Region Of 16S rRNA Gene Research Articles

Comparative metataxonamic analyses of seeds and leaves of traditional varieties and hybrids of cucumber (Cucumis sativus L.) reveals distinct and core microbiome

Profiling the endophytic microbiome of different tissues and varieties of agricultural crops can help to understand i) the tissue specific and varietal specific microbes associated with the plants ii) their potential role in growth, stress tolerance, disease resistance, and yield of the plants. Comparative microbiome profiling across various varieties and hybrids will also be useful to identify the plant's core microbiome. The main objective of the work is to profile and study the microbiome of traditional varieties in comparison with hybrids of cucumber, which would help to understand the microbiome structure in developing consortia to engineer the microbiome of modern hybrids, for useful phenotypes. Metataxonomic sequencing of bacteria and fungi using 16S rRNA gene and ITS regions respectively were carried out in seed and leaf samples of cucumber traditional varieties and modern hybrids. Among bacteria, Prevotella, Bacteroides, Lactobacillus, Dialester, and Fecalibacterium, and among fungal genera, Pichia, Aspergillus, Phaeoisariopsis, Candida, and Malassezia belonged to the core microbiome of cucumber. Modern hybrids were rich in antibiotic producing and toxic pollutant degrading bacteria. Many of the fungi and bacteria observed in the study are well known plant growth promoting microorganisms and play role in offering disease resistance. Some of the bacteria and fungi have beneficial roles in human gut thus revealing the dietary importance of cucumber. The microbes identified in the current study will be useful starting point to develop a consortia to engineer the cucumber microbiome for growth, yield and stress tolerance traits.

First report of a 'Candidatus Phytoplasma aurantifolia'-related strain associated with faba bean phyllody symptoms in India.

Vicia faba L. commonly known as broad bean or faba bean is one of the most widely grown protein rich legume crops. Out of more than 50 faba bean-producing countries, about 90% production is concentrated in the Asian, European Union (EU), and African region (FAO, 2020). Owing to its high nutritional value, both the fresh pods and dry seeds are consumed. During March 2022, some plants with little leaf and phyllody symptoms such as leaf-like floral structures were observed in the experimental fields of Indian Agricultural Research Institute (IARI), New Delhi (Fig. 1 a, b, c). The twig samples were collected from two individual symptomatic and one from asymptomatic plant. DNA was extracted using CTAB (cetyl trimethyl ammonium bromide) method (Ahrens and Seemüller, 1992; Marzachi et al. 1998) and examined for the association of phytoplasma through nested PCR using the universal primers P1/P7 and R16F2n/R16R2 targeting the 16SrRNA gene (Deng and Hiruki 1991; Gundersen and Lee 1996) and the other set of primers secAfor1/secArev3 and secAfor2/secArev3 targeting secA gene (Hodgetts et al. 2008). The DNA from symptomatic plants resulted the amplicons of 1200bp and 840bp specific to 16S rRNA and secA gene respectively. The gel purified PCR products were cloned into pGEM®-T Easy Vector system (Promega) and outsourced for Sanger sequencing at Agri Genome Labs, Kerala, India. The resultant 16S rRNA sequences (GenBank Acc. No. OP978231, OP978232) and secA sequences (ON715392 and ON715393) were examined through NCBI BLASTn analysis. The 16S rRNA sequences of the V. faba strains shared a minimum of 99.85% similarity with the phytoplasma strain causing little leaf and phyllody disease of sesame in India (MW622017) and a maximum of 100% sequence identity with the Vigna radiata phyllody and necrosis phytoplasma strain of Jodhpur (OP935760) India, whereas the secA gene sequences showed 100% identity with Tephrosia purpurea witches'-broom phytoplasma (MW603929) from China and a minimum of 91.14% similarity with 'Candidatus Phytoplasma aurantifolia' (MW020541) from India. The pairwise comparison results were completely in support of the corresponding phylogenetic sequence analysis results of 16SrRNA and secA gene sequences of faba bean strains in comparison with other strains retrieved from GenBank database, wherein the faba bean strains got clustered with 16SrII-D subgroup related strains (Fig. 2 a and b). Virtual RFLP analysis through iPhyClassifer tool through in silico digestion of R16F2n/R2 region of 16S rRNA gene of the faba bean strain using 17 restriction endonuclease enzymes resulted in the RFLP profiles similar to that of the profile of phytoplasma subgroup 16SrII-D (Y10097: papaya yellow crinkle) used as reference strain with a similarity coefficient value of 1.0. All the results of this investigation confirmed the association of 'Candidatus phytoplasma aurantifolia' (16SrII-D) with the diseased faba bean plants in this study. Previous reports of phytoplasma infecting faba bean include a group 16SrIII strain detected in Spain in 2004 (Castro and Romero), a subgroup 16SrII-D strain detected in Sudan in 2012 (Alfaro-Fernandez et al.), a group 16SrII strain detected in Saudi Arabia in 2014 (Al-Saleh and Amer), and subgroup 16SrIII-J strains detected in Egypt in 2014 (Hamed et al.) and in Peru in 2021 (Torres-Suarez et al.). To the best of our knowledge, these findings, document the first report of the association of 'Candidatus Phytoplasma aurantifolia' (subgroup 16SrII-D) with faba bean plants in India. This report necessitates further research on the status of distribution of this phytoplasma strain in other locations and hosts in the country so as to develop possible strategies to contain its further spread and management of the disease.

