16S rRNA Analysis Research Articles

ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.

Microbiome differential abundance analysis remains a challenging problem despite multiple methods proposed in the literature. The excessive zeros and compositionality of metagenomics data are two main challenges for differential abundance analysis. We propose a novel method called "Analysis of Differential Abundance by Pooling Tobit Models" (ADAPT) to overcome these two challenges. ADAPT interprets zero counts as left-censored observations to avoid unfounded assumptions and complex models. ADAPT also encompasses a theoretically justified way of selecting non-differentially abundant microbiome taxa as a reference to reveal differentially abundant taxa while avoiding false discoveries. We generate synthetic data using independent simulation frameworks to show that ADAPT has more consistent false discovery rate control and higher statistical power than competitors. We use ADAPT to analyze 16S rRNA sequencing of saliva samples and shotgun metagenomics sequencing of plaque samples collected from infants in the COHRA2 study. The results provide novel insights into the association between the oral microbiome and early childhood dental caries. The R package ADAPT can be installed from Bioconductor at https://bioconductor.org/packages/release/bioc/html/ADAPT.html or from Github at https://github.com/mkbwang/ADAPT. The source codes for simulation studies and real data analysis are available at https://github.com/mkbwang/ADAPT_example. The supplementary notes and figures are compiled together in a PDF document. The supplementary tables are combined in an excel file. Both the PDF document and the excel file are available online.

Molecular Identification, Histopathology and Antibiotic Susceptibility Profiling of Aeromonas veronii Isolated from Oreochromis niloticus in Bangladesh.

Tilapia (Oreochromis niloticus) is the most widely cultured freshwater fish species in Bangladesh and worldwide. However, commercial tilapia culture systems face increasing challenges from bacterial infections. The objective of this study was to identify the bacterial isolates from infected tilapia inan intensive cage culture farm located along the Shitalakshya River in Bangladesh. Infected fish samples were collected and underwentcomprehensive clinical and post-mortem investigations, followed by phenotypic, biochemical and molecular identification of the bacterial isolates, as well as histopathological and antibiotic susceptibility examinations. Phenotypic and biochemical characterization showed similarities of the -collected isolates with Aeromonas veronii. Moreover, molecular analysis of the bacterial conserved region 16S rRNA also confirmed these isolates as A. veronii. The analysed 16S rRNA sequence (GenBank accession no. PP832815) showed a close relationship (100% identity) with A. veronii from China (GenBank accession no. MT071624) in the NCBI BLAST search, and in the phylogenetic tree, they grouped in a single clade. This close genetic relationship is also supported by the low genetic distance between the isolates. Histopathological analysis revealed gross pathological changes like necrosis, hypertrophy and inflammation in muscle tissues. The isolates were found to be sensitive to multiple antibiotics but resistant to trimethoprim and sulphamethoxazole. This study investigated the presence of A. veronii infection in tilapia (O. niloticus) in an intensive cage culture farm in Bangladesh.

Asiaticoside improves depressive-like behavior in mice with chronic unpredictable mild stress through modulation of the gut microbiota.

Asiaticoside, the main active ingredient of Centella asiatica, is a pentacyclic triterpenoid compound. Previous studies have suggested that asiaticoside possesses neuroprotective and anti-depressive properties, however, the mechanism of its anti-depressant action not fully understood. In recent years, a growing body of research on anti-depressants has focused on the microbiota-gut-brain axis, we noted that disruption of the gut microbial community structure and diversity can induce or exacerbate depression, which plays a key role in the regulation of depression. Behavioral experiments were conducted to detect depression-like behavior in mice through sucrose preference, forced swimming, and open field tests. Additionally, gut microbial composition and short-chain fatty acid (SCFA) levels in mouse feces were analyzed 16S rRNA sequencing and gas chromatography-mass spectrometry (GC-MS). Hippocampal brain-derived neurotrophic factor (BDNF) and 5-hydroxytryptamine receptor 1A (5-HT1A) expression in mice was assessed by western blotting. Changes in serum levels of inflammatory factors, neurotransmitters, and hormones were measured in mice using ELISA. This study revealed that oral administration of asiaticoside significantly improved depression-like behavior in chronic unpredictable mild stress (CUMS) mice. It partially restored the gut microbial community structure in CUMS mice, altered SCFA metabolism, regulated the hypothalamic-pituitary-adrenal axis (HPA axis) and inflammatory factor levels, upregulated BDNF and 5-HT1A receptor protein expression, and increased serum serotonin (5-hydroxytryptamine, 5-HT) concentration. These findings reveal that asiaticoside exerts antidepressant effects via the microbiota-gut-brain axis. These results suggested that asiaticoside exerts antidepressant effects through the microbiota-gut-brain axis in a CUMS mouse model.

