in k-strategist bacteria compared to MT. However, no significant effect on alpha diversity was observed as a result of tillage. no variations in phyla composition were observed attributable to crop, as the primary distinctions were identified among legume crops, which were associated with different sampling times. Therefore, our conclusion is that over this period, NT did not promote microbial diversity in the upper soil layers, despite notable shifts in bacterial composition occurring across seasonal time points in both tillage management systems.

Effect of soil microbial community structure on the chemical compositions of different soil organic matter fractions in land uses of the Pearl River Estuary

Understanding the interactions between the dynamics of soil organic matter (SOM) and soil microbial communities is important for predicting the stability and fate of estuarine SOM following anthropogenic disturbance. However, current knowledge on the influence of microbial communities on the chemical compositions of different SOM fractions in estuarine land uses still remains incomplete. In this study, we used high-throughput sequencing, Fourier transform infrared spectroscopy, UV–Vis absorption, and fluorescence spectroscopy to investigate soil microbial communities and characterize the chemical compositions of bulk SOM and water-extractable organic matter (WEOM) across different land uses (artificial forests (AF), farmland (FL), natural wetland (NW), construction land (CL), and abandoned land (AL)) in the Pearl River Estuary. The results showed that the bulk SOM in FL and AL exhibited comparable or higher levels of aromatic functional groups (aromatic CH and aromatic CC) compared to other land uses. The HIX and SUV254 indexes further confirmed that AF and FL had more aromatic and hydrophobic WEOM. Apart from FL, where anthropogenic humus constituted the largest proportion, the WEOM fraction predominantly consist of three components in the following order across all land uses, ordered as anthropogenic humus < microbial humus < protein humus. The chemical compositions of the different SOM fractions showed a stronger correlation with the dominant bacterial phylum composition, especially for the WEOM fraction, compared to the fungal composition. Meanwhile, our findings demonstrate that bacterial diversity showed a stronger relationship with the chemical composition of WEOM compared to abundance. Overall, this study sheds light on the impact of land use on the quantity and quality of SOM fractions, underscoring the varying influence of microorganisms on the chemical compositions of different SOM fractions within estuarine environments.

Soil Bacterial Community Structure and Function Prediction of Millet/Peanut Intercropping Farmland in the Lower Yellow River

The objective of this study was to explore the microecological variability in farmland soil fertility in response to millet-peanut intercropping patterns by clarifying the effects of millet-peanut 4:4 intercropping on soil bacterial community structure and its diversity, as well as to provide a reference basis for promoting ecological restoration and arable land quality improvement in the lower Yellow River farmland. The Illumina MiSeq high-throughput sequencing technology and QIIME 2 platform were used to analyze the differences in bacterial community composition and their influencing factors in five soils[sole millet (SM), sole peanut (SP), intercropping millet (IM), intercropping peanut (IP), and millet-peanut intercropping (MP)] and to predict their ecological functions. The results showed that the α-diversity of intercropping soil bacterial communities differed from that of monocropping, though not significantly, whereas the β-diversity was significantly different (P<0.05). A total of 7081 ASVs were obtained from all soil samples, classified into 34 phyla, 109 orders, 256 class, 396 families, 710 genera, and 1409 species, of which 727 ASVs were shared, accounting for 24.5% to 27.8% in five soil species. The bacterial communities of millet-peanut intercropping and its monocropping soils were similar in phylum composition but varied in relative abundance. All five soils were dominated by the Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, with a relative abundance of 79.40%-81.33%. Soil organic carbon and alkaline nitrogen were the most important factors causing differences in the structures of the five soil bacterial communities at the phylum and genus levels, respectively. The PICRUSt functional prediction revealed that the relative abundance of primary functional metabolism was the largest (78.9%-79.3%), and the relative abundance of secondary functional exogenous biodegradation and metabolism fluctuated the most (CV=3.782%). In terms of the BugBase phenotype, the relative abundance of oxidative stress-tolerant bacteria increased in intercropping millet or peanut soils compared to that in the corresponding monocultures and significantly increased in intercropping millet soils compared to that in sole millet (P<0.05). Oxidative stress-tolerant, Gram-positive, and aerobic phenotypes were highly significantly positively correlated with each other (P<0.01), and all three showed highly significant negative correlations with potential pathogenicity and Gram-negative and anaerobic phenotypes (P<0.01). This showed that millet-peanut intercropping resulted in differences in soil bacterial community diversity, abundance, and metabolic functions and the possibility of reducing the occurrence of potential soil diseases. It can be used to regulate the soil microbiological environment to promote ecological restoration and sustainable development of farmland in the lower Yellow River.