EPIZOOTIC SITUATION OF HEMOPARASITIC DISEASES OF FARM ANIMALS IN IRKUTSK REGION

Background. Cattle anaplasmosis and babesiosis and theileriosis of horses are a group of natural focal vector-borne diseases that cause significant economic damage to livestock and horse breeding around the world. On the territory of the Baikal region these diseases and their pathogens remain little explored.
 Purpose – to study the epizootic situation of blood-parasitic diseases of farm animals in the Irkutsk region, to establish the species affiliation of the identified pathogens and their genetic diversity.
 Materials and methods. For the presence of Babesia spp./Theileria spp. and Anaplasma spp. has been researched659 horse blood samples, 579 sheep blood samples, 25 goat blood samples and 647 cattle blood samples. For the detection of babesia and theileria, nested two-round PCR with primers from the 18S rRNA gene region was used, and for the detection of anaplasma DNA with primers from the 16S rRNA gene region. For study the genetic diversity of the identified pathogens, selective sequencing of samples was carried out with subsequent phylogenetic analysis.
 Results. The DNA of Anaplasma spp. was detected in blood samples of small ruminants from 12 districts of the region. The infection rate of sheep and goats was 68.7±1.9% and 68%±9.3%, respectively. Nucleotide sequences of the 16S rRNA gene fragment were determined in 68 A. ovis samples from the blood of sheep and goats. The researched sequences were conservative for the studied gene and differed from each other in two heterozygous sites of the gene(T/C and G/A nucleotide substitutions).They corresponded to the sequences of the prototype strain Haibei (CP015994), as well as to the A. ovis sequences previously found in the blood of sheep from Altai (Russia) and Mongolia, deer and D. niveus and D. nuttalli ticks from China.
 DNA of Babesia spp./Theileria spp. found in blood samples of horses from 13 districts of the region. The average infection of horses was 64.2%±1.9%. Two etiological agents of equine piroplasmosis were found in the blood of the examined horses: T. equi (genetic groups A and E) and B. caballi. Definite sequences of the B. caballi 18S rRNA gene (700–1146 bp) were identical to each other and differed by at least ten substitutions and one deletion from the sequences available in the GenBank database. However, the greatest similarity was observed with B. caballi sequences found in the blood of a horse from Brazil (KY952238), ticks from Kazakhstan (MN907451) and China (MN173021).
 The results indicate that DNA of Anaplasma and Babesia in the blood of cattle have not been identified.
 Conclusion: The data received evidence a wide distribution of foci of small cattle anaplasmosis and piroplasmosis of horses in the Irkutsk region and the need to continue monitoring their epizootic condition.

The urogenital microbiome in chronic kidney disease patients on peritoneal dialysis

Introduction and objectivesDiabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters. Materials and methodsMid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3–V4 region of the bacterial 16S rRNA gene. Correlations with the patients’ clinical data and inflammatory profile were performed. ResultsCKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups. Depletion of Gardnerella, Staphylococcus, Corynebacterium, Lactobacillus or Dermabacter populations correlated with CKD-PD patients with history of diabetes, history of peritonitis and altered levels of sCD14. ConclusionsOur results highlight urogenital microbiome as a potential partner and/or marker in the overall health state of CKD-PD patients.