8513 Toxic Metals Are Associated With Increased Diabetes And Obesity Through Gut Microbiota Changes In Five African-Origin Populations

Abstract Disclosure: J. Jorgensen: None. C. Choo-Kang: None. L. Issa: None. J.A. Gilbert: None. G. Ecklu-Mensah: None. A. Luke: None. K. Bedu-Addo: None. T. Forrester: None. P. Bovet: None. E.V. Lambert: None. D. Rae: None. M. Argos: None. Y. Dai: None. R.M. Sargis: None. L.R. Dugas: None. B.T. Layden: None. Obesity is associated with an increased risk for cardiometabolic diseases, such as type 2 diabetes mellitus (T2D). Prior research has shown an association between toxic metals/metalloid (hereafter, “metals”) exposures, including arsenic (As), lead (Pb), mercury (Hg), and cadmium (Cd), and increased T2D risk. Importantly, metal exposure has been suggested to impact the gut microbiome. Gut microbiome composition and metabolism are key to the development and progression of obesity and diabetes, thus we propose a potential novel interaction via the gut microbiota between metals and T2D, although the exact pathway remains unclear. We studied a large African-origin cohort from Ghana, South Africa, Jamaica, Seychelles, and the US (n=188, 51% female, mean age=43.0±6.5 yr). Analyzing 16S rRNA Amplicon sequencing, anthropometrics, and creatinine-adjusted urinary metal levels, we observed metal levels were significantly associated with country of origin and in most countries were significantly associated with decreased microbial diversity. Metal levels were highest in Ghana and lowest in the US, and were significantly different between Ghana and the US for As and Pb (p-value < 2.2e-16). Individually, Pb levels were significantly associated with fasting blood glucose and BMI, As levels were associated with T2D diagnosis, and Hg levels were associated with obesity diagnosis. Pb levels were significantly associated with a lower proportion of potential acetate- and butyrate-producing microbial strains. Similarly, As levels were associated with decreased proportion of potential butyrate-producing genera. Microbial strains in individuals with high Pb levels showed significant association with obesity and T2D risk and strains in individuals with significant high As levels were associated with only T2D risk. Hg and Cd were not significantly associated with microbes and clinical status. These taxa are significantly associated with increased heme metabolism. With this study, we aimed to begin to describe the effect of metals and the risks for obesity and diabetes through its action within the gut microbiome. We demonstrate that toxic metal exposures were associated with differences in the gut microbiome and predicted metabolism that may also be associated with increased obesity and T2D risk. Presentation: 6/1/2024

Characterization of Photobacterium damselae subsp. damselae isolated from diseased Asian seabass (Lates calcarifer) and the preliminary development of a formalin-killed cell vaccine.

Asian seabass (Lates calcarifer) is an economically important fish species that is widely cultivated in Thailand. However, aquaculture of Asian seabass is limited by infectious diseases. One of the most serious diseases is photobacteriosis, caused by Photobacterium damselae. Vaccination is recognized as an efficient disease prevention and pathogen control method for strengthening the aquaculture industry. To promote vaccine development, the characterization of pathogenic bacteria and their pathogenesis is required. In this study, isolates of P. damselae were obtained from commercial aquaculture farms in Thailand during 2019-2021. Analyses of 16S rRNA and the urease subunit alpha genes identified the isolates as P. damselae subsp. damselae (Phdd). Antibiotic susceptibility analyses showed that all Phdd isolates were resistant to amoxicillin (10 μg). Haemolysis and phospholipase activities were used to categorize P. damselae into three groups based on their biological activities. The pathogenicity of four candidates (SK136, PD001, PD002 and T11L) was tested in Asian seabass. Isolate SK136 showed the highest virulence, with a lethal dose (LD50) of 1.47 × 105 CFU/fish, whereas isolate PD001 did not show any virulence. Genotypic characterization, based on multi-locus sequence typing analysis, demonstrated that all candidates were novel strains with new sequence types (64, 65, 66 and 67). Preliminary vaccination using formalin-killed cells (FKCs) protected Asian seabass from artificial challenges. Taken together, these results provide fundamental knowledge for vaccine development against Phdd infection in Asian seabass.

