Higher Relative Abundance Research Articles

Molecular composition of direct coal liquefaction products obtained from the Shenhua industrial plant

The China Shenhua company has built and operated the only large industrial direct coal liquefaction (DCL) plant in the world for 15 years, with an oil product capacity of one million tons per year. However, there is insufficient information on the chemical composition of its products. In this study, the liquefaction product, including the distillate oil and the vacuum residue, as well as the circulating solvent were characterized by gas chromatography – mass spectrometry (GC–MS) and high-resolution mass spectrometry. The liquefaction oil has lower H/C ratio and higher oxygen and nitrogen contents compared to hydrogenation products derived from petroleum. The major component of the liquefaction oil is middle-temperature distillate, which is approximately 70 wt% concentrated in the range of 200–350 °C. Pyrene and perhydropyrene are the most abundant compounds in the liquefaction oil. Hydrocarbons with 1–4 aromatic rings were detected in the liquefaction oil, with skeletons of benzene, biphenyl, naphthalene, fluorene, phenanthrene, pyrene, etc.. Various partially hydrogenated and perhydrogenated aromatic compounds were identified in the oils and they even constitute the major component of the circulating solvent. 2,3-Dihydro-1H-phenalene was also found in high-relative abundance in the oils and has potential to be used as a marker for coal liquefaction produced through hydrogenation processes. Partially hydrogenated polycyclic aromatics exhibit higher dehydrogenation activity compared to tetralin. The organic component in the vacuum residue account for around 60 wt%, with toluene insoluble matter accounting for more than one third. The toluene soluble fraction has an H/C ratio of 0.82 and is mainly composed of aromatic with 4–8 rings. The molecular size and condensation degree of the residue are much higher than those of other fossil fuel-derived aromatic-rich substances. Further studies are necessary to evaluate whether aromatic hydrocarbons with such a high condensation degree are suitable for producing high-performance carbon materials.

Antibiotics and their associations with antibiotic resistance genes and microbial communities in estuarine and coastal sediment of Quanzhou Bay, Southeast China

The antibiotic concentrations spanned from 11.2 to 173.8 ng/g, with quinolones and tetracyclines being observed to be prevalent. The amount of microbial biomass as determined by Phospholipid fatty acid (PLFA) ranged from 2.92 to 10.99 mg kg−1, with G- bacteria dominating. A total of 254 distinct ARGs and 10 MEGs were identified, with multidrug ARGs having the highest relative abundance (1.18 × 10−2 to 3.00 × 10−1 copies/16S rRNA gene copies), while vancomycin and sulfonamide resistance genes were the least abundant. Results from canonical-correlation analyses combined with redundancy analysis indicated that macrolides were significantly related to the shifts of microbial community structure in sediments, particularly in G+ bacteria that were more sensitive to antibiotic residues. It was observed that sulfonamide ARGs had a greater correlation with residual antibiotics than other ARGs. This study provided a field evidence that multiple residual antibiotics from coastal sites could cause fundamental shifts in microbial community and their associated ARGs.

Dysbiosis of oral microbiome persists after dental treatment-induced remission of periodontal disease and dental caries.

Oral diseases, such as periodontal disease and dental caries, have a high risk of recurrence and are considered to be related to dysbiosis of the oral microbiome and metabolome. It is, therefore, important to understand the state of the oral microbiome and metabolome after disease treatment to prevent recurrence. The current study sought to clarify whether oral dysbiosis improves the following remission of symptoms by dental treatment. To this end, the salivary microbiome and metabolome of healthy participants were compared to those with periodontal disease, dental caries, or both (concurrent). Saliva was collected as mouth-rinsed water and the microbiome was measured using 16S rRNA gene targeted sequencing and metabolome using capillary electrophoresis-time-of-flight mass spectrometry. Comparisons with healthy participants were performed before and after treatment, and several months after transition to self-care. Dental treatment significantly improved the oral health condition of each group; several months after treatment, oral health did not deteriorate. However, even after remission, the salivary microbiome of the two groups (oral disease and healthy) differed significantly. Additionally, after remission, significant differences, compared with healthy participants, remained in the relative abundances of disease-related bacteria and nitrate-reducing bacteria. After remission, significant differences were observed in the salivary metabolome in the healthy group in terms of threonate and pyrimidine metabolism-related component concentrations, which are assumed to reflect the high relative abundance of periodontal disease-related bacteria in the microbiome. Oral microbiome dysbiosis persisted even after dental treatment-induced disease remission with a sustained increased risk of disease when compared with healthy participants. IMPORTANCE We characterized the oral conditions, salivary microbiome, and metabolome after dental treatment by investigating the state after treatment completion and transition to self-care. Dental treatment improved oral health conditions, resulting in oral disease remission; however, the imbalanced state of the salivary microbiome continued even after remission. Although the results of this study are preliminary, owing to the small number of participants in each group when compared to larger cohort studies, they indicate that the risk of disease may remain higher than that of healthy participants, thereby demonstrating the importance of removing dental plaque containing disease-related bacteria using appropriate care even after treatment completion. We also identified bacterial species with relative abundances that differed from those of healthy participants even after remission of symptoms, which may indicate that the maturation of certain bacterial species must be controlled to improve the oral microbiome and reduce the risk of disease recurrence.