Effects of Ramadan intermittent fasting on gut microbiome: is the diet key?

Much research has been conducted regarding the impact of diet on the gut microbiota. However, the effects of dietary habits such as intermittent fasting are unclear. This study aimed to investigate the effect of intermittent fasting during Ramadan on the gut microbiota. The study was conducted on 12 healthy adult individuals who practiced fasting 17 h per day for 29 consecutive days during the month of Ramadan. To determine the dietary intake of individuals, a 3-day dietary record was kept at the beginning and end of the study. Reads that passed quality filtering were clustered, and custom-prepared 16S rRNA gene regions of bacteria associated with the human microbiome were used as a reference. Consensus sequences were created, and genus-level taxonomic annotations were determined using a sequence identity threshold of 95%. The correlations between the dietary intake measurements of the participants and the respective relative abundance of bacterial genera were investigated. The results showed that Firmicutes were higher in abundance in the gut microbiota before fasting among participants, while they were significantly lower in abundance at the end of Ramadan fasting (p < 0.05). Proteobacteria were significantly higher in abundance at the end of the month of Ramadan (p < 0.05). Fasting was associated with a significant decrease in levels of seven genera: Blautia, Coprococcus, Dorea, Faecalicatena, Fusicatenibacter, Lachnoclostridium, and Mediterraneibacter. Conversely, the abundances of two bacterial genera were enhanced at the end of the fasting month: Escherichia and Shigella. The results of the dietary intake analysis showed that a negative correlation was detected for three comparisons: Ihubacter and protein (rho = -0.54, p = 0.0068), Fusicatenibacter and vegetables (rho = -0.54, p = 0.0042), and Intestinibacter and nuts (rho = -0.54, p-value = 0.0065). The results suggest that even when the fasting period during Ramadan is consistent, the types of food consumed by individuals can affect the gut microbiota.

Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems

Soil microbes play a crucial role in soil organic matter decomposition and nutrient cycling and are influenced by management practices. Therefore, quantifying the impacts of various agricultural management practices on soil microbiomes and their activity is crucial for making informed management decisions. This study aimed to assess the impact of various management systems on soil bacterial abundance and diversity, soil enzyme activities and carbon mineralization potential in wheat-based systems. To accomplish this, soil samples from 0 to 15 cm depth were collected from ongoing long-term field trials in eastern Oregon region under wheat (Triticum aestivum L.)-fallow (WF), WF with different tillage (WT), wheat-pea (Pisum sativum L.) (WP), WF under different crop residue management (CR) and natural undisturbed/unmanaged grassland pasture (GP). These trials consisted of an array of treatments like tillage intensities, nitrogen rates, organic amendments, and seasonal residue burning. This study was a part of the Soil Health Institute’s North American Project to Evaluate Soil Health measurements (NAPESHM). Bacterial community structure was determined using amplicon sequencing of the V4 region of 16SrRNA genes and followed the protocols of the Earth Microbiome Project. In addition, extracellular enzyme activities, and carbon mineralization potential (1d-CO2) were measured. Among different trials, 1d-CO2 in WT, WP, and CR studies averaged 53%, 51% and 87% lower than GP systems, respectively. Enzyme activities were significantly greater in GP compared to the other managements and followed similar trend as respiration. We observed higher evenness in GP and higher richness in spring residue burning treatment of CR study. Our results indicated that species evenness is perhaps a better indicator of soil health in comparison to other indices in dryland wheat systems.

Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire.

