Bacterial Operational Taxonomic Units Research Articles

Detection of cardiovascular disease using explainable artificial intelligence and gut microbiota data

Purpose:Gut microbiota are defined as the microbial population of the intestines. They include various types of bacteria which can influence and predict the existence or onset of some specific diseases. Therefore, it is a common practice in medicine to analyze the gut microbiota for diagnostic purposes by analyzing certain measurable biochemical features associated with the disease under investigation. However, the evaluation of all the data collected from the gut microbiota is a labor-intensive process. Artificial Intelligence (AI) may be a helpful tool to identify the hidden patterns in gut microbiota for the detection of disease and other classification problems. Methods:In this study, we propose a deep neural model based on a one-dimensional convolutional neural network (1D-CNN) to detect cardiovascular disease using bacterial taxonomy and OTU (Operational Taxonomic Unit) table data. The developed AI method is compared to classical machine learning algorithms, regression, boosting algorithms and a deep model, Tabular Network (TabNet), developed for tabular data and obtained outperforming classification results. Results:According to AUC (Area Under Curve) values, boosting and regression methods outperformed the classical machine learning methods. However, the highest value of 97.09 AUC was obtained with the developed 1D-CNN model by using bacterial taxonomy data even with less then expected number of samples. Using explainable AI, nine bacteria were identified which the models find important for classification. Conclusion:The proposed method is robust and well adapted to taxonomy data in tabular form. It can be easily adapted to detect other diseases by using taxonomy data. The study also investigated the effect on barcode sequence for the classification, but the result showed that barcode sequences do not contribute to the bacterial taxonomy data for the estimation of CVD disease.

Microbial community analysis of sand filters used to treat mine water from a closed uranium mine.

Rapid sand filters (RSFs) are employed in a drinking water treatment to remove undesirable elements such as suspended solids and dissolved metal ions. At a closed uranium (U) mine site, two sets of tandemly linked paired RSF systems (RSF1-RSF2 and RSF1-RSF3) were utilized to remove iron and manganese from mine water. In this study, a 16S rRNA-based amplicon sequencing survey was conducted to investigate the core microbes within the RSF system treating the mine water. In RSF1, two operational taxonomic units (OTUs) related to methanotrophic bacteria, Methylobacter tundripaludum (relative abundance: 18.1%) and Methylovulum psychrotolerans (11.5%), were the most and second most dominant species, respectively, alongside iron-oxidizing bacteria. The presence of these OUTs in RSF1 can be attributed to the microbial community in the inlet mine water, as the three most abundant OTUs in the mine water also dominated RSF1. Conversely, in both RSF2 and RSF3, Nevskia sp., previously isolated from the Ytterby mine manganese oxide producing ecosystem, became dominant, although known manganese-oxidizing bacterial OTUs were not detected. In contrast, a unique OTU related to Rhodanobacter sp. was the third most abundant (8.0%) in RSF1, possibly due to selective pressure from the radionuclide-contaminated environment during RSF operation, as this genus is known to be abundant at nuclear legacy waste sites. Understanding the key bacterial taxa in RSF system for mine water treatment could enhance the effectiveness of RSF processes in treating mine water from closed U mines.

Can Phytoremediation-Induced Changes in the Microbiome Improve Saline/Sodic Soil and Plant Health?

Increasing soil salinity and/or sodicity is an expanding problem in the Northern Great Plains (NGP) of North America. This study investigated the impact of phytoremediation on the soil microbiome and if changes, in turn, had positive or negative effects on plant establishment. Amplicon sequencing and gas chromatograph/mass spectrometer analysis compared root metabolites and microbial composition of bulk vs. rhizosphere soils between two soil types (productive and saline/sodic). Beta-diversity analysis indicated that bacterial and fungal communities from both the bulk and rhizosphere soils from each soil type clustered separately, indicating dissimilar microbial composition. Plant species also influenced both root-associated bacterial and fungal communities with separate clustering of operational taxonomic units (OTUs) identified. Canonical correlation analysis (CCA) found a clear association between specific soil characteristics and soil types. Bacterial and fungal OTUs from productive soil were correlated with greater %Ca Sat, %H Sat, and potassium (ppm), especially for OTUs differentially enriched in productive soil. Both bacterial and fungal OTUs from saline/sodic soil are associated with increased Ca (ppm), soil pH, %Na Sat and CEC. Metabolite analysis showed that kochia (Bassia scoparia) roots from the saline/sodic soil had a 4.4-fold decrease in pantothenate accumulation (p = 0.004). Moreover, two endophytic bacterial isolates, a Bacillus spp. and a previously uncultured halophile, isolated from creeping foxtail (Alopecurus arundinaceus) grown in saline/sodic soil and used as buckwheat (Fagopyrum esculentum) seed inoculants, significantly increased seed germination by >30% and vigor index by 0.2 under osmotic stress (0.2 M NaCl) (p < 0.05). This study revealed the importance of soil, root-associated, and endophytic microbiomes. Using native microbes as seed inoculants may help in establishment and growth of species used for phytoremediation of saline/sodic soil.

