Number Of Operational Taxonomic Units Research Articles

Effects of high-grain diet feeding on mucosa-associated bacterial community and gene expression of tight junction proteins and inflammatory cytokines in the small intestine of dairy cattle

The objective of this study was to investigate changes in the composition of mucosa-associated bacterial community, the morphology of the small intestinal epithelia, and the gene expressions of junction proteins and inflammatory cytokines in the small intestines of dairy cattle fed a high-grain (HG) diet. A total of 12 ruminally cannulated Holstein cows in mid-lactation were randomly fed either a conventional (CON) diet (40% concentrate, dry matter basis) or an HG diet (60% concentrate, dry matter basis) for 4 wk. At the end of the feeding trial, all the cows were slaughtered and then examined for changes in the small intestinal mucosa-associated bacterial communities using 16S full-length amplicon sequencing. Furthermore, the gene expression of tight junction proteins and inflammatory cytokines in the small intestinal epithelium were studied using real-time quantitative PCR. The results of nonmetric multidimensional scaling plots showed that an HG diet altered the composition of mucosa-associated bacterial communities in the jejunum and ileum. The HG feeding only increased the numbers of operational taxonomic units in the mucosa-associated bacterial community in the jejunum. At the genus level, the HG diet increased the abundance of uncultured Succinivibrionaceae and Lachnospiraceae incertae sedis in the duodenal mucosa, whereas the proportions of Veillonella and Selenomonas increased in the jejunal mucosa. Compared with the CON group, the proportions of Acetitomaculum in both the jejunal and the ileal mucosa were higher in the HG group. Analysis via PICRUSt2 (version 2.2.0-b) suggested that the HG diet increased the abundance of genes related to biodegradation of xenobiotics in the jejunal mucosa and the abundance of genes related to immune disease in the ileal mucosa. Additionally, the group fed an HG diet had higher concentrations of lipopolysaccharides in the jejunal and ileal digesta. The HG feeding caused a downregulation of the mRNA expression of occludin and ZO-1 in the jejunal epithelium, as well as of claudin-1, claudin-4, and ZO-1 in the ileal epithelium. Moreover, the HG diet caused an increase in the mRNA expression of IL-1β, IL-2, and IFN-γ in the jejunal epithelium, but a higher expression of IL-2 and IFN-γ in the ileal epithelium. Correlation analysis revealed that the alteration of lipopolysaccharide levels and mucosa-associated bacterial community might partly contribute to changes in the expression of the epithelial cytokines in the jejunum and ileum during HG feeding. These findings suggest that microbiota residing in the small intestine provide essential health benefits to host dairy cattle.

Unraveling Nitrogen Fixing Potential of Endophytic Diazotrophs of Different Saccharum Species for Sustainable Sugarcane Growth.