Investigation of the oral microbiome of children associated with dental caries: A systematic study

ObjectiveThe present study aims to investigate the variations in dental caries (DC) related microbiome abnormality and metabolomics shift in children. DesignThe patients were divided into two groups healthy control (C) and highly affected DC children based on inclusion and exclusion criteria. Saliva samples were collected and used for the taxonomic and functional characterization of oral microbiota. ResultsMetatranscriptomics analysis revealed the alterations and composition of oral microbiota in the C and DC groups. Relative abundance in the C group was associated with Firmicutes, Actinobacteria, and Bacteroidetes. Whereas, the microbial composition in the DC group was found to be considerably altered with increases in the abundance of the Proteobacteria (25%), Fusobacteria (15%), and Cyanobacteria (8%) while decreases in the abundance of Firmicutes (10%) and Bacteroidetes (23%). Alterations in the phylum composition were positively and negatively correlated with several metabolites of sugars (such as fructose, sorbose, ribose, allose, and mannose) and amino acids (such as arginine, lysine, tryptophan, and proline). Moreover, in comparison with the C group, the metabolic shift of the DC group was different with an increase in certain tricarboxylic acid cycle intermediates levels, and a decrease in fatty acid. Such alterations can enhance the growth of oral pathogens and contribute to DC development. ConclusionsThe findings of this study suggest that an altered abundance of Actinobacillus, Fusobacterium, and Shuttleworthia can serve as biomarkers of DC in children.

Grazing Effects of Xenocypris davidi Bleeker (Cyprinidae, Cypriniformes) on Filamentous Algae and the Consequent Effects on Intestinal Microbiota

Filamentous algae are present in seawater and freshwater ecosystems worldwide. Their growth poses a serious threat to water environments and fishery production, especially Chinese mitten crab and red swamp crayfish culturing. To explore safe and ecological treatment methods, we comparatively studied the grazing effects of Xenocypris davidi Bleeker on Cladophora (one species) and Spirogyra (two species) in indoor glass tanks and examined the intestinal microbiota related to digestion and absorption. The results showed that the fish was more receptive to Spirogyra than to Cladophora, and the intake rates of different species of Spirogyra varied. Fish weight increased slightly after feeding with Spirogyra, and the levels of total nitrogen and total phosphorus in water increased significantly ( p &lt; 0.05 ) relative to the initial values. Intestinal microbiota diversity and richness varied after feeding with three filamentous algal species, and the similarity increased after feeding with two Spirogyra species. The microbial species detected in this study belonged to 40 phyla and 838 genera. The clustering characteristics of different groups and subgroups were obvious based on the microbial phylum composition. Significant differences in the relative abundance rates of eight nutrition-related metabolism functions were found among groups and subgroups ( p &lt; 0.05 ). The correlations between intestinal microbiota and metabolism functions were analyzed, and some meaningful correlations were revealed. The results presented in this study provided a meaningful reference on the control of the overgrowth of filamentous algae in aquaculture waters by the biomanipulation method.

N2O emission associated with shifts of bacterial communities in riparian wetland during the spring thawing periods.

Soil freeze-thaw processes lead to high nitrous oxide (N2O) emissions and exacerbate the greenhouse effect. The wetlands of the Inner Mongolia Plateau are in the pronounced seasonal freeze-thaw zone, but the effect of spring thaw on N2O emissions and related microbial mechanisms is still unclear. We investigated the effects of different periods (freeze, freeze-thaw, and thaw) on soil bacterial community diversity and composition and greenhouse gas emissions during the spring freeze-thaw in the XiLin River riparian wetlands in China by amplicon sequencing and static dark box methods. The results showed that the freeze-thaw periods predominantly impact on the diversity and composition of the bacterial communities. The phyla composition of the soil bacteria communities of the three periods is similar in level, with Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria dominating the microbial communities. The alpha-diversity of bacterial communities in different periods varies that the freezing period is higher than that of the freeze-thaw period (p < .05). Soil total carbon, soil water content, and microbial biomass carbon were the primary factors regulating the abundance and compositions of the bacterial communities during spring thawing periods. Based on functional predictions, the relative abundance of nitrification and denitrification genes was higher in the freezing period than in the thawing period, while the abundance was lowest in the freeze-thawing period. The correlation results found that N2O emissions were significantly correlated with amoA and amoB in nitrification genes, indicating that nitrification may be the main process of N2O production during spring thaw. This study reveals potential microbial mechanisms of N2O emission during spring thaw and provides data support and theoretical basis for further insight into the mechanism of N2O emission during spring thaw.