Ligilactobacillus Salivarius improve body growth and anti-oxidation capacity of broiler chickens via regulation of the microbiota-gut-brain axis

Certain strains of probiotic bacteria can secret functional substances namely digestive enzymes and functional peptides to regulate physiological conditions such as digestion and anti-oxidation, which are often incorporated in industrial broiler chick production. However, few studies have detailed the action mechanisms and effects of these bacteria on regulating growth and anti-oxidation levels in broiler chickens. Ligilactobacillus salivarius is a strain of probiotic bacteria used as dietary supplement. In the present study, Ligilactobacillus salivarius was evaluated for its secreted digestive enzymes in vitro. To detailed evaluate the action mechanisms and effects of gastrointestinal tract (GIT) microbiota on alleviating anti-oxidation levels of broiler chickens through the gut-brain axis. Ligilactobacillus salivarius was cultured and supplemented in the food of broilers to evaluate the probiotic effect on growth and anti-oxidation by modulation of gut microbial composition and its functional metabolites using metagenomic and metabolomic assays. Biochemical results showed that Ligilactobacillus salivarius secreted digestive enzymes: protease, lipase, and amylase. Broiler chickens with Ligilactobacillus salivarius supplemented for 42 days, showed increased body weights, a reduced oxidative status, decreased malondialdehyde levels, and improved activities rates of total superoxide dismutase, glutathione peroxidase IIand IV improved. The microbial composition of caecum was more abundant than those broiler without probiotics supplementation, owing 400 of total number (489) of bacterial operational taxonomic units (OTU). The genera of Lactobacillus, Megamonas, Ruminoccoccaceae, Ruminococcus, Alistipes and Helicobacter shared the dominant proportion of Candidatus _Arthromitus compared with the control chickens. These functional bacteria genera assisted in the transportation and digestion of amino acids, carbohydrates, and ions, synthesis of cellular membranes, and anti-oxidation. Uncultured_organism_g_ Anaerosporobacter, Lactobacillus salivarius, uncultured_bacterium_g_ Ruminococcaceae_UCG-014, uncultured_bacterium_g_ Peptococcus were strongly and positively correlated with body growth performance and anti-oxidation. A metabonomic assay suggested that the secreted of gamma-aminobutyric acid and monobactam was metabolized according to the Kyoto Encyclopedia of Genes and Genomes analysis. In conclusion, Ligilactobacillus salivarius optimized microbial composition of the caecum and secreted functional peptides through gut-brain axis to improve the body growth and antioxidation of broiler chicken.

Geochemistry and metagenomics analyses of bacterial community structure in selected waste dumpsites in Lagos Metropolis, Nigeria