Effects of xylo-oligosaccharide supplementation on the production performance, intestinal morphology, cecal short-chain fatty acid levels, and gut microbiota of laying hens

This study investigated the effects of xylo-oligosaccharide supplementation on the production performance, intestinal morphology, cecal short-chain fatty acid levels, and gut microbiota of laying hens. A total of 800 Lohmann pink layers, each 48 wk old, were randomly divided into 5 dietary treatment groups, namely XOS at 0 (CON), 100 (XOS1), 200 (XOS2), 300 (XOS3) and 400 (X0S4) mg/kg. The experimental period was 24 wk. The results revealed that the egg production rate and the number of eggs laid by each layer between 1 to 12 wk increased as the XOS concentration increased (Plinear < 0.05). The sand-shell egg percentage decreased significantly from 1 to 12 wk in the XOS1, XOS2, and XOS3 groups (PANOVA < 0.05). Compared with the CON group, the 4 XOS dosage groups presented significant increases in the villus height and the ratio of villus height to crypt depth in the jejunum (PANOVA < 0.05), whereas a linear decrease in jejunal crypt depth (Plinear < 0.05) was noted. In addition, XOS supplementation significantly increased the concentrations of butyric acid and isovaleric acid in the caeca (PANOVA < 0.05). High-throughput sequencing analysis of bacterial 16S rRNA revealed that dietary XOS supplementation influenced the cecal microbiota. The alpha diversity analysis indicated that the richness of cecal bacteria was greater in the laying hens fed XOS. The modulation of the cecal microbiota composition upon the addition of XOS was characterized by an increased abundance of Firmicutes and Bifidobacteriaceae, and decreased abundance of Bacteroidetes. At the genus level, dietary XOS supplementation resulted in decreases in the abundances of Bacteroides and Rikenellaceae_RC9_gut_group and an increase in the abundance of Lactobacillus. In conclusion, dietary XOS supplementation improved the production performance of laying hens by increasing the production of short-chain fatty acids and improving their intestinal morphology, which was achieved mainly through changes in the composition of the intestinal microbiota. The recommended level of XOS in the diet of laying hens is 200 mg/kg.

Exploration of the Molecular and Phylogenetic Aspects of Brucella intermedia (Ochrobactrum intermedia)

Brucella bacteria are among the oldest known zoonotic pathogens and they have become iconic case studies in infectious diseases. Genome comparisons have led to the reclassification of the genus Ochrobactrum, with its individual species now being categorized as Brucella. This study aims to isolate and molecularly identify Ochrobactrum intermedia from Iraqi patients. One hundred seventy urine samples were collected from patients with various conditions suspected of brucellosis. Based on identification by the VITEK compact system, two of the bacterial isolates were identified as Brucella intermedia (Ochrobactrum intermedia) species. This was confirmed by polymerase chain reaction using genus-specific primers for the 16S rRNA and recA genes which are specific for B.intermedia. The 16S rRNA gene sequences were aligned using BLAST and the BioEdit program. It was observed that there was a remarkable 99% similarity among the Brucella intermedia sequences. The affiliation of the two novel strains of B. intermedia, identified as Brucella intermedia strain BC-TCC 16S ribosomal RNA gene (OP415407) and Brucella intermedia strain Baghdadies 16S ribosomal RNA gene (OP415409), was confirmed through the analysis of both 16S rRNA and recA genes. These findings suggest that the use of 16S RC-PCR and sequencing in clinical settings can improve patient care by increasing the sensitivity of detection and identification of bacterial pathogens, resulting in more diagnoses of bacterial infections. By studying novel strains in a phylogenetic tree, researchers can learn more about the diversity of a species and can identify potential new threats to human and animal health.