The effect of long-term controlled-release urea application on the relative abundances of plant growth-promoting microorganisms

Controlled-release urea (CRUs), including polymer-coated urea (PCU), sulfur-coated urea (SCU), and polymer/sulfur dual layer-coated urea (PSCU), have been demonstrated to increase crop yield and nitrogen use efficiency (NUE). However, the effects of long-term application of CRUs on soil microbial community and function remain unclear. In this study, a 12-year (2009–2021) 24-season wheat -maize rotation lysimeter experiment was studied to investigate the effects of PCU, SCU, and PSCU on soil microbial community composition and function. Wheat was grown, soil chemical properties were analyzed, and soil biological properties including enzyme activities and microbial community structure and function at the wheat filling stage were determined in 2021. The results showed that soil organic matter (SOM) contents were markedly increased by 3.1∼5.0% under the CRUs compared to conventional urea. Meanwhile, some carbon, nitrogen, and sulfur cycle enzyme activities, including cellulase (CE), urease and arylsulfatase (AS), were significantly enhanced by 23.4∼32.4%, 6.6∼32.1%, and 2.5∼3.7% under the CRUs compared to conventional urea, respectively. Redundancy analysis indicated that changes in bacterial and fungal communities were driven by SOM. Co-occurrence network analysis showed that wheat growth promotion by the CRUs was strongly linked to the high relative abundance (Z-score) of bacterial and fungal module 1, which included such plant growth-promoting microorganisms (PGPMs) as Arthrobacter, Bryobacter, Bradyrhizobium, Microscypha, and Marasmius. Compared with PCU, SCU and PSCU showed a better effect in increasing the relative abundances of PGPMs while inhibiting the growth of nitrobacteria, denitrifying bacteria, and plant pathogens, thereby better promoting wheat yields and reducing N loss and plant disease. Of the three CRUs, SCU and PSCU have significantly increased SOM, which provided sufficient substrate for the growth of PGPMs, thus increasing wheat yield. This study provides a support for long-term CRUs application and sustainable agriculture.

The role of the gut microbiome in weight-gain in schizophrenia patients treated with atypical antipsychotics: Evidence based on altered composition and function in a cross-sectional study

ObjectivesWe aimed to explore the interconnection between the weight-gain in schizophrenia patients with atypical antipsychotic treatment and gut microbiome. MethodsThis study employed a cross-sectional design, encompassing a total of 88 schizophrenia patients with long-term atypical antipsychotic treatment. The 16S rRNA gene sequencing was used to identify gut microbiome contents. ResultsNo significant differences in alpha diversity between normal-weight and overweight schizophrenia treated with atypical antipsychotics. The beta diversity analysis showed that overweight patients clustered tightly while normal-weight patients clustered widely. For taxonomic composition, overweight patients had a lower relative abundance in Porphyromonadaceae at family level and Butyrivibrio at genus level, but higher relative abundance in Ruminococcus2 and Clostridium_XIVa at genus level than normal-weight patients. Function prediction revelated that four pathways (including Cell cycle, Non-homologous end-joining, Vibrio cholerae infection and Meiosis-yeast) were significantly different between groups. Correlation analysis indicated that Klebsiella, Butyrivibrio, Unassigned, Methanosphaera, Holdemania, Anaerotruncus were negatively, while Veillonella was positively correlated with BMI in patients. ConclusionOur findings offer evidence that perturbations in the gut microbiome composition, encompassing taxa such as Porphyromonadaceae, Butyrivibrio, Ruminococcus2, and Clostridium_XIVa, in conjunction with distinct functional pathways including Cell cycle, Non-homologous end-joining, Vibrio cholerae infection, and Meiosis-yeast, might contribute to the weight-gain in schizophrenia treated with atypical antipsychotics.