Dumpsites are reservoirs of persistent organic pollutants (POPs) and heavy metals (HMs), constituting environmental hazards to humanity. Autochthonous microorganisms in dumpsites exhibit various degrees of responses to contaminants. Unfortunately, there is a dearth of information on the types and concentration of pollutants and the array of microorganisms in these dumpsites which may play important roles in the metabolism of such pollutants or other community processes. Therefore, determining the microbial community structure in such contaminated sites across a municipality is essential for profiling the taxa that would serve as consensus degraders of the pollutants. In this study, soil samples from three dumpsites (Cele, CS; Solous, SS; and Computer Village, CVS) were characterized for geochemical properties using GC-MS, MP-AES, and other analytical protocols, while the dynamics of bacterial communities were evaluated based on their 16S rRNA gene barcodes. A significant difference in the bacterial communities was observed among the dumpsites in relation to the extent of pollution caused by POPs and HMs. CVS, with the highest HM contamination, was rich in Actinobacteria (41.7%) and Acidobacteria (10.2%), in contrast to CS and SS. Proteobacteria (34.1%) and Firmicutes (20%) were the dominant phyla in CS (highest POP contamination), while Bacteroidetes (45.5%) and Proteobacteria (39.9%) were dominant in SS soil. Bacillus was the dominant genus in the most polluted dumpsite. Canonical correspondence analysis revealed that polycyclic aromatic hydrocarbons (PAHs) and HMs shaped the structure of the bacterial operational taxonomic units (OTUs) in the most polluted dumpsite. Out of a total of 706 OTUs, 628 OTUs exhibited a significant correlation (>50%) with benzo(b)fluoranthene, azobenzene, dibenzofurans, pyrene, dibenzo(a,l)pyrene, Cu, and Zn. In particular, Proteobacteria (Achromobacter sp. and Serratia sp.), Bacteroidetes (Zhouia sp.), and Firmicutes (Bacillus sp.) were suggested to be pivotal to the ecophysiology of dumpsite soils contaminated with POPs and HMs. The results generally underscored the importance of metagenomic and physicochemical analyses of polluted systems in enabling correlations for useful prediction of drivers of such ecosystems. This will further improve our understanding of the metabolic potential and adaptation of organisms in such systems.

Gut microbial signatures are associated with Lynch syndrome (LS) and cancer history in Druze communities in Israel

Lynch syndrome (LS) is a hereditary cancer syndrome caused by autosomal dominant mutations, with high probability of early onset for several cancers, mainly colorectal cancer (CRC). The gut microbiome was shown to be influenced by host genetics and to be altered during cancer development. Therefore, we aimed to determine alterations in gut microbiome compositions of LS patients with and without cancer. We performed fecal microbiome analyses on samples of LS and non-LS members from the Druze ethnoreligious community in Israel, based on both their LS mutation and their cancer history. Our analysis revealed specific bacterial operational taxonomic units (OTUs) overrepresented in LS individuals as well as bacterial OTUs differentiating between the LS individuals with a history of cancer. The identified OTUs align with previous studies either correlating them to pro-inflammatory functions, which can predispose to cancer, or to the cancer itself, and as such, these bacteria can be considered as future therapeutic targets.

Forest restoration decouple soil C:N:P stoichiometry but has little effects on microbial biodiversity globally

AbstractIntroductionForest restoration is an effective way to promote ecosystem functions and mitigate climate change. However, how forest restoration affect soil C:N:P stoichiometry and microbial biodiversity, as well as their linkage across contrasting forest types globally remains largely illusive.Materials and MethodsHere we conducted a global meta‐analysis by synthesizing 121 published papers with 1649 observations to explore how forest restoration affect soil C:N:P stoichiometry and microbial biodiversity globally.ResultsForest restoration significantly increased soil total carbon (C), nitrogen (N) and phosphorus (P) content, whereas having no significant impact on most microbial diversity indicator, except for an enhancement in bacterial operational taxonomic unit and fungal Simpson. Meanwhile, forest restoration effects on soil C:N:P stoichiometry varied with different forest types, with promoting more soil C and P in ectomycorrhizal than those in arbuscular mycorrhizal forests. Meanwhile, forest restoration induced changes in soil N and P were positively correlated with microbial Shannon index. More importantly, forest restoration effects on soil C:N:P stoichiometry and microbial biodiversity were regulated by climate factors such as mean annual temperature and mean annual precipitation.ConclusionOur results highlight the crucial role of forest restoration in decoupling the biogeochemical cycles of C, N and P through changes in microbial biodiversity. Therefore, incorporating the decouple effects of forest restoration on soil C:N:P stoichiometry into Earth system models may improve predictions of climate–forest feedbacks in the Anthropocene.

Synthesis and application of a compound microbial inoculant for effective soil remediation.