Sugarcane (Saccharum officinarum L.) is one of the world’s highly significant commercial crops. The amounts of synthetic nitrogen (N2) fertilizer required to grow the sugarcane plant at its initial growth stages are higher, which increases the production costs and adverse environmental consequences globally. To combat this issue, sustainable environmental and economic concerns among researchers are necessary. The endophytic diazotrophs can offer significant amounts of nitrogen to crops through the biological nitrogen fixation mediated nif gene. The nifH gene is the most extensively utilized molecular marker in nature for studying N2 fixing microbiomes. The present research intended to determine the existence of novel endophytic diazotrophs through culturable and unculturable bacterial communities (EDBCs). The EDBCs of different tissues (root, stem, and leaf) of five sugarcane cultivars (Saccharum officinarum L. cv. Badila, S. barberi Jesw.cv Pansahi, S. robustum, S. spontaneum, and S. sinense Roxb.cv Uba) were isolated and molecularly characterized to evaluate N2 fixation ability. The diversity of EDBCs was observed based on nifH gene Illumina MiSeq sequencing and a culturable approach. In this study, 319766 operational taxonomic units (OTUs) were identified from 15 samples. The minimum number of OTUs was recorded in leaf tissues of S. robustum and maximum reads in root tissues of S. spontaneum. These data were assessed to ascertain the structure, diversity, abundance, and relationship between the microbial community. A total of 40 bacterial families with 58 genera were detected in different sugarcane species. Bacterial communities exhibited substantially different alpha and beta diversity. In total, 16 out of 20 genera showed potent N2-fixation in sugarcane and other crops. According to principal component analysis (PCA) and hierarchical clustering (Bray–Curtis dis) evaluation of OTUs, bacterial microbiomes associated with root tissues differed significantly from stem and leaf tissues of sugarcane. Significant differences often were observed in EDBCs among the sugarcane tissues. We tracked and validated the plethora of individual phylum strains and assessed their nitrogenase activity with a culture-dependent technique. The current work illustrated the significant and novel results of many uncharted endophytic microbial communities in different tissues of sugarcane species, which provides an experimental system to evaluate the biological nitrogen fixation (BNF) mechanism in sugarcane. The novel endophytic microbial communities with N2-fixation ability play a remarkable and promising role in sustainable agriculture production.

Long‐term ground cover affects soil bacterial community and carbon metabolism in the Loess Plateau, China

AbstractFarmland mulching can maintain soil nutrients, which plays a positive role in agricultural planting in the arid area. However, the composition of the soil microbial community and the C cycle involved is unclear under farmland mulching. Based on the Changwu Agro‐Ecological Experiment Station, this study set up a long‐term positioning experiment to explore the effect on soil bacterial community structure and C metabolism capacity. In this study, we include five treatments: control uncovered (CK), plastic film mulching (PF), high amount of straw mulching carried out in July, August, and September every year (St90), low amount of straw mulch throughout the growth period (S45), and high amount of straw cover throughout the growth period (S90). We combined Illumina MiSeq sequencing and Biolog‐ECO technology to analyze the functional characterization of soil bacterial community composition in terms of C source metabolism. The results indicated that the soil bacteria showed a high degree of epistatic clustering, and the operational taxonomic unit numbers of soil bacteria decrease as St90, S45, PF, CK, and S90. Redundancy analysis showed that soil available P, NH4+–N, soil moisture content were the main environmental factors affecting bacterial community composition. Proteobacteria, Acidobacteria, and Actinobacteria are the main dominant flora in this area. Soil bacterial C metabolism was highest under PF treatment. Structural equation modeling (SEM) shows that surface cover has direct and indirect effects on bacterial C metabolism capacity and diversity through soil physicochemical properties. Reasonable mulching methods have a positive effect on the sustainable development of agro‐ecosystems in arid areas.

Influence of DNA extraction kits on freshwater fungal DNA metabarcoding.

BackgroundEnvironmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes.MethodsDNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples.ResultsNo PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.

Monocot diet sources drive diversity of gut bacterial communities in Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae

AbstractMicrobiome research is currently gaining tremendous interest on the impact of diets and environment to influence life traits of several hosts. Full understanding of the insect ecology and characterization of gut microbial community including their natural enemies is vital for development of novel insect pest management strategies. This study examined the gut bacterial communities of Fall armyworm (FAW) Spodoptera frugiperda reared in the laboratory with three monocot plant diets (Sugarcane [M1], maize [M2] and onion [M3]) using 16S rRNA gene sequencing. The study revealed variations in the structure and community of the gut bacterial biota of FAW larvae reared with three monocot plants. Diet sources greatly altered the structure of the gut bacterial community. Three alpha diversity indices (observed species richness Chao1 and ACE) showed significant differences among the various diet groups. The principal component analysis revealed a moderate distinction in bacterial communities of the FAW larvae reared with the three monocot plants. Higher numbers of operational taxonomic units (OTUs) were observed in sugarcane diet (M1). The bacterial communities of all the larvae groups were dominated by phylum Firmicutes. A redundancy analysis (RDA) indicated that neutral detergent fibre (NDF) (p < 0.0005) was the most significant factors influencing the community distribution of gut bacteria of FAW larvae. Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis predicted that chemoheterotrophy, fermentation, aerobic chemoheterotrophy and aromatic compound degradation were the prominent putative functions of FAW larvae gut bacteria communities. Chemoheterotrophy was the most dominant putative functions predicted and was higher in sugarcane diet. Furthermore, the complexity of the network structure was higher in M1 while the modularity was higher in maize diet. The different monocot diets had a considerable impact on bacterial composition in the gut of Fall armyworm larvae and their ecological and functional relevance are discussed.