Effect of biofilm thickness on the activity and community composition of phosphorus accumulating bacteria in a moving bed biofilm reactor

Can biofilms enhance the rates of phosphorus removal in wastewater treatment? In order to narrow the scientific gap on the effect of biofilm thickness on the activity and microbial community of phosphorus-accumulating bacteria, this study investigated biofilms of 30 to 1000 µm thickness in a moving bed biofilm reactor. Measurements on 5 different biofilm carriers showed that biomass-specific phosphorus release and uptake rates increased as a function of biofilm thickness for biofilms thinner than about 110 µm but were lower for thicker biofilms of about 550–1000 µm. The reduced phosphorus uptake and release rates in the thickest biofilms can result from substrate mass transfer limitations whereas the low activity in the thinnest biofilms can be related to a too high turnover rate in the biofilm due to heterotrophic growth. Additionally, the microbial ecology of the different biofilms confirms the observed phosphorus uptake and release rates. The results from the full-length 16S rRNA gene sequencing of the bacterial community showed that the thicker biofilms were characterized by higher relative abundance (40–58%) of potential phosphorus accumulating genera Zoogloea, Acinetobacter, Dechloromonas and Ca. Accumulibacter. In contrast, the thinner biofilms were dominated by the genus Ferribacterium (34–60%), which might be competing with phosphorus-accumulating bacteria as indicated by the relatively high acetate uptake rates in the thinner biofilms. It is concluded that there is an optimal biofilm thickness of 100–500 µm, at which the phosphorus accumulating bacteria have the highest activity.

Reconstruction of Gut Bacteria in Spodoptera frugiperda Infected by Beauveria bassiana Affects the Survival of Host Pest.

Spodoptera frugiperda (Lepidoptera: Noctuidae) is a migratory agricultural pest that is devastating on a global scale. Beauveria bassiana is a filamentous entomopathogenic fungus that has a strong pathogenic effect on Lepidoptera pests but little is known about the microbial community in the host gut and the dominant populations in fungus-infected insects. B. bassiana AJS91881 was isolated and identified from the infected larvae of Spodoptera litura. The virulence of AJS91881 to the eggs, larvae, pupae and adults of S. frugiperda was measured. Moreover, the gut microbial community diversity of healthy and fungus-infected insects was analyzed. Our results showed that after treatment with B. bassiana AJS91881, the egg hatching rate, larval survival rate and adult lifespan of the insects were significantly reduced, and the pupae rigor rate was significantly increased compared to that of the control group. Additionally, the gut microbial community was reconstructed after B. bassiana infection. At the phylum and genus level, the relative abundance of the Proteobacteria and Serratia increased significantly in the B. bassiana treatment group. The KEGG function prediction results showed that fungal infection affected insect gut metabolism, environmental information processing, genetic information processing, organism systems and cellular processes. Fungal infection was closely related to the metabolism of various substances in the insect gut. Serratia marcescens was the bacterium with the highest relative abundance after infection by B. bassiana; intestinal bacteria S. marcescens inhibited the infection of insect fungi B. bassiana against the S. frugiperda. The presence of gut bacteria also significantly reduced the virulence of the fungi against the insects when compared to the group with the larvae fed antibiotics that were infected with fungal suspension (Germfree, GF) and healthy larvae that were infected with fungal suspension prepared with an antibiotic solution (+antibiotic). In conclusion, the reconstruction of the insect intestinal bacterial community is an indispensable link for understanding the pathogenicity of B. bassiana against S. frugiperda. Most importantly, in the later stage of fungal infection, the increased abundance of S. marcescens in the insect intestine inhibited the virulence of B. bassiana to some extent. The findings aid in understanding changes in the gut microbiota during the early stages of entomopathogenic fungal infection of insects and the involvement of insect gut microbes in host defense mediated by pathogenic fungal infection. This study is also conducive to understanding the interaction between entomopathogenic fungi, hosts and gut microbes, and provides a new idea for the joint use of entomopathogenic fungi and gut bacteria to control pests.