Currently, there is a noticeable scarcity of applications that harness composite microbial inoculants to stimulate straw decomposition, nitrogen fixation, and crop growth. This study addresses this gap by selecting and coculturing three bacterial strains to create a composite microbial inoculant named HY-1. This innovative inoculant exhibits multifunctional capabilities, including nitrogen fixation, straw decomposition, and crop growth promotion. Furthermore, we aimed to explore its impact on soil microbial communities. The results showed that the optimal preparation conditions for the compound microbial inoculant HY-1 were 28.5 ± 0.6°C, pH = 7.34 ± 0.40, and bacteriophage ratio 1:2:1 (Microbacterium: Streptomyces fasciatus: Bacillus amyloliquefaciens). Compared to single strains, the combination exhibited higher levels of cellulose-degrading and nitrogen-fixing enzyme activity, increased the straw degradation rate by 37.91% within 180days, and significantly promoted the growth of corn seedlings. Under the condition of straw return, the compound bio-fungicide HY-1 effectively improved the soil microbial diversity. At that time, the soil had the highest number of unique bacterial operational taxonomic units (166), and the abundance of Proteobacteria in the soil increased by 7.24%, while that of Acidobacteriota decreased by 2.27%. The biosynthetic function of the cell wall/membrane/periplasm and the metabolic function of transporting inorganic ions were significantly enhanced. In this study, we discovered that employing coculturing techniques to produce the composite microbial inoculant HY-1 and applying it in the field effectively compensates for the limitations of single-strain inoculants, which often exhibit fewer functions and less pronounced effects. This approach demonstrates significant potential for enhancing the quality of agricultural soils.

PSXII-26 Effect of Different Supplements Plus Phytogenic Additives on Ruminal Bacterial Community of Grazing Beef Cattle

Abstract Changes in ruminal microbial community can affect animal productivity, nutrient utilization efficiency, and environmental impact. This study aimed to evaluate the effect of two levels of supplementation plus a blend of phytogenic additives (essential oils, saponins, and spices) on the ruminal bacterial community in beef cattle grazing tropical pastures. The experiment was conducted at the Beef Cattle Sector of UNESP, Jaboticabal-BR, and lasted 84 days. Nine castrated Nellore steers (body weight of 262 ± 31.2 kg) cannulated in the rumen were assigned to 3 simultaneous 3 × 3 Latin square designs. Animals were kept on pasture of Urochloa brizantha cv. Marandu during the rainy season. The treatments included ad libitum mineral supplementation (MS) as the control group, added mineral supplementation of 0.1% of body weight per day plus Cargill phytogenic blend (AMSP), and energetic-protein supplementation, 0.3% of body weight per day plus Cargill phytogenic blend (EPSP). Ruminal samples were collected on day 26 of each experimental period. A mix of liquid and solid rumen content (6 mL) was taken before supplementation and immediately frozen in liquid nitrogen. Total genomic DNA was extracted using the Quick-DNA Fecal/Soil Microbe kit. The V3-V4 hypervariable regions of the bacterial 16S rRNA gene were amplified using universal primers 341F and 806R. The PCR fragments were submitted to sequencing on an Illumina NovaSeq 6000 PE 250 platform. The sequences were processed using mothur, grouped into operational taxonomic units (OTUs) using a similarity cut-off value of 97%, and the bacterial OTUs were classified using the SILVA database. Bacterial community composition was compared between treatments using a Kruskal–Wallis test and Wilcoxon’s post-hoc test using Rstudio. A total of 27 phyla, 224 families, and 577 genera were assigned by the taxonomic analysis of the ruminal bacterial community (Figure 1). The phyla Bacteroidetes (44.45 ± 9.43) and Firmicutes (42.50 ± 7.18) represent over 86% of the total relative abundance in the rumen of Nellore steers and were not influenced by the supplementation (P ≥ 0.250). The relative abundances of the Spirochaetes phylum, Spirochaetaceae family, and Treponema genus decreased in the rumen of AMSP supplemented animals (P ≤ 0.037) and were similar between MS and EPSP (Figure 2). Additionally, the EPSP supplementation resulted in decreased relative abundances of TM7, TM7 family Incertae sedis, and TM7 genus Incertae sedis relative abundances compared with those in MS (P = 0.031) but not between AMSP and EPSP supplementations. The addition of phytotherapy blend in the supplements led to decreased SR1, SR1 family Incertae sedis, and SR1 genus Incertae sedis abundances in the rumen (P ≤ 0.012). This study indicates that the relative abundance of the dominant phyla was not affected by the supplementation levels, but the addition of the phytogenic blend in the supplement decreased the relative abundances of specific bacterial phyla, families, and genera,

PSXI-30 Ruminal Bacterial Diversity Indexes of Grazing Beef Cattle Receiving Different Supplements Plus Phytogenic Additives