Biodegradation of linear alkylbenzene sulfonate contamination by pseudomonas aeruginosa isolates

Linear alkylbenzene sulphonate (LAS), a surfactant frequently incorporated into detergent formulations, typically ends up in wastewater treatment facilities after use. The present study aims to investigate the efficacy of bacteria isolated from Iraqi wastewater in removing LAS. This strain was identified as Pseudomonas aeruginosa by genetic analysis (16S rRNA). Three LAS concentrations (25, 50, and 100 mg/l) were employed in this investigation, along with three temperatures (30, 35, and 40 oC) and pH values (5, 7, 9). The LAS anionic surfactant demonstrated optimal biodegradation by Pseudomonas aeruginosa at a temperature of 30 °C and at pH levels of 7 and 9, with removal percentages of 93.76% and 90.4%, respectively, at a concentration of 25 mg/l of LAS. The study's findings demonstrated the possibility and importance of using aerobic biodegradation to remove LAS from actual effluents. This bacterium is useful for bioremediation because of its capacity to break down LAS.

Molecular characterization of ‘Candidatus Phytoplasma australasiaticum’ associated with ornamentals, amaranthus, French bean and sunhemp crops and development of rapid LAMP assay for detection

Phytoplasma is one of the most economically important pathogens, causing significant yield losses in many crops worldwide. During a survey in Bengaluru rural and Chikkabalpura areas of Karnataka, India, a total of 33 symptomatic plant samples including ornamentals, amaranthus, french bean, and sunhemp displaying phytoplasma symptoms were collected and confirmed as infected with phytoplasma through PCR targeting the 16S rRNA and secY genes. Pairwise sequence comparison and phylogenetic analysis of 16S rRNA and secY gene sequences confirmed the presence of ‘Candidatus Phytoplasma australasiaticum’ in antirrhinum, chrysanthemum, china aster, dianthus, amaranthus, french bean, and sunhemp. In-silico restriction fragment length polymorphism (RFLP) analysis indicated that phytoplasma strains infecting Antirrhinum, China aster, Dianthus, French bean, and Sunhemp represented distinct variants within the 16SrII phytoplasma group, with a threshold similarity coefficient of less than 0.98. A loop-mediated isothermal amplification (LAMP) assay was developed for detecting phytoplasma strains infecting the four ornamentals and other studied crops, targeting the phytoplasma 16S rRNA gene sequence with detection in 60 min. The comparative testing of LAMP products using various nucleic acid dyes and a colorimetric dye (hydroxy naphthol blue) confirmed the presence of phytoplasmas in symptomatic samples. This LAMP assay offers superior ease of use, cost-effectiveness, and rapid results for detecting phytoplasmas in symptomatic plants.

Ganoderma lucidum polysaccharide promotes broiler health by regulating lipid metabolism, antioxidants, and intestinal microflora

Ganoderma lucidum polysaccharides (GLP) are the primary bioactive macromolecular compounds of Ganoderma lucidum, possessing antioxidant and immunomodulatory effects. Hot water extract of Juncao-substrate Ganoderma Lucidum residue (HWE-JGLR) is abundant in GLP. There are few research reports on the application of HWE-JGLR in animal husbandry. Therefore, this study aims to investigate the effects of HWE-JGLR supplementation on growth performance, serum biochemistry, the antioxidant function of serum and liver, and the intestinal microbiota of yellow-feathered broilers. The control group was fed a corn-soybean meal basal diet, while the HJ I, II, and III groups received diets supplemented with 0.25 %, 0.5 %, and 1 % of HWE-JGLR, respectively. Results showed that HWE-JGLR increased the serum HDL-C content and decreased the TG content in broilers. Moreover, HWE-JGLR enhanced the antioxidant function by the Keap1-Nrf2/ARE signaling pathway and the antioxidative enzyme in broilers. In addition, the cecum of the metagenomic analysis of 16S rRNA showed that the relative abundance of no-rank Ruminococcacea was increased in the HJ I group. Our findings indicate that HWE-JGLR has strong potential for development as a green feed additive based on its functions of lipid-lowering, antioxidation, and the modulation of gut microbiota composition.

Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis.

The relationship between dysbiosis of the gastrointestinal microbiota and gastric cancer (GC) has been extensively studied. However, microbiota alterations in GC patients vary widely across studies, and reproducible diagnostic biomarkers for early GC are still lacking in multiple populations. Thus, this study aimed to characterize the gastrointestinal microbial communities involved in gastric carcinogenesis through a meta-analysis of multiple published and open datasets. We analyzed 16S rRNA sequencing data from 1,642 gastric biopsy samples and 394 stool samples across 11 independent studies. VSEARCH, QIIME and R packages such as vegan, phyloseq, cooccur, and random forest were used for data processing and analysis. PICRUSt software was employed to predict functions. The α-diversity results indicated significant differences in the intratumoral microbiota of cancer patients compared to non-cancer patients, while no significant differences were observed in the fecal microbiota. Network analysis showed that the positive correlation with GC-enriched bacteria increased, and the positive correlation with GC-depleted bacteria decreased compared to healthy individuals. Functional analyses indicated that pathways related to carbohydrate metabolism were significantly enriched in GC, while biosynthesis of unsaturated fatty acids was diminished. Additionally, we investigated non-Helicobacter pylori (HP) commensals, which are crucial in both HP-negative and HP-positive GC. Random forest models, constructed using specific taxa associated with GC identified from the LEfSe analysis, revealed that the combination of Lactobacillus and Streptococcus included alone could effectively discriminate between GC patients and healthy individuals in fecal samples (area under the curve (AUC) = 0.7949). This finding was also validated in an independent cohort (AUC = 0.7712). This study examined the intratumoral and fecal microbiota of GC patients from a dual microecological perspective and identified Lactobacillus, Streptococcus, Roseburia, Faecalibacterium and Phascolarctobacterium as intratumoral and intestinal-specific co-differential bacteria. Furthermore, it confirmed the validity of the combination of Lactobacillus and Streptococcus as GC-specific microbial markers across multiple populations, which may aid in the early non-invasive diagnosis of GC.

Reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) into a novel genus as Eshraghiella crossota gen. nov., comb. nov.

The reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) as Eshraghiella crossota gen. nov., comb. nov. is proposed within the family Lachnospiraceae. This reclassification is based on differences revealed through the analysis of 16S rRNA, groEL, recA, and rpoB genes, as well as genome sequences, distinguishing it from other Butyrivibrio species. Comparative analysis showed that B. crossotus exhibited digital DNA-DNA hybridization (dDDH) values of 19.40-27.20% and average nucleotide identities based on blast (ANIb) values of 67.06-67.64% with other Butyrivibrio species. These values are significantly below the species delineation thresholds (dDDH, 70%; ANIb, 95-96%), justifying the proposed reclassification. Additionally, the results of the average amino acid identity (AAI) analysis indicated that this species shares 59.22-60.17% AAI with the other species of the genus Butyrivibrio, which is below the AAI threshold (65%) for a genus boundary. In addition, biochemical and morphological characteristics also support the proposal that this species is different from other species of the genus Butyrivibrio. The type strain is ATCC 29175T (DSM 2876T=T9-40AT).