Dietary plant soot supplementation improves the intestinal health status of farmed American eels (Anguilla rostrata)

The current study evaluated the effect of different dietary plant soot supplementation levels on the intestinal health status of American eels (Anguilla rostrata) cultured in concrete tanks. Nine concrete fish tanks were randomly divided into three groups and fed the diets with plant soot (PS) supplementation levels at 0, 3 g/kg, and 5 g/kg, respectively. After a feeding trial for 60 days, the intestinal tissues were sampled to measure health status parameters. The D-lactate level and DAO activity in the serum of the PS5 group were significantly lower than those of the PS0 group (P <0.05). Compared with the PS0 group, the villi length of the intestine in both PS3 group and PS5 group increased significantly (P<0.05). The muscular thickness of the intestine of the PS5 group was significantly higher than the PS0 group (P<0.05). The microvillus density of the intestine of the American eel was increased obviously in the PS5 group. The intestinal microbiota composition of plant soot groups was beneficially regulated with certain probiotics’ higher relative abundances and some pathogenic bacteria’ lower relative abundance. In conclusion, dietary 5 g/kg plant soot supplementation could benefit the intestinal health of farmed American eels.

Comparison of the broncoalveolar lavage fluid proteomics between foals and adult horses.

Neonates have different cellular composition in their bronchoalveolar lavage fluid (BALF) when compared to foals and adult horses; however, little is known about the non-cellular components of BALF. The objective of this study was to determine the proteomic composition of BALF in neonatal horses and to compare it to that of foals and adult horses. Bronchoalveolar lavage fluid samples of seven neonates (< 1 week age), four 5 to 7-week-old foals, and six adult horses were collected. Quantitative proteomics of the fluid was performed using tandem mass tag labeling followed by high resolution liquid chromatography tandem mass spectrometry and protein relative abundances were compared between groups using exact text. A total of 704 proteins were identified with gene ontology terms and were classified. Of these, 332 proteins were related to the immune system in neonates, foals, and adult horses. The most frequent molecular functions identified were binding and catalytic activity and the most common biological processes were cellular process, metabolic process, and biological regulation. There was a significant difference in the proteome of neonates when compared to foals and to adult horses. Neonates had less relative expression (FDR < 0.01) of many immune-related proteins, including immunoglobulins, proteins involved in the complement cascade, ferritin, BPI fold-containing family B member 1, and macrophage receptor MARCO. This is the first report of equine neonate BALF proteomics and reveals differential abundance of proteins when compared to BALF from adult horses. The lower relative abundance of immune-related proteins in neonates could contribute to their susceptibility to pulmonary infections.

Leaf Endophyte Community Composition and Network Structures Differ Between Tolerant and Susceptible English Boxwood

Differential tolerance of English boxwood to boxwood blight has been linked to the ratio of culturable bacterial and fungal dominance in the leaf tissue of representative samples. To further understand how the whole endophyte communities may involve the tolerance of large samples, we extracted DNA from healthy leaf tissue of previously identified 28 tolerant (T), 41 moderately tolerant (M), and 21 susceptible (S) English boxwood plants, then sequenced associated bacterial and fungal amplicons using the Nanopore MinION platform. The endophyte community did not differ in diversity among the T, M, and S plants but differed in the abundance of bacteria and fungi, particularly between T and S samples. The bacterial genera Brevundimonas and Ammonifex had higher relative abundance in the T and M communities than in the S community, in which the fungal genera Botrytis and Thermothelomyces and family Chaetomiaceae were more dominant. The same results were obtained when mother and daughter samples in the T community were compared with controls in the S community, suggesting bacteria as a work force in the T community. Cooccurrence network analyses revealed that the T network had more fungal hubs but was less complex, with more positive connections than the S network, suggesting that the T community was supported by a healthier network. The resistance of English boxwood to blight is likely attributed to bacteria dominance and a synergic community network. This study is foundational to constructing synthetic communities and using whole communities of tolerant plants through vegetative propagation for microbe-modulated immunity.