Prescribed burn is a management tool that influences the physical structure and composition of forest plant communities and their associated microorganisms. Plant-associated microorganisms aid in host plant disease tolerance and increase nutrient availability. The effects of prescribed burn on microorganisms associated with native ecologically and economically important tree species, such as Cornus florida L. (flowering dogwood), are not well understood, particularly in aboveground plant tissues (e.g., leaf, stem, and bark tissues). The objective of this study was to use 16S rRNA gene and ITS2 region sequencing to evaluate changes in bacterial and fungal communities of five different flowering dogwood-associated niches (soil, roots, bark, stem, and leaves) five months following a prescribed burn treatment. The alpha- and beta-diversity of root bacterial/archaeal communities differed significantly between prescribed burn and unburned control-treated trees. In these bacterial/archaeal root communities, we also detected a significantly higher relative abundance of sequences identified as Acidothermaceae, a family of thermophilic bacteria. No significant differences were detected between prescribed burn-treated and unburned control trees in bulk soils or bark, stem, or leaf tissues. The findings of our study suggest that prescribed burn does not significantly alter the aboveground plant-associated microbial communities of flowering dogwood trees five months following the prescribed burn application. Further studies are required to better understand the short- and long-term effects of prescribed burns on the microbial communities of forest trees.

Antibacterial activities and characteristics of some marine fungi strains isolated from Co To beach, Quang Ninh province

Resistance to pathogenic bacteria may lead to serious health problems. Scientists found that discovering novel antimicrobial compounds is possible by exploring rarely investigated environments. Therefore, this work focused on isolating and identifying some fungal strains collected from the Co To sea. We tested whether such strains can produce compounds with vital activities, including antibacterial and antifungal. The antimicrobial activity of the marine fungi crude extracts was performed by the Bioassay method in a 96-well tray. The minimum inhibitory concentration (MIC) test results showed that 22 strains of marine fungi from samples with different geographic coordinates and 20/22 strains had antibacterial activity against at least two strains of microorganisms tested. The biological evaluation revealed that strains M257 and M238 inhibited 4 to 5 tested strains with MIC values equal to or lower than positive controls. Using a BLAST analysis in the GenBank database, morphological comparisons of the two selected candidate strains with similar known species and phylogenetic analyses were conducted on the 18S rRNA gene regions, and maximum likelihood revealed that M257 belongs to Talaromyces genus, and M238 belongs to Aspergillus penicillioides. The isolates were analyzed in a phylogenetic tree based on MegaX software.

First report on mycetoma in Turkana County-North-western Kenya.

Mycetoma is one of the six Neglected Tropical Diseases that are prevalent in Turkana County (northwest Kenya). The aim of the study was to estimate the prevalence of mycetoma in the county, as well as to describe the main causative agents involved in the disease using methods affordable locally. Based on the data collected by the team of cooperative medicine Cirugia en Turkana (Surgery in Turkana), a specific study for mycetoma was started during the 16th humanitarian medicine campaign in February 2019. Patients with suspected mycetoma were studied at the Lodwar County Referral Hospital (LCRH). After informing the patient and getting their consent, the lesions were examined and sampled (mainly by biopsy) and clinical data were recorded. Samples were washed in sterile saline solution and cut in fragments. Some of these were inoculated on Sabouraud Dextrose Agar, Malt Extract Agar, and diluted Nutrient Agar plates. One fragment of each sample was used for DNA extraction. The DNA and the rest of the fragments of samples were kept at -20°C. All cultures were incubated at room temperature at the LCRH laboratory. The DNA obtained from clinical samples was submitted to PCR amplification of the ITS-5.8S and the V4-V5 16S rRNA gene region, for the detection and identification of fungi and bacteria respectively. From February 2019 till February 2022, 60 patients were studied. Most of them were men (43, 74,1%) between 13 and 78 y.o. (mean age 37). Half of the patients were herdsmen but, among women 40% (6) were housewives and 26.7% (4) charcoal burners. Lesions were mainly located at the feet (87.9%) and most of the patients (54; 93.1%) reported discharge of grains in the exudate, being 27 (46.6%) yellow or pale colored and 19 (32.8%) of them dark grains. Culture of clinical samples yielded 35 fungal and bacterial putative causative agents. Culture and molecular methods allowed the identification of a total of 21 causative agents of mycetoma (39.6% of cases studied). Most of them (17) corresponded to fungi causing eumycetoma (80.9%) being the most prevalent the genus Madurella (7; 41.2%), with two species involved (M. mycetomatis and M. fahalii), followed by Aspergillus (2; 11.8%). Other minority genera detected were Cladosporium, Fusarium, Acremonium, Penicillium, and Trichophyton (5.9% each of them). Actinobacteria were detected in 19.1% of samples, but only Streptomyces somaliensis was identified as a known agent of mycetoma, the rest being actinobacteria not previously described as causative agents of the disease, such as Cellulosimicrobium cellulans detected in two of the patients. Although Kenya is geographically located in the mycetoma belt, to our knowledge this is the first report on mycetoma in this country from 1973, and the first one for Turkana County.