Bacteria Community Inhabiting Heterobasidion Fruiting Body and Associated Wood of Different Decay Classes.

The microbiome of Heterobasidion-induced wood decay of living trees has been previously studied; however, less is known about the bacteria biota of its perennial fruiting body and the adhering wood tissue. In this study, we investigated the bacteria biota of the Heterobasidion fruiting body and its adhering deadwood. Out of 7,462 operational taxonomic units (OTUs), about 5,918 OTUs were obtained from the fruiting body and 5,469 OTUs were obtained from the associated dead wood. Interestingly, an average of 52.6% of bacteria biota in the fruiting body was shared with the associated dead wood. The overall and unique OTUs had trends of decreasing from decay classes 1 to 3 but increasing in decay class 4. The fruiting body had the highest overall and unique OTUs number in the fourth decay class, whereas wood had the highest OTU in decay class 1. Sphingomonas spp. was significantly higher in the fruiting body, and phylum Firmicutes was more dominant in wood tissue. The FAPROTAX functional structure analysis revealed nutrition, energy, degradation, and plant-pathogen-related functions of the communities. Our results also showed that bacteria communities in both substrates experienced a process of a new community reconstruction through the various decay stages. The process was not synchronic in the two substrates, but the community structures and functions were well-differentiated in the final decay class. The bacteria community was highly dynamic; the microbiota activeness, community stability, and functions changed with the decay process. The third decay class was an important turning point for community restructuring. Host properties, environmental factors, and microbial interactions jointly influenced the final community structure. Bacteria community in the fruiting body attached to the living standing tree was suppressed compared with those associated with dead wood. Bacteria appear to spread from wood tissue of the standing living tree to the fruiting body, but after the tree is killed, bacteria moved from fruiting body to wood. It is most likely that some of the resident endophytic bacteria within the fruiting body are either parasitic, depending on it for their nutrition, or are mutualistic symbionts.

OP-10 Gut microbiota dysbiosis as a driver of inflammation in Ocular Mucous Membrane Pemphigoid.

Gut microbiome profiles between OcMMP patients (n=49) and healthy controls (n=40) were compared by extracting DNA from faecal samples and amplified for the V4 region of the 16S rRNA gene followed by Illumina Miseq platform sequencing. Sequencing reads were processed using the bioinformatics pipeline available in the mothur v.1.44.1 software. Using multivariable model and adjustment for participant factors, OcMMP cohort was found to be associated with lower number of operational taxonomic units (OTUs) and Shannon Diversity Index when compared to healthy controls. OcMMP OTUs were found to be significantly correlated with both the bulbar conjunctival inflammation score (p=0.03) and the current use of systemic immunotherapy (p=0.02). Linear discriminant analysis effect size scores found Streptococcus and Lachnoclostridium enriched in OcMMP. By contrast, healthy controls were enriched with Oxalobacter, Clostridia uncultured genus-level group (UCG) 014, Christensenellaceae R-7 group and butyrate-producing bacteria such as Ruminococcus, Lachnospiraceae, Coprococcus, Roseburia, Oscillospiraceae UCG 003, 005, NK4A214 group (Log10 LDA score <2, FDR-adjusted p<0.05). In conclusion, OcMMP patients have gut dysbiosis that correlated with bulbar conjunctival inflammation and the use of systemic immunotherapies. This provides a framework for future longitudinal deep phenotyping studies on the role of the gut microbiome in the pathogenesis of OcMMP. Low L, Suleiman K, Shamdas M, Bassilious K, Poonit N, Rossiter AE, Acharjee A, Loman N, Murray PI, Wallace GR, Rauz S. Gut dysbiosis in ocular mucous membrane pemphigoid. Front. Cell. Infect. Microbiol. 2022;12:780354. https://doi.org/10.3389/fcimb.2022.780354.