Investigation of the rotational spectrum of CD3OD and an astronomical search toward IRAS 16293-2422

Solar-type prestellar cores and protostars frequently display large amounts of deuterated organic molecules and, in particular, high relative abundances of doubly and triply deuterated isotopologs. Recent findings on CHD2OH and CD3OH toward IRAS 16293–2422 suggest that even fully deuterated methanol, CD3OD, may be detectable as well. However, searches for CD3OD are hampered in particular by the lack of intensity information from a spectroscopic model. The objective of the present investigation is to develop a spectroscopic model of CD3OD in low-lying torsional states that is sufficiently accurate to facilitate searches for this isotopolog in space. We carried out a new measurement campaign for CD3OD involving two spectroscopic laboratories that covers the 34 GHz–1.1 THz range. A torsion-rotation Hamiltonian model based on the rho-axis method was employed for our analysis. Our resulting model describes the ground and first excited torsional states of CD3OD well up to quantum numbers J ⩽ 51 and Ka ⩽ 23. We derived a line list for radio-astronomical observations from this model that is accurate up to at least 1.1 THz and should be sufficient for all types of radio-astronomical searches for this methanol isotopolog. This line list was used to search for CD3OD in data from the Protostellar Interferometric Line Survey of IRAS 16293–2422 obtained with the Atacama Large Millimeter/submillimeter Array. While we found several emission features that can be attributed largely to CD3OD, their number is still not sufficiently high enough to establish a clear detection. Nevertheless, the estimate of 2 × 1015 cm−2 derived for the CD3OD column density may be viewed as an upper limit that can be compared to column densities of CD3OH, CH3OD, and CH3OH. The comparison indicates that the CD3OD column density toward IRAS 16293–2422 is in line with the enhanced D/H ratios observed for multiply deuterated complex organic molecules.

Investigating the effect of anode materials on the performance and microbial community in an integrated chamber-free microbial fuel cell

Conventionally, there are two basic configurations for microbial fuel cell (MFC), one with anode and cathode chambers, as known as dual-chamber MFC, one with only anode chamber and a air–cathode, called single-chamber MFC. However, electrode materials' complex configuration and high resistance limit their practical applications in power generation and wastewater purification. To this end, we constructed three MFCs using carbon felt, Ni/Ti, and Ag-Ni/Ti as anodes based on our previously constructed integrated chamber-free MFC (iMFC). After 21 days of operation, the Ag-Ni/Ti-MFC performed best in bioelectricity output and removal of target pollutants. The bioelectricity output parameters were an open-circuit voltage of 0.773 V, a maximum current density of 552.1429 mA/m2, and a power density of 426.8064 mW/m2. Furthermore, the MFC achieved removals of 67.90% for the chemical oxygen demand (COD), 55.20% for total nitrogen (TN), and 61.83% for ammonia nitrogen (NH3-N). Introducing silver nanoparticles to the transmembrane and outer membrane boosted the charge extraction efficiency in the MFCs. Moreover, 16S rDNA analysis indicated that typical electricity-producing bacteria, including Comamonas, Paraclostridium, and Asaccharospora, had a higher relative abundance in the Ag-Ni/Ti-MFC anode than in other anodes. Overall, the surface structure of different anode materials plays a critical role in bioelectricity generation and wastewater purification using iMFC by affecting the mass transfer of substrates and metabolites.

Italian ryegrass (Lolium multiflorum L.)-rice (Oryza sativa L.) rotation promotes the nitrogen cycle in the rice rhizosphere through dominant ammonia-oxidizing bacteria