Abstract The addition of phytogenic compounds that have antimicrobial activity in cattle supplements can promote changes in ruminal bacterial diversity. This study aimed to evaluate the effect of two levels of supplementation plus a blend of phytogenic additives (essential oils, saponins, and spices) on the measures of alpha and beta diversity in the rumen of beef cattle grazing tropical pasture. The experiment was carried out in the Beef Cattle Sector of UNESP, Jaboticabal-BR. The trial lasted 84 days and nine castrated Nellore steers (body weight of 262 ± 31.2 kg) cannulated in the rumen were assigned in 3 simultaneous 3 × 3 Latin square designs. Animals were kept on the pasture of Urochloa brizantha cv. Marandu in the rainy season. The treatments were: ad libitum mineral supplementation (MS) as control group; added mineral supplementation, 0.1% of body weight per day plus Cargill phytogenic blend (AMSP); and energetic-protein supplementation, 0.3% of body weight per day plus Cargill phytogenic blend (EPSP). Ruminal samples were collected on day 26 of each experimental period. A mix of liquid and solid rumen content (6 mL) was taken before supplementation, placed in cryogenic tubes, and immediately frozen in liquid nitrogen. All samples were stored at −80 °C until DNA extraction and analysis. Total genomic DNA was extracted using the Quick-DNA Fecal/Soil Microbe Miniprep kit. The V3-V4 hypervariable regions of the bacterial 16S rRNA gene were amplified primers 341F (CCTACGGGNGGCWGCAG) and 806R (GGACTACHVGGGTWTCTAAT). The PCR fragments were submitted to sequencing on an Illumina NovaSeq 6000 PE 250 platform. The sequences were processed using mothur, grouped into operational taxonomic units (OTUs) using a similarity cut-off value of 97%, and the bacterial OTUs were classified using the SILVA database. Alpha diversity indices including Shannon, Simpson, Fisher, Chao1, and ACE, were calculated using the phyloseq package, while beta diversity was determined using the vegan package, both in Rstudio. Alpha diversity indices were compared between treatments using a non-parametric Kruskal–Wallis test and Wilcoxon’s post-hoc test. Beta diversity was tested using permutational multivariate analysis of variance (PERMANOVA) based on the Bray-Curtis similarity index. The AMSP and EPSP did not affect measures of alpha diversity (Figure 1), such as Shannon and Fisher indices (P = 0.219) as well as the richness index measured using Chao1 and ACE (P ≥ 0.363). A negative effect of supplementation on alpha diversity (P = 0.004) was only observed with Simpson’s Index of Diversity. Additionally, the supplementation did not change the beta-diversity of the ruminal bacterial community based on Bray–Curtis similarity index (P = 0.510; Figure 2). In conclusion, the addition of phytogenic compounds in the two levels of supplementation showed only a minor impact on the alpha diversity in the rumen of grazing beef cattle.

Evaluation of 16S rRNA gene primer pairs for bacterial community profiling in an across soil and ryegrass plant study

AbstractIntroductionAs microbes play important roles in many hosts and niches, linking microbiota across niches is becoming an important area of research. Studying microbiota across multiple niches would allow understanding of ecosystem‐level interactions and potential points of better manipulation for agriculture gains. However, a suitable methodology to characterize microbiota from vast different niches is currently lacking. We used the plant shoot and soil as two important niches for this case study.Materials and MethodsConsidering the important linkage plant play in connecting above‐ and below‐ground ecosystems and challenges of working with plant microbiota, we first compared three commonly used 16S ribosomal RNA gene primer pairs targeting V3–V4 or V5–V7 regions coupled with Illumina sequencing for bacterial communities associated with ryegrass shoot. Then the selected primer was used to amplify bacterial communities in soil and rhizosphere samples for comparison with the commonly used 338F/806R. Finally, core operational taxonomic units (OTUs) across soil and plant niches were identified.ResultsPrimer pair 799F/1193R amplified the lowest number of plant organelle sequences (<0.2% of total sequences) and consistently showed the highest α‐diversity compared with 338F/806R and 335F/769R. For soil and rhizosphere samples, 799F/1193R also demonstrated significantly higher α‐diversity indices compared with 338F/806R. The bacterial phyla commonly detected by both primer pairs comprised >97% of the total relative abundance in soil and rhizosphere samples. In addition, the differences in bacterial communities of the soil and rhizosphere samples were more evident when using 799F/1193R than 338F/806R. Using the 799F/1193R data set, 50 core bacterial OTUs were identified across soil, rhizosphere and shoot niches, whereas only 38 core OTUs were identified when using 338F/806R. Most of these core OTUs were dominant in either shoot or soil niche.ConclusionPrimer pair 799F/1193R is suitable for bacterial community studies targeting ryegrass plant and soil microbiota, in particular for cross‐niches studies.

Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields.

Over the years, the microbial community of maize (Zea mays) rhizosphere has been extensively studied; however, the role of microdiversity sustain rhizosphere-associated microbial species distribution from root surface to bulk soil in mature maize is still unclear. Although operational taxonomic units (OTUs) have been used to classify species, amplicon sequence variants (ASVs) have been shown to be effective in representing microdiversity within OTUs at a finer genetic scale. Therefore, the aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients from root surface to bulk soil at the OTU and ASV levels. Here, the microbial community structures of bulk, loosely bound, and tightly bound soil samples from maize rhizosphere were examined at OTU and ASV levels. The results showed that OTU and ASV methods exhibited similar microbial community structures in rhizosphere. Additionally, different ecotypes with varying distributions and habitat preferences were observed within the same bacterial OTU at the ASV level, indicating a rich bacterial microdiversity. In contrast, the fungal community exhibited low microdiversity, with no significant relationship between fungal microdiversity and persistence and variability. Moreover, the ecotypes observed within the bacterial OTUs were found to be positively or negatively associated with environmental factors, such as soil organic carbon (SOC), NO3 --N, NH4 +-N contents, and pH. Overall, the results showed that the rich microdiversity could sustain the distribution of rhizosphere-associated bacterial species across environmental gradients from root surface to bulk soil. Further genetic analyses of rhizosphere-associated bacterial species could have considerable implications for potential mediation of microdiversity for sustainable crop production.

What microbes do we eat with traditional fermented sour porridge from China?

Sour porridges are a kind of fermented cereal food consumed widely, especially in Asia and Africa. They hold a rich source of beneficial bacterial communities exposed to humans, which needs to be studied more. We analyzed the microbiota of five representative sour porridges from China using 16S rDNA amplicon, quantitative polymerase chain reaction (qPCR), and fluorescence in situ hybridization (FISH) visualization. Firmicutes was the most abundant phylum. Genera Lactobacillus and Acetobacter were the richest among the five sour porridges. All the sour porridge samples shared 12 bacterial operational taxonomic units (OTUs), mainly belonging to Lactobacillus, Acetobacter, Weissella, and Enterococcus. Distinct bacterial communities colonized each sour porridge. Significant correlation existed between the microbiota composition and the chemical properties of sour porridge—the content of amino acid (AA), protein (P), flavonoid (F), reducing sugar (RS) and starch (S). Overall, on average, approximately 108 bacterial 16S rDNA numbers were quantified in one gram of sour porridge. Based on the 16S rDNA profile, microbial functions were primarily involved in carbohydrate and amino acid metabolism, sensory system, signaling molecules and interactions. The results indicate that about 1011 bacterial cells were consumed with one bowl of sour porridge of 300 g weight. Sour porridge samples made in the laboratory also verified the order of magnitude of the study. The research provided what and how many microbes consumers eat with sour porridge and a reference for the fermentation improvement of sour porridge.

Relative contribution of season, site, scion and rootstock genotype, and susceptibility to European canker to the variability in bacterial and fungal communities in apple leaf scar tissues

AbstractNeonectria ditissima infects apple trees through wounds, causing European canker. In the UK, the most important entry site for N. ditissima is leaf scar. Specific apple endophytes may contribute to cultivar resistance/tolerance to the pathogen. We assessed the relative effect of location, sampling time (season), and rootstock/scion genotype on bacterial and fungal endophyte communities in the apple leaf scar tissues of current‐season extension shoots and identified Operational Taxonomic Units (OTUs) with differential abundance between canker resistant and susceptible scions, and between rootstocks. Leaf scar tissues were sampled from two orchards at three times (10/2018, 06/2019 and 10/2019) for eight scion cultivars, each grafted onto two rootstocks, for profiling 16S and ITS rRNA regions. Endophyte composition was primarily affected by season (autumn vs. spring) and location (sites and blocks within site). There was a significant reduction in the community size in the spring, particularly for fungi, and species turnover between autumn and spring. This seasonal dynamics suggest that to protect leaf scars from N. ditissima infection in the autumn specific endophytes suppressing canker may have to be augmented annually around the leaf‐fall time. Scion and rootstock genotypes had limited effects on the endophyte community. A group of resistant cultivars differed from a group of susceptible ones in the relative abundance of many bacterial and fungal OTUs, most of which had low reads numbers. Nevertheless, several OTUs with high reads numbers differed in their relative abundance between resistant and susceptible scions, including OTUs from Sphingomonas, Methylobacterium, Vishniacozyma and Rhodotorula babjevae, and warrant further investigation for their potential role in host resistance/tolerance against N. ditissima.