Evaluation of the Zybio EXS3000 mass spectrometry in routine identification of Clinical isolates

The matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been widely applied in routine clinical microbiology laboratories as an efficient and reliable technique for diagnostic purpose. In this work, we evaluated the performance of the newly developed Zybio EXS3000 (Zybio Inc., China) in microbial identification and compared it with VITEK MS (bioMérieux, France). For this study, a total of 1340 isolates from various clinical specimens were collected. These isolates were analyzed simultaneously on both EXS3000 and VITEK MS. The inconsistent or unidentifiable data were further identified using the help of either 16S rRNA gene or ITS region sequencing. During the study, we observed that EXS3000 and VITEK MS provided positive confirmatory diagnostics for 95.0% and 96.5% of the isolates, respectively, which were consistent with the sequencing results. However, it is worth noting that the EXS3000 system needs to improve the identification performance of Candida albicans in the follow-up. There are no significant differences between the two devices in terms of microbial identification performance. The advantage of EXS3000 over VITEK MS is in its ability to perform in significantly lesser time period. In conclusion, the results of this investigation showed that EXS3000 can be used to identify microorganisms in clinical microbiology laboratories.

Evaluating the diversity of the enigmatic fungal phylum Cryptomycota across habitats using 18S rRNA metabarcoding

Fungi in the phylum Cryptomycota have been recovered in numerous environmental DNA (eDNA) surveys but are only known from five described genera of intracellular parasites. These fungi are common in aquatic and soil habitats, but little is known about their relative diversity and specificity among particular habitats. We surveyed Cryptomycota from 80 eDNA samples including freshwater, soil, and marine habitats using Cryptomycota-preferential primers coupled with long-amplicon PacBio sequencing (1.2 kb of the 18S rRNA gene region). We found that freshwater samples were the most diverse, comprising 175 operational taxonomic units (OTUs) of Cryptomycota and also showed a high abundance of the related algae-parasitic group Aphelidiomycota, while marine samples were the least diverse with 25 OTUs. The composition of Cryptomycota communities was influenced by habitat, with freshwater and soil showing statistically distinct communities. Phylogenetic analyses showed that the present survey recovered most previously sampled major clades of Cryptomycota, but most (61%) OTUs were novel to this study, indicative of an extensive diversity of the group that remains largely uncharacterized.

Identifying the Microbiome of the Adenoid Surface of Children Suffering from Otitis Media with Effusion and Children without Middle Ear Effusion Using 16S rRNA Genetic Sequencing.

The upper respiratory tract harbors diverse communities of commensal, symbiotic, and pathogenic organisms, originating from both the oral and nasopharyngeal microbiota. Among the primary sites of microbial colonization in the upper airways are the adenoids. Alterations in the adenoid microbiota have been implicated in the development of various conditions, including secretory otitis media. This study aims to employ 16S rRNA genetic sequencing to identify the most common bacteria present on the surface of adenoids in children with otitis media with effusion and compare them with children without pathologies in the tympanic cavity. Additionally, we seek to determine and compare the bacterial diversity in these two study groups. A total of nineteen samples from the adenoid surfaces were collected, comprising two groups: thirteen samples from children without middle ear effusion and six samples from children with secretory otitis media. The libraries of the V3-V4 hypervariable region of the bacterial 16S rRNA gene was made and sequenced using MiSeq platform. The most prevalent phyla observed in both groups were Proteobacteria, Firmicutes, and Bacteroidetes. The most common bacterial genera identified in both groups were Haemophilus, Streptococcus, Moraxella, Fusobacterium, and Bordetella, with Fusobacterium and Moraxella being more prevalent in the groups that had no middle ear effusion, while Haemophulus and Streptococcus were more prevalent in the otitis media with effusion group, although not in a statistically significant way. Statistical analysis shows a trend towards bacterial composition and beta diversity being similar between the study groups; however, due to the limited sample size and unevenness between groups, we should approach this data with caution. The lack of prolific difference in bacterial composition between the study groups suggests that the role of the adenoid microbiome in the development of otitis media with effusion may be less significant.