The dominant ammonium bacteria established in different crop rotations are directly related to the conversion and utilization of nitrogen (N) in paddy soil. This study investigated the ammonia oxidation process in the rice rhizosphere of Italian ryegrass (Lolium multiflorum L.)-rice (IRR), celery (Apium graveolens)-rice (CLR) and winter fallow-rice (WFR) rotations in South China through the amoA functional gene analysis based on Miseq high-throughput sequencing platform and qPCR methods. The abundance of amoA gene in IRR was increased by 116.67 % (P < 0.05) and 42.76 % (P > 0.05) compared with CLR and WFR, respectively. Nitrosomonas became the dominant genus in the rhizosphere of IRR, with the highest relative abundance (59.30 %). The contents of soil organic matter, total N and nitrate nitrogen (NO3−-N) in the rice rhizosphere soil in IRR were significantly higher than other two treatments (P < 0.05) by 12.47–14.31 %, 16.88–25.00 %, and 97.48–159.60 %, respectively. Although lower microbial diversity was observed in IRR, the soil fluorescein diacetate hydrolysis enzyme activities and ammonia monooxygenase activities in the rice rhizosphere were higher in IRR than those in CLR and WFR (P < 0.05). Also, the soluble sugar and crude protein of milled rice were highest in IRR among the three rotation treatments (P < 0.05). The ammonia oxidation efficiency of ammonium-oxidizing bacteria was largely dependent on key taxa, such as Nitrosomonas (dominant genus in IRR), rather than the dynamics of AOB community structure. The key amoA-nitrifier taxa of the AOB community developed in IRR are capable of promoting rice production by improving soil N cycle efficiency and reducing the loss of N. Our findings illustrate the regulatory mechanism of IRR on the rice rhizosphere AOB community and reveal the important role of winter ryegrass in promoting soil nitrogen cycling during nutrient transformation of agricultural ecosystems in paddy fields.

Occurrence of putative Culicoides biting midge vectors (Diptera: Ceratopogonidae) inside and outside barns in Germany and factors influencing their activity

BackgroundAfter several years without bluetongue disease, a ruminant illness caused by Culicoides-borne bluetongue virus (BTV), two new autochthonous cases were reported in 2018 in Germany. By contrast, Schmallenberg virus (SBV), another Culicoides-borne virus pathogenic to ruminants, has continuously circulated in Germany since its first emergence in 2011. The disease outbreaks have triggered numerous studies on the biology of the Culicoides vectors, but many ecological details are still obscure.MethodsCulicoides biting midge species were collected with UV-light traps on 10 farms in Germany, with one trap inside and one trap outside barns on each of the farms. Traps were run once a week for 24 h from January to December 2019. Collected biting midges were morphologically identified, counted and statistically evaluated, with a focus on the Obsoletus Group and the Pulicaris Complex of the ceratopogonid genus Culicoides, which are believed to contain the major virus vectors. Temperature and relative humidity recorded at each trap were linked to the quantity of caught Culicoides. Correlations between relative Culicoides abundance and presence of livestock or type of husbandry were also investigated.ResultsA total of 38,886 Culicoides biting midges were trapped, with most of them belonging to the Obsoletus Group (51.0%) and the Pulicaris Complex (38.8%). The majority of captured specimens were collected in traps inside the barns. Obsoletus Group individuals were caught from late January to the last week of December while Pulicaris Complex individuals were captured from the end of March to early December. The lowest average temperatures at which members of the two groups were collected were 10.7 °C and 12.8 °C, respectively. While temperature had a statistically significant effect on the activity of both the Obsoletus Group and the Pulicaris Complex, relative humidity only significantly affected the activity of the latter. The presence of livestock significantly influenced the number of captured Obsoletus Group, but not of Pulicaris Complex specimens. Inside the barns, no statistical difference was found between numbers of caught Obsoletus Group and Pulicaris Complex specimens in livestock holdings with deep litter and manure scraper or slatted floor husbandry systems.ConclusionsThe almost year-round presence of Obsoletus Group biting midges and the demonstrated high relative abundance of other potential Culicoides vector species inside barns suggest a high risk of indoor virus transmission to ruminants should BTV or SBV circulate locally. Appropriate structural, organisational and vector control measures to reduce biting midge exposure should be implemented.Graphical

Comparative analysis of eukaryotic microbial communities associated with Acropora formosa, sediment, and seawater in a coral reef ecosystem of Whale island, Nha Trang bay, Vietnam