Isolation and identification of Acinetobacter lwoffii from the Chinese Giant Salamander (Andrias davidianus)

This study aimed to identify the primary pathogenic bacteria responsible for the mortality of the Chinese giant salamander (Andriasd davidianus). A pathogenic bacterium was isolated from a diseased Chinese giant salamander exhibiting typical symptoms under aseptic conditions and then identified by morphological examinations, biochemical analysis, and the sequence analysis of bacterial 16S rRNA. Artificial infection testing was then conducted to determine the pathogenicity of the isolated bacteria strain. Drug susceptibility tests were conducted using the agar diffusion method. The isolated pathogenic bacteria, named DN-2, was successfully identified as Acinetobacter lwoffii. The artificial infection showed that the typical symptoms of the disease could be replicated as the ones originally occurred, and this bacterium exhibited high pathogenicity to the Chinese giant salamander. In the Chinese giant salamander, the median lethal dosage (LD50) of A. lwoffii DN-2 for A. davidianus was determined to be 4.63×104 CFU/g. Drug sensitivity testing showed that these bacteria were highly sensitive to erythromycin, gentamicin, neomycin, streptomycin, midecamycin, ciprofloxacin, piperacillin, florfenicol, doxycycline, carbenicillin, and sulfanilamide. In summary, A. lwoffii was identified as the primary pathogen responsible for the demise of A. davidianus. Our study first presents how these bacteria harm Chinese giant salamanders.

Utilization of 16Sr RNA and secA genes for molecular discernment of 'Candidatus Phytoplasma australasiaticum' strain associated with linseed germplasm in India.

The growing prevalence of phytoplasma associated symptoms on linseed or flax (Linum usitatissimum L.) germplasm at Indian Council of Agricultural Research- National Bureau of Plant Genetic Resources (ICAR-NBPGR) fields was noticed during the 2019-22 growing seasons. The characteristic phytoplasma symptoms of phyllody, stem fasciation, stunting, along with floral and capsule malformations were observed in 41 linseed accessions grown at experimental fields of ICAR-NBPGR, Delhi. During 3years, the presence of phytoplasma in symptomatic linseed accessions was confirmed by nested-PCR assays utilizing 16S rRNA and secA gene-specific primers. The 16S rRNA and secA gene sequences of linseed phytoplasma strains from the representative symptomatic 41 linseed accessions exhibited 100% sequence identity among themselves and 99.93% and 99.82% sequence homology with reference strain, 'Candidatus Phytoplasma australasiaticum' (GenBank Accession: Y10097). Phylogenetic analysis of 16S rRNA and secA gene sequences clustered the linseed isolates with the peanut witches' broom group belonging to 'Ca. P. australasiaticum' strains. The virtual RFLP analysis of 16S rRNA F2nR2 fragment (~1.2kb) of linseed phytoplasma strains further classified it into 16Sr group II, subgroup D. Our results suggested confirmation of the association of 'Ca. P. australasiaticum' strain (16SrII-D) in the linseed germplasm accessions from North India, which is the first report from India. The phytoplasma infection also reduced the growth and yield parameters of two linseed accessions (IC0498748 and EC0718851).

Whole genome–based comparative analysis of the genus Streptomyces reveals many misclassifications

Streptomyces species are experts in the production of bioactive secondary metabolites; however, their taxonomy has fallen victim of the tremendous interest shown by the scientific community, evident in the discovery of numerous synonymous in public repositories. Based on genomic data from NCBI Datasets and nomenclature from the LPSN database, we compiled a dataset of 600 Streptomyces species along with their annotations and metadata. To pinpoint the most suitable taxonomic classification method, we conducted a comprehensive assessment comparing multiple methodologies, including analysis of 16S rRNA, individual housekeeping genes, multilocus sequence analysis (MLSA), and Fast Average Nucleotide Identity (FastANI) on a subset of 409 species with complete data. Due to insufficient resolution of 16S rRNA and inconsistency observed in individual housekeeping genes, we performed a more in-depth analysis, comparing only FastANI and MLSA, which expanded our dataset to include 502 species. With FastANI validated as the preferred method, we conducted pairwise analysis on the entire dataset identifying 59 non-unique species among the 600, and subsequently refined the dataset to 541 unique species. Additionally, we collected data on 724 uncharacterized Streptomyces strains to investigate the uniqueness potential of the unannotated fraction of the Streptomyces genus. Utilizing FastANI, 289 strains could be successfully classified into one of the 541 Streptomyces species.Key points• Evaluation of taxonomic classification methods for Streptomyces species.• Whole genome analysis, specifically FastANI, has been chosen as preferred method.• Various reclassifications are proposed within the Streptomyces genus.Graphical abstract

Changes in microbial community structure of bio-fouled polyolefins over a year-long seawater incubation in Hawai'i.