Esophageal Microbiota and Nutritional Intakes in Patients With Achalasia Before and After Peroral Endoscopic Myotomy.

Background/AimsThe composition of the microbiota in the esophagus is only partially understood, especially in patients with achalasia. We aim to investigate the esophageal microbial community and nutritional intakes in patients with achalasia before and after peroral endoscopic myotomies (POEM).MethodsTwenty-nine patients were prospectively enrolled from 4 referral institutions across Korea. We collected esophageal samples (mucosal biopsies and retention fluid) and conducted dietary surveys for nutritional intake before and 8 weeks after POEM. The esophageal microbiota was analyzed by 16S rRNA gene sequencing targeting the V3-V4 region.ResultsOut of the 105 samples from 29 patients, 99 samples were subjected to microbial bioinformatic analysis after quality control, which excluded samples with no amplification or low-quality sequence data. The overall esophageal microbial compositions of patients with achalasia showed that Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the dominant phyla, representing over 95% of the total phyla in all groups. At the genus level, Streptococcus was the most abundant in all groups. The observed operational taxonomic unit number was significantly higher in the retention fluid than in the tissue biopsies. However, the esophageal microbial composition showed no significant changes 8 weeks post POEM. The dietary survey analysis showed that nutritional intake significantly improved post POEM.ConclusionThis study determined the unique esophageal microbial composition of patients with achalasia, and also found that the microbial composition did not significantly change after POEM in the short-term, despite a significant improvement in the nutritional intake.

Niche differentiation of comammox Nitrospira in sediments of the Three Gorges Reservoir typical tributaries, China

Complete ammonia oxidizer (Comammox) can complete the whole nitrification process independently, whose niche differentiation is important guarantee for its survival and ecological function. This study investigated the niche differentiation of comammox Nitrospira in the sediments of three typical tributaries of the Three Gorges Reservoir (TGR). Clade A and clade B of comammox Nitrospira coexisted in all sampling sites simultaneously. The amoA gene abundance of clade A and B was gradually increased or decreased along the flow path of the three tributaries with obvious spatial differentiation. The amoA gene abundance of comammox Nitrospira clade A (6.36 × 103 − 5.06 × 104 copies g−1 dry sediment) was higher than that of clade B (6.26 × 102 − 6.27 × 103 copies g−1 dry sediment), and the clade A amoA gene abundance was one order of magnitude higher than that of AOA (7.24 × 102 − 6.89 × 103 copies g−1 dry sediment) and AOB (1.44 × 102 − 1.46 × 103 copies g−1 dry sediment). A significant positive correlation was observed between comammox Nitrospira clade A amoA gene abundance and flow distance (P < 0.05). The number of operational taxonomic units (OTUs) in two sub-clades of clade A accounted for the majority in different tributaries, indicating that clade A also had population differentiation among different tributaries. This study revealed that comammox Nitrospira in the sediments of TGR tributaries have niche differentiation and clade A.2 played a more crucial role in comammox Nitrospira community.

Bladder Microbiota Are Associated with Clinical Conditions That Extend beyond the Urinary Tract.