Sodium levels and grazing pressure shape natural communities of the intracellular pathogen Legionella

BackgroundLegionella are parasites of freshwater protozoa, responsible for Legionellosis. Legionella can be found in a variety of aquatic environments, including rivers, lakes, and springs, as well as in engineered water systems where they can potentially lead to human disease outbarks. Legionella are considered to be predominantly freshwater organisms with a limited ability to proliferate in saline environments. Exposure of Legionella to high sodium concentrations inhibits growth and virulence of laboratory strains, particularly under elevated temperatures. Nonetheless, Legionella have been identified in some saline environments where they likely interact with various protozoan hosts. In this work, we examine how these selection pressures, sodium and grazing, help shape Legionella ecology within natural environments. Utilizing Legionella-specific primers targeting a variable region of the Legionella 16S rRNA gene, we characterized Legionella abundance, diversity, and community composition in natural spring clusters of varying sodium concentrations, focusing on high sodium concentrations and elevated temperatures.ResultsWe observed the highest abundance of Legionella in spring clusters of high salinity, particularly in combination with elevated temperatures. Legionella abundance was strongly related to sodium concentrations. The Legionella community structure in saline environments was characterized by relatively low diversity, compared to spring clusters of lower salinity. The community composition in high salinity was characterized by few dominant Legionella genotypes, not related to previously described species. Protozoan microbial community structure and composition patterns resembled those of Legionella, suggesting a common response to similar selection pressures. We examined Legionella co-occurrence with potential protozoan hosts and found associations with Ciliophora and Amoebozoa representatives.ConclusionsOur results indicate that selection forces in saline environments favor a small yet dominant group of Legionella species that are not closely related to known species. These novel environmental genotypes interact with various protozoan hosts, under environmental conditions of high salinity. Our findings suggest that alternative survival mechanisms are utilized by these species, representing mechanisms distinct from those of well-studied laboratory strains. Our study demonstrate how salinity can shape communities of opportunistic pathogens and their hosts, in natural environments, shedding light on evolutionary forces acting within these complex environments.Dch3Ld1J5jASmW1xvkYvDBVideo

Composition of soil bacterial communities associated with urban stormwater detention basins and their predicted functional roles in N cycle.

Stormwater detention basins serve as vital components in mitigating the adverse effects of urban runoff, and investigating the microbial dynamics within these systems is crucial for enhancing their performance and pollutant removal capabilities. The aim of this study was to examine and compare the soil bacterial communities in two stormwater detention basins located on the Edwards Aquifer in Bexar County, Texas, USA, and evaluate how soil physiochemical properties may affect them. Each basin soil was sampled in two different seasons at varying depths and the structure of microbial communities was examined using paired end Illumina sequencing using V3 and V4 region of 16S rRNA gene. PICRUSt2 was used to predict functional genes in the nitrogen cycle. In addition, soil physicochemical properties such as pH, carbon, nitrogen, and phosphorus and particle size were examined. A beta diversity analysis revealed that basins had distinctive microbial communities. Additionally, soil particle size, phosphorus and ammonia significantly correlated with some of the dominant phyla in the basins. Proteobacteria and Acidobacteria showed a positive correlation with the relative abundances of nitrogen-cycling genes, while Actinobacteria showed a negative correlation. This study evaluated the associations between soil physicochemical properties and microbial community dynamics in stormwater basins. The study also predicts the relative abundance of nitrogen cycling genes, suggesting shared functional traits within microbial communities. The findings have implications for understanding the potential role of microbial communities in nitrogen cycling processes and contribute to developing sustainable stormwater management strategies and protecting water quality in urban areas.

Red imported fire ant nesting affects the structure of soil microbial community.