In this study, eukaryotic microbial communities associated with coral Acropora formosa and its natural surroundings, sediment and seawater, in a coral reef ecosystem of Whale Island, Nha Trang Bay, Vietnam were investigated. First, genetic material was taken from Acropora formosa’s surface mucus layer (SML) as well as the sediment underneath and seawater above the colonies from four different sampling locations in a coral reef ecosystem. Subsequently, the data were sequenced using 18S rRNA gene amplicon sequencing method. Sequences (reads) were then analyzed in Rstudio version 4.2.0. Bioinfomatic tools such as DADA2 pipeline clustered the sequences into amplicon sequence variants (ASVs), to which the taxonomy was assigned using SILVA 132 database. The majority of the sequences was categorized at the kingdom and phylum levels, but fewer sequences were identified at genus and species level. The visualization of the results revealed changes in abundance and composition of the eukaryotic communities in all samples. The results demonstrated that phylum Dinoflagellata had the highest relative abundance in coral samples. Meanwhile, Ochrophyta was the most prevalent phylum in seawater samples. Notably, after filtering out the sequences with abundance less than 2%, only genus Symbiodinium appeared significantly in coral samples. The composition of samples from coral sampling sites was more consistent. The same was true for samples of seawater, whereas the composition of sediment samples varied more. Alpha and beta diversity indices confirmed that there were significant differences (p &lt; 0.05) in abundance and composition of eukaryotic communities among three different habitats. These findings come as the first effort to explore the diversity of eukaryotic communities in different habitats and could be valuable for further study in functional profiling or metabolic functions of microbial communities in the coral ecosystem.

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.

Bacterial community structure and predicted function in the rhizosphere of wild and cultivated date palms: Effects of Fertilizers on Composition and Functionality

This study investigated bacterial diversity in date palm rhizosphere and assessed the influence of different fertilizers on diversity using metagenomics. A total of 6356 Operational Taxonomic Units (OTUs) and 1164425 sequences were analyzed across 27 samples. The findings revealed variations in microbial community phylogeny among similar cultivars from different farms, except for the Khalas cultivar, suggesting minor influence of genotype on microbial community structure. Wild date palms exhibited more unique OTUs, in contrast, cultivated date palms had a higher number of OTUs and diversity. Moreover, different fertilizer treatments had varying effects on bacterial diversity. For example, organic and bio-organic fertilizers positively influenced specific bacterial groups, including delta-proteobacteria, acidobacteria-Gp3, Anaerolinaea, and Clostridia. Conversely, combining high concentrations of chemical fertilizers with other types did not show significant effects. Classes such as Bacilli, Nitrospira, Deltaproteobacteria, Spartobacteria, and Thermomacrobia exhibited high relative abundances in treatments with high chemical fertilizer concentrations. Our analysis revealed potential pathways related to carbon, nitrogen, phosphorus, phenol, sulfur, and antimicrobial compounds. Interestingly, these pathways and functions varied across different date palm cultivars. Our findings suggest that date palm cultivars shape the rhizosphere by selectively influencing bacterial communities consistently across other locations. These modulated bacterial communities can potentially provide enhanced benefits to the host. Importantly, this study was the first to investigate the soil bacterial diversity of wild date palms, giving valuable insights into the microbial community associated with this specific context.

Causal relationship between gut microbiota and type 2 diabetes: a two-sample Mendelian randomization study.

Studies showed that development of gut microbial dysbiosis has a close association with type 2 diabetes (T2D). It is not yet clear if there is a causal relationship between gut microbiota and T2D. The data collected from the published genome-wide association studies (GWASs) on gut microbiota and T2D were analyzed. Two-sample Mendelian randomization (MR) analyses were performed to identify causal relationship between bacterial taxa and T2D. Significant bacterial taxa were further analyzed. To confirm the findings' robustness, we performed sensitivity, heterogeneity, and pleiotropy analyses. A reverse MR analysis was also performed to check for potential reverse causation. By combining the findings of all the MR steps, we identified six causal bacterial taxa, namely, Lachnoclostridium, Oscillospira, Roseburia, Ruminococcaceae UCG003, Ruminococcaceae UCG010 and Streptococcus. The risk of T2D might be positively associated with a high relative abundance of Lachnoclostridium, Roseburia and Streptococcus but negatively associated with Oscillospira, Ruminococcaceae UCG003 and Ruminococcaceae UCG010. The results of MR analyses revealed that there were causal relationships between the six different genera and T2D. And the reverse MR analysis did not reveal any evidence of a reverse causality. This study implied that Lachnoclostridium, Roseburia and Streptococcus might have anti-protective effect on T2D, whereas Oscillospira, Ruminococcaceae UCG003 and Ruminococcaceae UCG010 genera might have protective effect on T2D. Our study revealed that there was a causal relationship between specific gut microbiota genera and T2D.