Background. Since the discovery of the human urinary microbiota (UM), alterations in microbial community composition have been associated with various genitourinary conditions. The aim of this exploratory study was to examine possible associations of UM with clinical conditions beyond the urinary tract and to test some of the conclusions from previous studies on UM. Methods. Catheterised urine samples from 87 men were collected prior to endoscopic urological interventions under anaesthesia. The composition of the bacterial community in urine was characterized using the hypervariable V4 region of the 16S rRNA gene. Samples from 58 patients yielded a sufficient amount of bacterial DNA for analysis. Alpha diversity measures (number of operational taxonomic units, ACE, iChao2, Shannon and Simpson indices) were compared with the Kruskal–Wallis test. Beta diversity (differences in microbial community composition) was assessed using non-metric dimensional scaling in combination with the Prevalence in Microbiome Analysis algorithm. Results. Differences in bacterial richness and diversity were observed for the following variables: age, diabetes mellitus, dyslipidemia, smoking status and single-dose preoperative antibiotics. Differences in microbial community composition were observed in the presence of chronic kidney disease, lower urinary tract symptoms and antibiotic prophylaxis. Conclusions. UM appears to be associated with certain clinical conditions, including those unrelated to the urinary tract. Further investigation is needed before conclusions can be drawn for diagnostics and treatment.

DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera).

BackgroundThe hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy.MethodsA morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies.ResultsSequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.

Gut Dysbiosis in Ocular Mucous Membrane Pemphigoid.

Mucous Membrane Pemphigoid is an orphan multi-system autoimmune scarring disease involving mucosal sites, including the ocular surface (OcMMP) and gut. Loss of tolerance to epithelial basement membrane proteins and generation of autoreactive T cell and/or autoantibodies are central to the disease process. The gut microbiome plays a critical role in the development of the immune system. Alteration in the gut microbiome (gut dysbiosis) affects the generation of autoreactive T cells and B cell autoantibody repertoire in several autoimmune conditions. This study examines the relationship between gut microbiome diversity and ocular inflammation in patients with OcMMP by comparing OcMMP gut microbiome profiles with healthy controls. DNA was extracted from faecal samples (49 OcMMP patients, 40 healthy controls), amplified for the V4 region of the 16S rRNA gene and sequenced using Illumina Miseq platform. Sequencing reads were processed using the bioinformatics pipeline available in the mothur v.1.44.1 software. After adjusting for participant factors in the multivariable model (age, gender, BMI, diet, proton pump inhibitor use), OcMMP cohort was found to be associated with lower number of operational taxonomic units (OTUs) and Shannon Diversity Index when compared to healthy controls. Within the OcMMP cohort, the number of OTUs were found to be significantly correlated with both the bulbar conjunctival inflammation score (p=0.03) and the current use of systemic immunotherapy (p=0.02). The linear discriminant analysis effect size scores indicated that Streptococcus and Lachnoclostridium were enriched in OcMMP patients whilst Oxalobacter, Clostridia uncultured genus-level group (UCG) 014, Christensenellaceae R-7 group and butyrate-producing bacteria such as Ruminococcus, Lachnospiraceae, Coprococcus, Roseburia, Oscillospiraceae UCG 003, 005, NK4A214 group were enriched in healthy controls (Log10 LDA score < 2, FDR-adjusted p <0.05). In conclusion, OcMMP patients have gut dysbiosis correlating with bulbar conjunctival inflammation and the use of systemic immunotherapies. This provides a framework for future longitudinal deep phenotyping studies on the role of the gut microbiome in the pathogenesis of OcMMP.