The red imported fire ants (RIFA, Solenopsis invicta) have become a well-known invasive species that poses significant ecological and economic threats globally. As of recent times, the geographic scope of its invasion in China is rapidly expanding, thereby aggravating the extent and severity of its detrimental effects. The importance of soil microorganisms for maintaining soil health and ecosystem function has been widely acknowledged. However, the negative impact of RIFAs on soil microbial communities and their functions has not yet been fully understood. In this study, we sequenced the V3-V4 variable region of the bacterial 16S rRNA gene in soil samples collected from three types of RIFA nests to investigate the impact of RIFA invasion on soil microbial diversity and composition. The results of alpha diversity analysis showed that the normal soil without nests of RIFAs exhibited the highest level of diversity, followed by the soil samples from RIFA-invaded nests and abandoned nests. Taxonomy and biological function annotation analyses revealed significant differences in microbial community structure and function among the different samples. Our findings demonstrate that RIFA invasion can significantly alter soil microbial community composition, which could ultimately affect ecosystem function. Therefore, effective management strategies are urgently needed to mitigate the negative impact of invasive species on native ecosystems.

Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species.

The oil sands mining operations in Alberta have produced billions of m3 of tailings which must be reclaimed and integrated into various mine closure landforms, including terrestrial landforms. Microorganisms play a central role in nutrient cycling during the reclamation of disturbed landscapes, contributing to successful vegetation restoration and long-term sustainability. However, microbial community succession and response in reconstructed and revegetated tailings remain largely unexplored. This study aimed to monitor the structural and functional responses of microbial communities in tailings subjected to different capping and vegetation strategies over two growing seasons (GS). To achieve this, a column-based greenhouse experiment was conducted to investigate microbial communities in tailings that were capped with a layer (10 or 30 cm) of peat-mineral mix (PMM) and planted with either upland or wetland communities. DNA metabarcoding analysis of the bacterial 16S rRNA gene and fungal ITS2 region as well as shotgun metagenomics were used to asses the impact of treatments on microbial taxonomy and functions, respectively. Results showed that tailings microbial diversity and community composition changed considerably after two GS compared to baseline samples, while communities in the PMM capping layer were much more stable. Likewise, several microbial functions were significantly enriched in tailings after two GS. Interestingly, the impact of capping on bacterial communities in tailings varied depending on the plant community, leading to a higher number of differentially abundant taxa and to a decrease in Shannon diversity and evenness in the upland treatment but not in the wetland treatment. Moreover, while capping in the presence of wetland vegetation increased the energy-related metabolic functions (carbon, nitrogen, and sulfur), these functions were depleted by capping in the upland treatment. Fungi represented a small proportion of the microbial community in tailings, but the relative abundance of several taxa changed over time, while the capping treatments favored the growth of some beneficial taxa, notably the root endophyte Serendipita, in both upland and wetland columns. The results suggest that selecting the right combination of capping material and vegetation type may contribute to improve below-ground microbial processes and sustain plant growth in harsh environments such as oil sands tailings.

Identification and Characterization of Pseudomonas aeruginosa 16S rRNA Gene Isolated from Contaminated Soil With Oil Residues

Pseudomonas aeruginosa was isolated from fifty soil samples were collected from different sites of contaminated soil with oil residues in Ministry of science& technology. Morphological, biochemical tests and 16S rRNA genes sequencing was performed for bacterial isolates identification. Thirty (30) isolates of P. aeruginosa bacteria were confirmed according to morphological, biochemical tests. For molecular analysis, all isolates that tested positive for P. aeruginosa underwent amplification of the 16S rRNA gene using previously described primers that amplified a particular DNA fragment of 956 bp. PCR product was delivered to Macrogen Corporation - Korea for Sanger sequencing utilizing an automated DNA sequencer called the ABI3730XL. The results were emailed to us, and we used geneious software to analyze them. The investigation of phylogenetic relationships between different strains of Pseudomonas aeruginosa has frequently been conducted on the sequencing of the 16S rRNA gene region, which is a viable technique for species identification. To determine the degree of genetic similarity between the organisms, a distance tree was built. Consequently, gene sequencing of the 16S rRNA region was an appropriate method for isolating isolates at the molecular level. The a novel local strain of Ps. aeruginosa which isolated from contaminated soil with oil residues samples (MSZ. IRQ20) and we will registration of isolate in GenBank under accession number of MT832126.1. Distance Tree Using Blast Tool in the Geneious software.