Lime-treated urine improves sunflower growth without shifting soil bacterial communities

Urine contains high concentrations of nitrogen and phosphorus, which can be utilized as fertilizer in sustainable agriculture, forestry, and landscaping. Before urine application, the nitrogen can be stabilized with calcium hydroxide (lime), which raises the pH and inhibits urea hydrolysis. However, the impact of lime-treated urine on plants and soils remains unclear. Here, lime-treated urine diluted 1:10 with water was applied to soils with sunflowers (Helianthus annuus L.), and growth and soil bacterial diversity was examined at 2 months. We show that lime-treated urine significantly increased sunflower growth up to 85 %, plant biomass up to 151 %, leaf area up to 137 %, and the number of leaves per plant by 2.5 compared to untreated plants. No major differences in bacterial Shannon or Simpson diversity indices were detected between treatment groups, though small shifts in phyla composition were observed, depending on treatment and plant presence. This work demonstrates that recycled urine can effectively be used for the fertilization of non-food crops and landscaping plants.

MO573: Diet Quality Components and Gut Microbiota of Peritoneal Dialysis Patients

Abstract BACKGROUND AND AIMS Diet has been recognized as an important determinant of microbiota composition. In CKD, nutrients such as fiber and protein have been shown to influence the microbiota profile. However, since nutrients are not ingested in isolation, the overall assessment of diet, reflecting the synergy of nutrients, may potentially modify the relationship between the diet and gut microbiota. Therefore, our aim was to evaluate whether the quality of diet and its components associate with alpha diversity of gut microbiota and phyla composition in peritoneal dialysis (PD) patients. METHOD In this cross-sectional study, patients undergoing automated PD for at least 3 months, aged 18–75 years and clinically stable were enrolled. Those who were using prebiotics, probiotics, symbiotics and antibiotics within a period of 30 days before the study were not included. Participants received sterile materials to collect the feces sample and were instructed to keep it refrigerated and bring to the clinic within a period of 12 h. To evaluate α-diversity and phyla microbial profile, 16S ribosomal DNA was PCR-amplified and sequenced on an IlluminaMiSeq platform. The diet quality index (DQI), validated for the healthy Brazilian population, was calculated from a 3-day food record. This index is based on the energy density of 11 components (sugars and sweets; beef and pork; refined grains and breads; animal fat; poultry, seafood and eggs; whole grains, breads, tubers and roots; fruits; non-starchy vegetables; legumes and nuts; milk and dairy products and vegetable oils). Each component is scored from 0 to 5 or 10, and a final score ranged from 0 (worse) to 100 (better) is obtained. RESULTS Thirty-seven patients were included [52.4 ± 13.7 years; 54% men; 70% with diabetes; PD vintage 18.0 (5.0–46.5) months]. The distribution of gut microbiota's phyla is presented in Figure 1. Mean DQI was 47.8 ± 12.2, indicating that most of the patients (76%) were in an intermediate quality of diet. DQI was not associated with age, gender, PD vintage, BMI or the presence of diabetes. As can be seen in Table 1, although no association was found between DQI total score with the gut microbiota α-diversity indexes, the energy density of some components of DQI tended or was associated with those indexes. DQI total score was also not associated with any specific phyla, but the energy density of the components ‘sugars and sweets’ was negatively associated with Bacteroidetes (r= −0.389, P = 0.017) and positively with Firmicutes (r = 0.468, P = 0.003), while the inverse was observed for ‘legumes and nuts’, Bacteroidetes (r = 0.358, P = 0.029) and Firmicutes (r = −0.333, P = 0.044). CONCLUSION A healthier diet, with a larger amount of ‘whole grains, breads, tubers and roots’ and ‘legumes and nuts’ and, lower in ‘sugars and sweets’, seems to contribute to the α-diversity or Bacteroidetes colonization in peritoneal dialysis patients.

The Microbiome of Suaeda monoica and Dipterygium glaucum From Southern Corniche (Saudi Arabia) Reveals Different Recruitment Patterns of Bacteria and Archaea

Soil and plant interact differently in response to the same stress (e.g., salinity) and recruit certain bacteria. The southern corniche (Saudi Arabia) has limited plant growth, which could be due to the high temperature and salinity. The study aimed to determine the soil microbiome of selected plants and the interactions between soil and these plants. Suaeda monoica and Dipterygium glaucum soil samples were collected from the crust (surface) and rhizosphere, while soil with no plant growth from the nearby area was used as control. High-throughput hypervariable V3–V4 region of the 16S rRNA gene was used to evaluate the shifts in soil microbiome due to growth of plant growth. The analysis detected up to 16% archaeal strains in S. monoica-associated samples, while D. glaucum and control samples contained 100% bacterial strains. The top 10 phyla composition of the soil samples were Proteobacteria, Actinobacteria, Firmicutes, Gemmatimonadota, Bacteroidota, Halobacterota, Cyanobacteria, Cloroflexi, Planctomycetota, and Myxococcota. The V3–V4 region analysis successfully clustered the 5 samples into 3 clusters (control, D. glaucum, and S. monoica) at higher-order classification but not at the species level due to unidentified bacteria. The main differences between soil samples were due to halophyte S. monoica samples containing high amounts of halophilic archaea and halophilic bacteria. This showed that selected plants interacted differently with the soil. EC- and KO-based analyses of functional genes and pathways showed that 5 pathways were specific to control, 11 pathways were observed only in D. glaucum samples, 12 pathways were expressed in S. monoica samples only, and 9 pathways were common in all samples. The study also detected numerous relatively novel genera in high abundance such as Aliifodinibius, Pontibacter, and Lacunisphaera. This showed that the soil in the sampling area is not well explored and that novel species could be isolated from the soil samples and used for future research.