Residual Bacteriome after Chemomechanical Preparation of Root Canals in Primary and Secondary Infections

IntroductionSecondary infections may be linked to the presence of residual microorganisms within dental root canals. The purpose of this study was to investigate the bacterial composition of primary and secondary root canal infections before and after chemomechanical treatment. MethodsSamples were collected before chemomechanical preparation (S1) and before obturation (S2) from 19 subjects (10 primary and 9 secondary infections). DNA was extracted, and the V3/V4 region of the 16S ribosomal RNA gene was amplified using the 347 F/803R primers and paired-end sequenced using the MiSeq (Illumina, San Diego, CA) instrument. ResultsSequencing analysis yielded partial 16S ribosomal RNA gene sequences that were taxonomically classified into 10 phyla and 143 genera. The most prevalent phyla in the S1 and S2 samples were Firmicutes and Bacteroides; however, when comparing between sample groups, Proteobacteria seem to have been enriched in secondary infections. The dominant genera in the primary S1 samples were Bacillus, Streptococcus, and Prevotella, whereas Bacillus, Streptococcus, and Selenomonas dominated the secondary infection S1 samples. Bacillus and Marinilactibacillus were the most dominant genera in the primary and secondary S2 samples. The mean number of operational taxonomic units per sample was 32,656 (±12,124 SD) and 37,113 (±16,994 SD) in the S1 and S2 samples, respectively. Alpha and beta diversities presented the same pattern within samples from both groups. ConclusionsGreat interindividual variations in the bacterial composition of the root canal biofilms were observed. There was no difference in the bacterial composition before and after treatment, although some genera survived and seem to be part of a residual microbiome. Our findings revealed a high diversity of the bacterial communities present in root canal infections after chemomechanical treatment, although the majority of the taxa detected were in low abundance.

Observation of the Gut Microbiota Profile in BALB/c Mice Induced by Plasmodium yoelii 17XL Infection.

Rodent malaria caused by Plasmodium yoelii 17XL (Py 17XL) is an ideal animal model for human malaria studies. Although the gut microbiota plays an important role in the occurrence and development of infectious diseases, the gut microbiota associated with Py 17XL infection remains unclear. In the current study, the gut microbiota composition of infected BALB/c mice was surveyed. Mouse fecal samples were collected at 0, 2, 5 days post-infection (dpi), and the gut microbiota was characterized by 16S rRNA sequencing. Operational taxonomic units (OTUs) were 634 ± 26 on average. Firmicutes and Bacteroidetes were typically predominant in the gut microbiota composition at the phylum level. Compared with the Ctrl, Firmicutes was significantly decreased after infection, while Bacteroidetes was notably increased. The most dominant family was Lactobacillaceae in all samples. The alpha diversity index showed that compared with that of the Ctrl, the observed OTU number was decreased at 2 dpi and then slightly increased at 5 dpi. LEfSe analysis revealed several bacterial taxa were notably related to Py-infected mice at the phylogenetic level. Several bacterial genera, such as Lactobacillus, were overrepresented in the Py-infected fecal microbiota at 2 dpi, while Muribaculaceae was overrepresented at 5 dpi. Moreover, Alistipes and Helicobacter were overrepresented at 5 dpi compared with 2 dpi. The results indicated Py infection could alter the gut microbiota composition of mice. Besides, biomarkers could serve as direct targets to elucidate their roles in the progression and pathogenesis of malaria and provide insights into studies of antimalarial drugs and malaria vaccines.

Effect of rapeseed straw-derived biochar on soil bacterial community structure at tillering stage of Oryza Sativa.

Numerous studies have reported the dynamics of microbes when biochar was applied, whereas the information on the alterations of bacterial community after application of rapeseed straw-derived biochar is limited. A pot experiment with two rapeseed straw-derived biochar application treatments (with biochar application at the rate of 200g/pot, C1, and without biochar application, 0g/pot, C0) was conducted. No significant differences were observed in the number of operational taxonomic units, observed species, Shannon index, Simpson index, Chao1, ACE, and phylogenetic diversity whole tree between the C1 and C0 treatments. Taxonomic analysis at the phylum level showed that the abundances of Bacteroidetes and Parcubacteria were higher in the C1 treatment compared to the C0 treatment, while Acidobacteria, Chloroflexi, Rokubacteria, Berkelbacteria, and Latescibacteria were observed with higher abundance in the C0 treatment compared to the C1 treatment. Taxonomic analysis at the genus level showed that the abundances of Gracilibacter, Lentimicrobium, unidentified Rikenellaceae, Hydrogenophaga, and Bacillus were higher in the C1 treatment compared to the C0 treatment, while Candidatus Solibacter, Candidatus Koribacter, and Lutispora abundances were found to be higher in the C0 treatment compared to the C1 treatment. Obvious clusters were observed between the C1 and C0 treatments in both principal component analysis and nonmetric multidimensional scaling. These results indicate that soil bacterial community was altered after rapeseed straw-derived biochar was applied.