A high-concentrate diet induces colonic inflammation and barrier damage in Hu sheep

Long-term feeding of a high-concentrate diet can induce subacute ruminal acidosis (SARA) in ruminants, which further leads to systemic inflammatory response. However, few studies have examined the effects of feeding a high-concentrate diet on the hindgut of ruminants. The purpose of this study was to investigate the effects of a high-concentrate diet on the composition of gut microbiota in colonic contents, inflammatory response, and barrier damage in the colon tissue of ruminants. A total of 12 healthy multiparous lactating Hu sheep were randomly allotted into the following 2 groups: a high-concentrate (HC) group (concentrate:forage = 7:3) and a low-concentrate (LC) group (concentrate:forage = 3:7). All sheep were fitted with ruminal fistulas. The formal feeding experiment lasted for 8 wk. After the feeding experiment, rumen fluid, portal vein blood, hepatic vein blood, colonic contents, and colon tissue samples were collected. The results showed that feeding the HC diet induced SARA in Hu sheep and significantly reduced pH in the colonic contents. The abundances of Firmicutes, Verrucomicrobiota, and Actinobacteriota decreased significantly, whereas those of Bacteroidota, Spirochaetota, and Fibrobacterota significantly increased in colonic contents. At the genus level, the relative abundances of 29 genera were significantly altered depending on the different type of diets. Analysis of the 10 bacterial genera with high relative abundance revealed that feeding the HC diet significantly reduced the abundance of UCG-005, Christensenellaceae R-7 group, UCG-010-norank, Monoglobus, [Eubacterium] coprostanoligenes group_norank, and Alistipes, whereas the abundances of Rikenellaceae RC9 gut group, Treponema, Bacteroides, and Prevotella increased. Compared with the LC group, feeding the HC diet significantly increased the concentration of LPS in rumen fluid, portal vein blood, hepatic vein blood, and colonic contents, and significantly upregulated the mRNA expression levels of proinflammatory cytokines in colon tissue, including TNF-α, IL-1β, IL-6, and IL-8, indicating the occurrence of inflammatory response in the colon tissue. In addition, the structure of colonic epithelial cells was loose, the intercellular space became larger, epithelial cells were exfoliated, and the mRNA and protein abundances of ZO-1, occludin, claudin-1, claudin-3, and claudin-4 were significantly decreased in the HC group, which was consistent with the results of immunohistochemistry. Furthermore, feeding the HC diet increased the ratios of DNA methylation and chromatin compaction in the promoter regions of occludin and claudin-1, which in turn inhibited their transcriptional expression. Therefore, the present study demonstrated that feeding an HC diet induced SARA in Hu sheep, altered the composition and structure of the microbial community in the colonic contents, induced an inflammatory response, and disrupted the intestinal mucosal barrier in the colonic tissue.

Effect of different types of volatile fatty acids on the performance and bacterial population in a batch reactor performing biological nutrient removal

Different ratios of four volatile fatty acids (VFAs) were used as the primary feed to a laboratory scale biological nutrient reactor during four operational stages. The reactor performed efficiently over 500 days of operation with over 90% dissolved phosphorus and over 98% ammonium-nitrogen (NH4+-N) removal. Through in the first experimental phase, acetate and propionate were present in a significant proportion as carbon sources, the relative abundance of Candidatus Accumulibacter, a potential polyphosphate accumulating organism, increased from 10% to 57% and the Defluviicoccus genus, a known glycogen accumulating organism (GAO), decreased from 41% to 5%. Further tests indicated the presence of denitrifying phosphorus accumulating organisms (DPAO) belonging to Clade IIC, that could use nitrite as the electron acceptor during P-uptake. In general, VFAs favored the increase of the genus Defluviicoccus and Candidatus Accumulibacter. High relative abundance of Defluviicoccus did not affect the stability and the performance of the BNR process.