Abundant Operational Taxonomic Units Research Articles

Impact of periodontal therapy on oral bacterial composition in individuals diagnosed with advanced periodontal disease.

Introduction. Negative changes in the microbial composition have been extensively studied in individuals with periodontal disease.Gap Statement. The changes in the oral microbiota after treating this disease are still unknown.Aim. We sought to elucidate the distinctive traits of salivary microbiota in individuals displaying healthy gums and those with severe periodontitis (SP) and examine the influence of periodontal therapy.Methodology. Periodontal pocket depths were examined to determine disease severity. The presence and quantity of oral Helicobacter pylori (associated with periodontal disease) were determined. Sequencing of 16S ribosomal DNA and bioinformatic analyses were performed to assess oral bacterial compositions in patients.Results. Sequencing analysis of 16S ribosomal DNA revealed a significant reduction in the abundance of operational taxonomic units (OTUs) and Chao1 and Abundance coverage-based estimator(ACE) indices in the oral cavities of individuals with SP compared to those of the healthy controls. However, these parameters showed significant recovery after appropriate treatment severe periodontitis after treatment (TSP). Additionally, the levels of harmful Bacillales and Spirochetes significantly increased, whereas the presence of beneficial Euryarchaeota significantly decreased in the SP group. The TSP group exhibited considerably augmented abundances of Burkholderiaceae and Veillonella, while noteworthy reductions in the pathogenic microbiota (Clostridia, Fusobacteria and Spirochaetes) were noticed compared to those of the SP group. Functionally, these modified OTUs were extensively implicated in 41 metabolic pathways.Conclusion. Our study demonstrates that nonsurgical periodontal therapy can effectively reduce the diversity of the oral microbiota, thereby potentially enhancing the treatment efficacy in patients with periodontal disease.

Effects of Microplastic on the Gastrointestinal Tract and Gut microbiome of Sprague Dawley Rats

ABSTRACT Nowadays there is evidence that animals are exposed to microplastics (MPs) via food, however there is not much known about their effect on tissue of gastrointestinal tract and on gut microbiome. In this study, adult male rats were fed with polyethylene MPs, mixed with standard pellet food for 24 days at different concentrations ranging from 0 to 1000 μg/day. At the end of experiment, rats were euthanized and histopathological investigation using light and electron microscopy and the gut microbiome was analyzed using MiSeq 16S rRNA amplicon sequencing. Microscopic analysis revealed significant impact of MPs on the intestine, including visible changes to the crypt area as well as reduction in mucus secretion. Autophagic vacuoles were observed in the livers of the rats fed with MPs at 100 µg/day. Oxidative stress was evident in rats fed with 1000 µg/day of MPs, as indicated by the presence of myeloid bodies in both intestinal and hepatic cells. The gut microbiome was also affected by MPs. Although, no distinct clusters were formed when the bacterial communities in the different treatments were ordinated by multidimensional scaling (NMDS), the diversity indices including operational taxonomic unit (OTU) richness and Chao1 exhibited an increasing trend with increasing MPs concentration. Pearson correlations revealed a linear increase in the relative sequence abundance of Clostridia (R=0.036, P=0.003) with increasing MPs concentration, but not in the case of other bacterial groups,. Lactobacillus faecis was the most abundant OTU in the entire dataset, and its relative abundance decreased significantly with increasing MPs concentration. We conclude that exposure to MPs can disrupt cellular function and disturb microbiome balance, and in the event of prolonged exposure, organisms might experience unpredictable effects.

Evaluation of corn fermented protein (CFP) on the fecal microbiome of cats.

Co-products from the ethanol industry, such as distillers dried grains with solubles (DDGS), can provide alternative protein sources for pet food. Corn fermented protein (CFP) is produced using post-fermentation technology to split the protein and yeast from fiber prior to drying. This results in a higher protein ingredient compared to DDGS, increasing its appeal for pet food. In addition, the substantial yeast component, at approximately 20-25%, may promote gut health through modulation of the microbiome and the production of short chain fatty acids. Therefore, the objective of this study was to determine the effect of CFP on the fecal microbiome of cats. The four experimental diets included a control with no yeast (T1) and diets containing either 3.5% brewer's dried yeast (T2), 2.5% brewer's dried yeast plus 17.5% DDGS (T3), or 17.5% CFP (T4). All diets except T1 were formulated to contain 3.5% yeast. Diets were fed to adult cats (n = 11) in an incomplete 4 x 4 replicated Latin square design. Cats were adapted to diet for 9 days followed by a 5-d total fecal collection. During each collection period, fresh fecal samples from each cat were collected and stored at -80°C until analysis. Fresh fecal samples (n = 44) were analyzed by 16S rRNA gene sequencing. Raw sequences were processed through Mothur (v.1.44.1). Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance was analyzed within the 50 most abundant operational taxonomic units (OTU) using a mixed model of SAS (v9.4, SAS Institute, Inc., Cary, NC). Diet was the fixed effect and cat and period were random effects. Results were considered significant at P < 0.05. Alpha-diversity indices (Observed, Chao1, Shannon, Simpson) and beta-diversity metric (principal coordinate analysis) were similar for all treatments. Predominant phyla were Firmicutes (66%), Bacteroidetes (25%), Actinobacteria (8%), Proteobacteria (0.64%), and Desulfobacteria (0.54%). The relative abundance of Firmicutes and Actinobacteria was lower (P < 0.05) for T3 compared to T4 and T2, respectively. On a more specific phylogenic level, 17 genera resulted in differences (P < 0.05) among dietary treatments. Overall, this data indicates that compared to traditional yeast and distillers dried grains, CFP did not alter the overall diversity of the fecal microbiome of healthy adult cats over a 14-d period.

Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean.

Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.

Fungal composition associated with host tree identity mediates nutrient addition effects on wood microbial respiration.

Fungi are key decomposers of deadwood, but the impact of anthropogenic changes in nutrients and temperature on fungal community and its consequences for wood microbial respiration are not well understood. Here, we examined how nitrogen and phosphorus additions (field experiment) and warming (laboratory experiment) together influence fungal composition and microbial respiration from decomposing wood of angiosperms and gymnosperms in a subtropical forest. Nutrient additions significantly increased wood microbial respiration via fungal composition, but effects varied with nutrient types and taxonomic groups. Specifically, phosphorus addition significantly increased wood microbial respiration (65%) through decreased acid phosphatase activity and increased abundance of fast-decaying fungi (e.g., white rot), while nitrogen addition marginally increased it (30%). Phosphorus addition caused a greater increase in microbial respiration in gymnosperms than in angiosperms (83.3% vs. 46.9%), which was associated with an increase in Basidiomycota:Ascomycota operational taxonomic unit abundance in gymnosperms but a decrease in angiosperms. The temperature dependencies of microbial respiration were remarkably constant across nutrient levels, consistent with metabolic scaling theory hypotheses. This is because there was no significant interaction between temperature and wood phosphorus availability or fungal composition, or the interaction among the three factors. Our results highlight the key role of tree identity in regulating nutrient response of wood microbial respiration through controlling fungal composition. Given that the range of angiosperm species may expand under climate warming and forest management, our data suggest that expansion will decrease nutrient effects on forest carbon cycling in forests previously dominated by gymnosperm species.

211 Analysis of microbial communities from a commercial-size swine manure pit and their association with production of volatile organic compounds

Abstract Global pollution and emission concerns have been linked to concentrated animal feeding operations (CAFOs). Indeed, the U.S Environmental Protection Agency (US EPA) warns that there is a significant danger to human health, soil, and water quality from CAFOs. Volatile organic compounds (VOCs), which are amongst air contaminants that pose a serious risk, are abundantly produced in swine manure pits. While VOC emissions from swine manure have been well studied, the microbial species responsible for their production remain mostly uncharacterized. Thus, a deeper comprehension of the microorganisms responsible for VOC production in swine manure pits may help in the development of management approaches that target the microbiome in these environments. In this context, this study aimed to identify the major bacterial species populating the manure pit of a commercial-size swine wean-to-finish research facility. Manure collected from two sampling locations at different time points were analyzed using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. An analysis of the most highly represented microorganisms identified 24 bacterial Operational Taxonomic Units (OTUs), with only four showing a species-level nucleotide sequence identity to currently known or valid species. As these results indicated that the majority of bacterial species from this manure pit were unknown, a metagenomics approach was used to assemble partial to full length genomes from the two most abundant OTUs: Pit_9-00239 [5.09% - 19.44%; Clostridium saccharoperbutylacetonicum (96.60%)] and Pit_ 7-00035 [5.58% - 17.30%; Bacteroides eggerthii (87.66%)]. From genome assembly analysis, 979 contigs were generated for a combined length of 12,367,510 bp, which together included 21,776 coding sequences. Predicted metabolic functions from these contig sets included pathways involved in carbohydrate utilization (glycolysis), vitamin synthesis (riboflavin), and butyrate production (volatile fatty acids). Notably, an enzyme responsible for the production of indole, a common VOC produced from swine manure pits, was also identified. Together, the results from this analysis provide insights on metabolic capabilities of abundant bacterial species from manure pits. These can in turn be used for the future development of management strategies or products that can reduce VOC emissions that result from swine CAFO manure storage.