Cropping practices manipulate soil bacterial structure and functions on the Qinghai–Tibet Plateau

There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai–Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae–legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae–legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai–Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.

Effects of Feeding Frequency and Dietary Protein/Carbohydrate Ratios on Gilthead Seabream (Sparus aurata) Intestinal Functionality and Health

The present study evaluated the effects of feeding frequency (FF) and dietary protein/carbohydrate (P/CH) ratios on intestinal histomorphology, microbiota profile, and digestive and oxidative stress-related enzyme activities of gilthead seabream (Sparus aurata). To this purpose, two practical diets were formulated: one with 50% P and 10% CH (P50/CH10) and other with 40% P and 20% CH (P40/CH20). Triplicate groups of fish with9.1±0.01 gwere fed these diets for 60 days until visual satiation at a FF of 1, 2, or 3 meals per day. Distal intestine histomorphology was not affected by diet composition or FF. However, the pyloric caeca (PC) of fish fed 1 meal per day presented more gut fold height alterations than the other groups, except in fish fed diet P50/CH10 3 meals per day, where no changes was observed. Fish fed diet P40/CH20 3 meals per day also presented higher PC submucosa cellularity than the other groups. Fish fed diet P40/CH20 presented a higher number of operational taxonomic units, microbial richness, and diversity indices than fish fed diet P50/CH10. Amylase was the only measured digestive enzyme affected by the experimental conditions, presenting higher activity in fish fed diet P50/CH10 once per day. Glucose-6-phosphate dehydrogenase activity was lower in fish fed 2 meals per day than only 1. While catalase activity was lower in fish fed 2 than 3 meals per day. Glutathione reductase activity was the only measured parameter affected both by dietary P/CH ratio and FF, being inferior in fish fed once per day the P50/CH10 diet than the P40/CH20 diet and, also in the P50/CH10 diet, to fish fed 1 than those fed 3 meals per day. Overall, no major interactions was observed between dietary P/CH ratio and FF; however, a P40/CH20 diet fed 2 meals per day might be recommended for gilthead seabream juveniles.

Effect of Dietary Plant Feedstuffs and Protein/Carbohydrate Ratio on Gilthead Seabream (Sparus aurata) Gut Health and Functionality

This study investigated, for the first time, the integrated effects of dietary protein source and protein/carbohydrate (P/CH) ratio on gilthead seabream gut histomorphology, microbiota composition, digestive enzymes activity, and immunological and oxidative stress-related gene expressions. Four isolipidic diets: two fishmeal-based (FM) and two plant feedstuff (PF)-based diets, with P/CH ratios of 50/10 or 40/20 each (FM-P50/CH10; FM-P40/CH20; PF-P50/CH10; PF-P40/CH20), were tested. PF-based diets lead to more histomorphological alterations than FM-based diets. P/CH ratio had no relevant effect on gut histomorphology. Gut mucosa of fish fed PF-based diets presented a higher number of operational taxonomic units, and richness and diversity indices, while the P/CH ratio did not affect those parameters. The α-amylase activity was lower in fish fed with PF-based diets and in fish fed the P40/CH20 diets. Regarding the immune-related genes, only cyclooxygenase-2 was affected, being higher in fish fed the P50/CH10 diets than the P40/CH20 diets. Fish fed the FM-based diets presented higher expression of glutathione reductase and glutathione peroxidase, while fish fed the P50/CH10 diet had higher expression of superoxide dismutase. In conclusion, PF-based diets can compromise gut absorptive and digestive metabolism, but decreasing the dietary P/CH ratio had little effect on the parameters measured.