Plastic waste, especially positively buoyant polymers known as polyolefins, are a major component of floating debris in the marine environment. While plastic colonisation by marine microbes is well documented from environmental samples, the succession of marine microbial community structure over longer time scales (> > 1 month) and across different types and shapes of plastic debris is less certain. We analysed 16S rRNA and 18S rRNA amplicon gene sequences from biofilms on polyolefin debris floating in a flow-through seawater tank in Hawai'i to assess differences in microbial succession across the plastic types of polypropylene (PP) and both high-density polyethylene (HDPE) and low-density polyethylene (LDPE) made of different plastic shapes (rod, film and cube) under the same environmental conditions for 1 year. Regardless of type or shape, all plastic debris were dominated by the eukaryotic diatom Nitzschia, and only plastic type was significantly important for bacterial community structure over time (p = 0.005). PE plastics had higher differential abundance when compared to PP for 20 bacterial and eight eukaryotic taxa, including the known plastic degrading bacterial taxon Hyphomonas (p = 0.01). Results from our study provide empirical evidence that plastic type may be more important for bacterial than eukaryotic microbial community succession on polyolefin pollution under similar conditions.

Diversity of plant pollen sources, microbial communities, and phenolic compounds present in bee pollen and bee bread.

The pollination of several crops, as well as wild plants, depends on honeybees. To get the nutrients required for growth and survival, honeybee colonies are dependent on pollen supply. Bee pollen (BP) is partially packed in honeycomb cells and processed into beebread (BB) by microbial metabolism. The composition of pollen is highly variable and is mainly dependent on ecological habitat, geographical origin, honey plants, climatic conditions, and seasonal variations. Although there are important differences between the BP and the BB, little comparative chemical and microbiological data on this topic exists in the literature, particularly for samples with the same origin. In this study, BP and BB pollen samples were collected from two apiaries located in the Campania and Molise regions of Southern Italy. Phenolic profiles were detected via HPLC, while antioxidant activity was determined by ABTS·+ and DPPH· assay. The next-generation sequencing (NGS) based on RNA analysis of 16S (rRNA) and internal transcribed spacer (ITS2) regions were used to investigate the microbial community (bacteria and fungi) and botanical origin of the BP and BB. Chemical analysis showed a higher content of flavonols in BP (rutin, myricetin, quercetin, and kaempferol), while in BB there was a higher content of phenolic acids. The NGS analysis revealed that the microbial communities and pollen sources are dependent on the geographical location of apiaries. In addition, diversity was highlighted between the microbial communities present in the BP and BB samples collected from each apiary.

Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism

BackgroundThe interplay between root-knot nematode (RKN) parasitism and the complex web of host-associated microbiota has been recognized as pivotal for effective management of the pest. However, studies assessing this relationship have focussed on the bacterial and fungal communities, neglecting the unicellular eukaryotic members. Here, we employed amplicon sequencing analysis of the bacterial 16S rRNA, fungal ITS and eukaryotic 18S rRNA genes, and comprehensively examined how the microbiome composition, diversity and networking developed with time in the rhizospheres and roots of RKN-inoculated and non-inoculated tomato plants.ResultsAs expected, infection with the RKN Meloidogyne incognita decreased plant growth. At individual timepoints, we found distinct bacterial, fungal and eukaryote community structures in the RKN-inoculated and non-inoculated rhizospheres and roots, and RKN inoculation affected several taxa in the root-associated microbiome differentially. Correlation analysis revealed several bacterial and fungal and few protist taxa that correlated negatively or positively with M. incognita. Moreover, network analysis using bacterial, fungal and eukaryotic data revealed more dynamic networks with higher robustness to disturbances in the RKN-inoculated than in the non-inoculated rhizospheres/roots. Hub taxa displayed a noticeable successional pattern that coincided with different phases of M. incognita parasitism. We found that fungal hubs had strong negative correlations with bacteria and eukaryotes, while positive correlations characterized hub members within individual kingdoms.ConclusionOur results reveal dynamic tomato-associated microbiomes that develop along different trajectories in plants suffering M. incognita infestation and non-infested plants. Overall, the results identify stronger associations between RKN and bacterial and fungal taxa than between eukaryotic taxa and RKN, suggesting that fungal and bacterial communities could play a larger role in the regulation of RKN. The study identifies several putative RKN-antagonistic bacterial and fungal taxa and confirms the antagonistic potential previously identified in other taxa.