Linking soil organic carbon mineralization to soil physicochemical properties and bacterial alpha diversity at different depths following land use changes

BackgroundAnthropogenic land use changes (LUCs) impart intensifying impacts on soil organic carbon (SOC) turnover, leading to uncertainty concerning SOC mineralization patterns and determining whether soils act as “source” or “sink” in the global carbon budget. Therefore, understanding the SOC mineralization characteristics of different LUC patterns and their potential influencing factors is crucial. An indoor incubation experiment was conducted to study the SOC mineralization patterns and their relevance to soil physicochemical properties, soil enzyme activity, SOC fractions, and bacterial alpha diversity. The soils were collected from two layers of five typical LUC patterns in Yellow Sea Forest Park, including four that were converted from wheat–corn rotation systems [a gingko plantation (G), a metasequoia plantation (M), a gingko–wheat–corn agroforestry system (GW), and a gingko–metasequoia system (GM)] and a traditional wheat–corn system (W).ResultsLUCs had significant and diverse impacts on the SOC content and SOC fraction contents and on soil enzyme activity. The cumulative SOC mineralization was significantly higher in the M systen than in the W and GW systems at 0–20 cm depth and higher in the G system than in the GW system at 20–40 cm depth after 60-day incubation. The mineralization ratio was highest in the W system and lowest in the GW system. The soil pH and bulk density had a significant negative correlation with the cumulative SOC mineralization, while the soil bacterial Shannon index had a significant positive correlation with cumulative SOC mineralization. Multiple stepwise linear regression analysis showed that the SOC mineralization potential was dominantly explained by the bacterial Shannon index and operational taxonomic units (OTUs). The GW system had lower potentially mineralizable SOC and higher SOC stability. Additionally, the incubation time and cumulative SOC mineralization were well fitted by the first-order kinetic equation.ConclusionsLUCs significantly changed SOC mineralization characteristics and the results highlighted the important roles of the bacterial community in soil carbon cycling, which contributes to the fundamental understanding of SOC turnover regulation.

Gut bacterial diversity in Vespa velutina and implications for potential adaptation in South Korea.

Invasive species such as the Yellow-legged hornet (Vespa velutina), along with four other Vespa species - V. analis, V. crabro, V. ducalis, and V. mandarinia, pose significant threats to the environment, economy, and human health. This study focuses on understanding the key factors contributing to the successful invasion of these species, particularly V. velutina, in South Korea. The analysis encompasses the gut bacterial communities and stable isotopes of carbon and nitrogen of the queen hornets, aiming to identify variances in gut microbial composition and food resource utilization. The gut bacterial communities in the five Vespa species were primarily composed of Proteobacteria, with Firmicutes and Bacteroidetes present. V. velutina and V. mandarinia had higher Firmicutes abundance at the phylum level, possibly indicating an increased capacity for dietary fiber breakdown and short-chain fatty acid production, providing them with a competitive edge. No significant differences in nitrogen and carbon stable isotope values were found among the five Vespa species, suggesting that they fed on similar food sources. However, V. velutina had a higher number of unique gut bacterial operational taxonomic units (OTUs), implying adaptation through the acquisition of a distinct gut bacterial set. Significant correlations were found between the observed index and the Shannon index, and between δ15N and the observed index, suggesting that the food source diversity may influence the gut bacterial community diversity. Our study offered valuable insights regarding the adaptation of V. velutina to its new environment in South Korea. The potential role of gut microbiota in the success of invasive species was elucidated. This information is crucial for the management of invasive species, targeted control methods, and implementing preventive regulations. Further studies with larger sample sizes and comprehensive sampling are required to gain a complete understanding of the gut microbiota of Vespa species and their adaptation to new environments. This article is protected by copyright. All rights reserved.

Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture.

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.

Can endophytic microbial compositions in cane roots be shaped by different propagation methods.

In practical production, cane stems with buds are generally used as seed for propagation. However, long-terms cane stems only easily lead to some problems such as disease sensitivity, quality loss, etc. Recently, cane seedings, which are produced by tissue culture were used in sugarcane production, but few studies on cane health related to tissue culture seedings. Therefore, to evaluate the immunity and health of sugarcanes growing from different reproduction modes, the endophytic microbial compositions in cane roots between stem and tissue culture seedlings were analyzed using high-throughput techniques. The results showed that the endophytic microbial compositions in cane roots were significant differences between stem and tissue culture seedlings. At the genus level, Pantoea, Bacillus, Streptomyces, Lechevalieria, Pseudomonas, Nocardioides, unclassified_f__Comamonadaceae enriched as the dominant endophytic bacterial genera, and Rhizoctonia, Sarocladium, Scytalidium, Wongia, Fusarium, unclassified_f__Phaeosphaer, unclassified_c__Sordariom, unclassified_f__Stachybot, Poaceascoma, Microdochium, Arnium, Echria, Mycena and Exophiala enriched as the dominant endophytic fungal genera in cane roots growing from the tissue culture seedlings. In contrast, Mycobacterium, Massilia, Ralstonia, unclassified_f__Pseudonocardiacea, norank_f__Micropepsaceae, Leptothrix and Bryobacter were the dominant endophytic bacterial genera, and unclassified_k__Fungi, unclassified_f__Marasmiaceae, Talaromyces, unclassified_c__Sordariomycetes and Trichocladium were the dominant endophytic fungal genera in cane roots growing from stem seedlings. Additionally, the numbers of bacterial and fungal operational taxonomic units (OTUs) in cane roots growing from tissue culture seedlings were significantly higher than those of stem seedlings. It indicates that not only the endophytic microbial compositions in cane roots can be shaped by different propagation methods, but also the stress resistance of sugarcanes can be improved by the tissue culture propagation method.

Sex-specific differences in symbiotic microorganisms associated with an invasive mealybug (Phenacoccus solenopsis Tinsley) based on 16S ribosomal DNA.

The ability of Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) to utilize a wide range of host plants is closely related to the symbiotic bacteria within its body. This study investigated the diversity of symbiotic microorganisms associated with the sap-sucking hemipteran insect. Using deep sequencing of the 16S rDNA gene and subsequent analysis with the Qiime software package, we constructed a comprehensive library of bacterial operational taxonomic units (OTUs). We compared the microbial communities of female and male adult mealybugs. Our results showed significant differences in bacterial composition between the sexes, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both female and male mealybugs. These results suggest that the diverse assemblage of symbiotic bacteria in P. solenopsis may be critical in enabling this insect to utilize a wide range of host plants by facilitating carbohydrate digestion and energy uptake.

Effects of parasitism by a parasitoid wasp on the gut microbiota in a predaceous lady beetle host.

The gut microbiota has an intimate relationship with insect hosts and this relationship can become complicated with parasitic organisms being involved with the host. To date there has been limited evidence for the relevance of parasitism of the host by parasitoids to host gut microbiota, especially in host insect predators. Here, our study examined gut microbiotas in larvae of the predaceous lady beetle, Coccinella septempunctata, in response to their parasitism by Homalotylus eytelweinii regarding the development progress of offspring parasitoids. Overall 58.5% of gut bacterial operational taxonomic units (OTUs) in the parasitized lady beetle were different from those in the unparasitized host. The phylum Proteobacteria abundance increased while Firmicutes decreased in parasitized hosts compared to the unparasitized. The abundance of genus Aeribacillus decreased substantially in the parasitized lady beetle across all stages of the offspring development compared to the unparasitized host. The α-diversity of the gut microbiota in a parasitized lady beetle larva increased at the early stage of offspring parasitoids and then returned over the intermediate and later stages. Analyses of β-diversity indicated that the gut microbial community in a parasitized lady beetle was distinct from that in an unparasitized one and different between early or middle and late stages of offspring parasitoids in parasitized hosts. Our results provide evidence for the relevance of the gut microbiota to interactions between a lady beetle host and its parasitoid. Our study provides a starting point for further investigations of the role the gut microbiota may play in host-parasitoid interactions. © 2023 Society of Chemical Industry.