Molecular Prevalence of Three Chicken Gastrointestinal Tract Pathogens and Phylogenetic Characterization of Tetratrichomonas gallinarum in Türkiye

Several species of parasites infect chickens and can cause economic losses. Histomonas meleagridis, its intermediate host Heterakis gallinarum, and Tetratrichomonas gallinarum are the most common parasites of poultry. The current study aimed to determine the molecular prevalence and phylogenetic relationships of H. meleagridis, He. gallinarum, and T. gallinarum in chickens in Central Anatolia Region of Türkiye. For this, a total of 100 fecal specimens from chickens were analyzed by using a PCR assay targeting the 18S rRNA gene region of H. meleagridis and T. gallinarum and the mtDNA COI gene region of He. gallinarum. PCR analysis identified T. gallinarum in 11 (1.1%) specimens, whereas other species were not found in all the examined specimens. Positive specimens were detected only in backyard chickens. Sequence analyses identified two novel genotypes named TRTgal1 and TRTgal3, and one known genotype (TRTgal2) of T. gallinarum. The TRTgal2 genotype was found to be identical to the human genotype (AY247746) and the four avian genotypes. Phylogenetic analyses of the obtained genotypes clustered in separate monophyletic clades. Our study provides the first data on T. gallinarum in chickens in Türkiye and contributes to public health with the identified zoonotic genotype and knowledge of the epidemiology of this parasite.

Molecular identification of Anaplasma platys in cattle by nested PCR.

Anaplasmosis is a zoonotic disease caused by Gram-negative bacterium from Anaplasmataceae family. Anaplasma causes high economic losses worldwide. 16S rRNA analysis was used to diagnose Anaplasma platys in Cattle. Phylogenetic tree and estimation of evolutionary divergence between A. platys isolates were performed. A total of 60 blood samples were collected from a cattle farm in AL-Diwaniyah province. 16S rRNA gene was identified using nested PCR. Overall, 40% of cattle that were chosen to collect the blood were identified to be infected with A. platys. The results have shown presence of targeting partial region of 16S rRNA gene in 24 samples out of 60. Sequencing results of 10 samples have revealed that the phylogenetic tree was divided in to two separate clades. Five isolates of A. platys-Iraq (accession no. OP646782, OP646783, OP646784, OP646790, and OP646791) were located in one clade with the A. platys-China (accession no. MN193068.1). While, five isolates (accession no. OP646785, OP646786, OP646787, OP646788, OP646789) were in different clade with two isolates of A. platys-Africa and A. platys-Zambia in distinct branches, close to the Rickettsiales. The phylogenetic study of A. platys sequences indicated that the isolates were collected from a cattle farm in Al-Dewaniyah were similar and close related to A. platys-China, A. platys-Zambia and A. platys-Africa). This study suggests that cattle can be considered a reservoir of A. platys.

Discovery of a new Hepatozoon species namely Hepatozoon viperoi sp. nov. in nose-horned vipers in Türkiye

Although Hepatozoon spp. remains the most prevalent intracellular protozoa infecting snakes, it was reported only in a few snake species of the Colubridae family in Türkiye. Moreover, studies on these hemoparasites are not available in venomous nose-horned vipers from Türkiye. In this study, we investigated Hepatozoon spp. in three individual Vipera ammodytes using morphological and molecular methods. Our results were positive for intraerythrocytic Hepatozoon spp. gamonts in all three snakes, exhibiting low parasitemia. The microscopic findings were further confirmed through molecular data. A genus-specific PCR assay targeting the 18S rRNA gene region of Hepatozoon spp., was performed using HemoF/HemoR and Hep300/Hep900 primers. The obtained sequences were concatenated and used in phylogenetic analyses in comparison with different Hepatozoon species. Although our (OP377741) isolate was separated into a different branch, it was clustered with the isolates of H. massardi (KC342526), H. cevapii (KC342525), and H. annulatum (ON262426) from Brazilian snakes. Moreover, gene similarity and pair-wise distance between our isolate and other Hepatozoon species infecting snakes were found to be 89.30–98.63% and 0.009–0.077, respectively. Hence, we reported a new species of Hepatozoon, namely Hepatozoon viperoi sp. nov. infecting V. ammodytes. Since the literature does not indicate the existence of such a Hepatozoon species in V. ammodytes in different countries, our data may contribute to the expanding knowledge of Hepatozoon species in snakes, providing new insights into the biodiversity of the haemogregarine protozoan parasite.