Pseudanabaena pruinosa sp. nov. (Pseudanabaenales, Cyanobacteria): an Arctic Pseudanabaena species with branched sheaths and central aerotopes

ABSTRACT This study focused on polyphasic evaluation of four psychrophilic Pseudanabaena strains collected from extreme environments characterized by freezing temperatures. The strains were isolated from hydroterrestrial and terrestrial ecosystems in Petuniabukta Bay (Billefjorden, Svalbard), growing as icy microbial soil crusts. In addition to their unique ecology, the phylogenetic analyses of 16S rRNA revealed that the strains form a monophyletic clade within the Pseudanabaena sensu stricto cluster; this clade was unambiguously separated from the other Pseudanabaena infrageneric units, showing <98.5% 16S rRNA sequence identity with the other Pseudanabaena strains available in GenBank and possessing a unique and different D1 ITS region. Polyphasic evaluation of these four strains led to the description of the new species Pseudanabaena pruinosa sp. nov. which can be morphologically distinguished by light microscopy by several unique apomorphic traits not previously detected in Pseudanabaena. These traits include: production of widened, anastomotic branched sheaths enveloping several trichomes into a filament, heteropolar filaments with long trichomes with more than 20 cells, richly pseudobranched filaments forming tree-like structures, production of both polar and central aerotopes, and ability to produce swollen cells and to undergo irregular cell division. The characters observed for Pseudanabaena pruinosa, never reported for other species of Pseudanabaena, substantially widen the taxonomic concept of this genus. Therefore, the description of Pseudanabaena pruinosa sp. nov. with its unique ecology and distinct phylogenetic position and morphological features, is a significant addition to cyanobacteriology and represents a starting point for further research into the evolution of the genus Pseudanabaena. The new combination Pseudanabaena gygaxiana (Casamatta & Johansen) Aleksovski, Krstić & Strunecký is proposed based on16S rRNA, supported by its shared phenotypic traits and similar ecology to Pseudanabaena pruinosa.

Isolation, Identification and Survival Strategy of &lt;i&gt;Dietzia maris&lt;/i&gt; MX2 Halotolerant Strain from the Yakshinskoe Mineral Salts Deposit

Halophilic and halotolerant microorganisms have a high biotechnological potential. They are producers of biologically active substances, stress-protective agents, hydrolytic enzymes, and are used for environmental bioremediation. At the same time, the characterization of novel halotolerant bacteria and the disclosure of their salt tolerance strategy are topical fundamental problems. In the present work, a new strain MX2 was isolated from the salt well brine of the Yakshinskoe potassium-magnesium salt deposit. The isolate is represented by aerobic gram-positive non-motile bacteria that do not produce spores. The cell morphology varies from cocci to short rods that are capable of producing V-shaped forms. Colonies on the surface of agar nutrient medium were circular with an entire edge and raised center, glistening and orange. Bacteria of strain MX2 are halotolerant microorganisms capable of growing at NaCl concentrations up to 9%. Strain MX2 was sequenced. Its size was estimated at 3747717 b. p., the number of protein-coding genes — 3562. Strain MX2 was identified as belonging to the species Dietzia maris based on analysis of 16S rRNA, gyrB, rpoB, recA, ppk gene sequences and using time-of-flight mass spectrometry (MALDI-TOF-MS). D. maris MX2 has complete metabolic pathways for the synthesis of ectoine, hydroxyectoine, and trehalose, as well as transport systems for ectoine, hydroxyectoine, trehalose, glycerol, glycerol-3-phosphate, L-proline, and glycine-betaine. Thus, to ensure the osmotic balance, D. maris MX2 uses the strategy of accumulating compatible organic solutes.