Effects of Nutrient Levels and Rice Cultivation on Taxonomic and Functional Diversity of Bacterial Communities in Flooded Soils of the Hanon Maar Crater, Korea

Agricultural land use may deteriorate soil bacterial diversity and function in an agroecosystem. This study aimed to explore the impact of agricultural disturbance on the taxonomic and functional diversity of soil bacteria using a high-throughput sequencing method. We examined the bacterial community diversity in five types of flooded soils in the Hanon Maar Crater from two types of canals characterized by different nutrient levels and three field types with a different rice cultivation history. Proteobacteria (43.2%), Chloroflexi (19.8%), Acidobacteria (15.8%), Actinobacteria (5.1%), and Nitrospirae (5.0%) were the dominant phyla (&gt;5%). The relative abundance of Actinobacteria was 7.1 times greater in the abandoned fields than in the polluted canal. Alpha diversity indices of taxonomic diversity showed strong negative correlations with C, N, and NH4+ levels. The 1.7-fold greater number of operational taxonomic units (OTUs) in abandoned fields than in paddy fields may be caused by factors other than nutrients. Functional analysis revealed that 11 putative functions, including cellulolysis and ligninolysis, were significantly affected by soil management. Functional diversity indices showed negative correlations with electrical conductivity (EC) and NH4+. Nitrogen input had a greater effect on bacterial taxonomic diversity than on functional diversity. Available P was positively correlated with the diversity indices. Taken together, these results suggest that keeping land fallow for more than 5 years and monitoring of C, N, and P levels are practical approaches for restoring taxonomic diversity but not functional diversity of soil bacteria. Our study demonstrated a decoupled response of taxonomic and functional diversity to rice cultivation, highlighting the necessity of further studies on the impact of decoupling on the stability of ecosystem functioning.

Composition, activity and diversity of bacterial and fungal communities responses to inputs of phosphorus fertilizer enriched with beneficial microbes in degraded Brunic Arenosol

AbstractAnthropogenic‐induced deterioration of soil health remains a global problem, resulting in a diminished productivity of agroecosystems. In order to improve soil quality, we investigated the impact of phosphorus biofertilizer on the microbiological parameters of soil (type Brunic Arenosol) degraded as a result of inappropriate cultivation and fertilization, characterized by low pH and decrease in K and Mg content. Two‐year field experiment included control treatment (FC) without microbial enrichment and FA100 (fertilizer amendment at optimal dose) and FA60 (fertilizer amendment at 40% reduced dose) treatments containing beneficial microorganisms. The results showed that the biofertilizer enhanced soil enzymatic activity (as expressed by the increased activities of urease, protease, acid phosphomonoesterase, and β‐glucosidase), increased number of operational taxonomic units associated with metabolic processes (including phosphorus related pathways and degradation of xenobiotics), improved crop yield, increased bacterial diversity, and changed the quantity of phytoavailable phosphorus in the soil. Biofertilizer also stimulated the occurrence of plant growth promoting microorganisms involved in phosphorus biotransformations, decomposition of organic matter, nitrogen fixation, and protection plants against pathogens. Next generation sequencing (NGS) and Biolog analyses showed that the composition of soil microbiome was affected also by soil sampling time, suggesting seasonal variations in the preferred carbon sources and level of C‐substrates utilization, and pointing the differences in the relative abundance of individual microbial groups at particular stages of the experiment. Taking into consideration the improvement of microbiological indicators of soil health, phosphorus biofertilizer seems to be effective approach to implement in sustainable agriculture linking soil microbiome quality with the general soil condition.