Distribution and Release of Volatile Organic Sulfur Compounds in Yangcheng Lake

Volatile organic sulfur compounds (VOSCs) function as a water–atmosphere link in the global sulfur cycle. It is generally believed that the vast majority of VOSCs are released from the ocean. However, due to the pervasive eutrophication and pollution of inland waters, the VOSC production and emission in rivers, lakes and reservoirs are attracting more attention. In this study, the temporal and spatial distributions of three VOSCs, including methanethiol, Dimethyl sulfide, and dimethyl disulfide in Yangcheng Lake, a eutrophic shallow lake, are investigated monthly and seasonally. Results show that VOSCs are higher in summer and autumn, with the western region as a hotspot. Our results show a positive correlation between VOSC and phytoplankton biomass (p &lt; 0.05). Interestingly, from algal phylum composition, all the phylum, except those with low biomass, played a positive effect on VOSCs’ concentration. We did not find any specific phylum or species of cyanobacteria that contributed solely to the VOSCs. The water-air effluxes of Dimethyl sulfide (DMS) are estimated by a stagnant film model. The DMS effluxes from Yangcheng Lakes were higher than deep lakes and similar to the ocean, indicating that VOSCs, particularly DMS, in those eutrophic shallow lakes were non-negligible.

Airway inflammation, dysbiosis and respiratory parameters are dependent of the route of sensitization in mouse model of asthma

Asthma is an inflammatory chronic disease of lower part of the airways which attempt more than 300 million of asthmatics are counted in the world, whose 70% with an allergic asthma. The diversity of asthmatic endotypes contributes to its complexity. Many factors are involved in the pathophysiology of asthma to explain its phenotype diversity, as environment, the allergen sensitization pathways and the key role of microbiota. In this context, the objective of this project is to determine the influence of the sensitization pathway on the endotype and severity of asthma. Using a mouse model of dust mite allergic asthma, we analyzed respiratory function by plethysmography and by lung resistance and compliance measurement. Then we explore lung tissue damage by histological studies and we analyzed the inflammation phenotype by flow cytometry. In addition, we defined the impact of the sensitization pathway on microbiota by 16S sequencing and barrier dysfunction. Our results show an influence of the sensitization pathway on respiratory function and on the inflammatory response. Indeed, we have shown that the nasal route induces the most severe asthma with pro-Th2 inflammation with a little Th17 but rather eosinophilic asthma. The cutaneous route induces severe asthma with a mixed Th2/Th17 infiltrate. While the oral route is more tolerogenic with less impairment of respiratory function, but with an inflammatory profile of the Th2 type with eosinophilia. Concerning microbiota dysbiosis, we notified some significant difference of gut and lung phylum composition between different sensitization pathways. Altogether, these results will demonstrate the link between sensitization pathway and asthmatic endotype by taking into account the mechanisms linking the immune response, the microbiota and the bronchial epithelial barrier. These results will ultimately make it possible to better target prevention strategies through immuno-intervention and the development of predictive markers and/or the selection of asthma endotypes.

Different Effects of Thermophilic Microbiological Inoculation With and Without Biochar on Physicochemical Characteristics and Bacterial Communities in Pig Manure Composting.

This study evaluated the effects of thermophilic microbiological inoculation alone (TA) and integrated with biochar (TB) on the physicochemical characteristics and bacterial communities in pig manure (PM) composting with wheat straw. Both TA and TB accelerated the rate of temperature increase during the PM composting. TA significantly reduced total nitrogen loss by 18.03% as opposed to TB which significantly accelerated total organic carbon degradation by 12.21% compared with the control. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the major phyla in composting. Variation of the relative abundance of genera depended on the composting period and treatment. The genera Lactobacillus (26.88–46.71%) and Clostridium_sensu_stricto (9.03–31.69%) occupied a superior position in the temperature rise stage, and Bacillus (30.90–36.19%) was outstanding in the cooling stage. Temperature, total nitrogen (TN), and ammonium nitrogen significantly influenced the bacterial phyla composition. TN, water content, and nitrite nitrogen were the main drivers of the bacterial community genera. Furthermore, our results demonstrated that microbiological consortia were resistant to high temperatures and could fix nitrogen for enriched Pseudomonas; however, when interacted with biochar, total organic carbon (TOC) degradation was accelerated for higher bacterial richness and diversity as well as overrepresented Corynebacterium.