227 Comparative analysis of rumen bacterial communities from bison heifers fed two forage-based diets of different quality

Abstract Bison have a demonstrated ability to thrive on low-quality forage, an attribute that distinguishes them from their domestic ruminant counterparts. This could be attributed to the capability of their rumen symbiotic microorganisms in extracting more nutrients out of plant biomass. To gain further insight into the role of the bison microbiome in this beneficial adaptation, the primary objective of this study was to determine the diversity and composition of ruminal bacteria in bison fed poor versus good quality forage-based diets. Ruminal content was collected by stomach tubing from 25 bison heifers fed good quality forage (GQG) during the summer (last week of June 2023) at the McGinley Ranch (Gordon, Nebraska, USA). The same individuals were then transitioned to low quality hay (PQG) in pen confinement for approximately 4 to 5 wk before resampling. Data generated from Illumina MiSeq (2×300) sequencing of PCR amplicons targeting the V1-V3 region of the 16S rRNA gene were analyzed using a combination of custom Perl scripts, and publicly available software (Mothur v.1.40, RDP classifier and NCBI Blast). Principal Coordinate Analysis (PCoA) showed a clear distinction in bacterial composition between the two types of forages (Figure 1). Further analysis of species-level operational taxonomic units (OTUs) was performed, and a total of 78,808 OTUs were identified across all samples. From the 20 most highly represented OTUs, the respective abundance of twelve OTUs showed significant differences between the two forage types (Kruskal-Wallis’s sum-rank test; P &amp;lt; 0.05). For example, OTUs SD_Bb-00014 (µGQG = 1.06% vs µPQG = 0.19%), and SD_Bb-00049 (µGQG = 0.98% vs µPQG = 0.08%) showed significant decreases in abundance when animals switched to PQG. Conversely, OTUs SD_Bb-00071 (µGQG = 0.2% vs µPQG = 2.71%), SD_Bb-00049 (µGQG = 0.68% vs µPQG = 1.67%) and OTUs SD_Bb-00148 (µGQG = 0.19% vs µPQG = 1.40%) exhibited a significant increase in abundance in response to the forage transition. Notably, only one of the assessed OTUs, SD_Bb-00071, showed high sequence identity to its closest valid relative, Fibrobacter succinogenes (98.41%). In contrast, most of the other highly represented OTUs were found to be very dissimilar to known species, suggesting that they might represent novel or currently uncharacterized bacterial species (Table 1). Together, these results demonstrate the significant impact of variations in nutritional value and forage quality on the composition of rumen bacterial communities in the North American bison. Poor forage quality appeared to favor bacterial species such as Fibrobacter succinogenes, known for its cellulolytic capabilities, presumably because of its greater efficiency in breaking down more resistant plant cell walls. Its ability and that of other abundant OTUs to efficiently convert plant fibers into assimilable nutrients is likely critical in allowing bison to perform better on poor-quality forage compared with domesticated ruminants.

Selection of the Dominant Endophytes Based on Illumina Sequencing Analysis for Controlling Bacterial Wilt of Patchouli Caused by Ralstonia solanacearum.

Bacterial wilt caused by Ralstonia solanacearum (RS) is one of the most devastating diseases in patchouli (Pogostemon cablin [Blanco] Benth.), which results in low yield and quality of patchouli. However, no stable and effective control methods have been developed yet. To evaluate the potential of dominant bacterial endophytes in biocontrol, the endophytic bacterial diversity of patchouli was investigated based on Illumina sequencing analysis, and the ability of isolates belonging to the dominant bacterial genera to control RS wilt of patchouli was explored in pot experiments. A total of 245 bacterial genera were detected in patchouli plants, with the highest relative abundance of operational taxonomic units belonging to the genus Pseudomonas detected in roots, leaves, and stems. The Pseudomonas isolates S02, S09, and S26 showed antagonistic activity against RS in vitro and displayed many plant growth-promoting characteristics, including production of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic acid deaminase and phosphate- and potassium-solubilizing capability. Inoculation of patchouli plants with the isolates S02, S09, and S26 significantly improved shoot growth and decreased the incidence of bacterial wilt caused by RS. The results suggest that screening of dominant bacterial endophytes for effective biocontrol agents based on Illumina sequencing analysis is more efficient than random isolation and screening procedures.

Comparison of Daily Versus Admission and Discharge Surveillance Cultures for Multidrug-Resistant Organism Detection in an Intensive Care Unit.

Admission and discharge screening of patients for asymptomatic gut colonization with multidrug-resistant organisms (MDROs) is a common approach to active surveillance, but its sensitivity for detecting colonization is uncertain. Daily rectal or fecal swab samples and associated clinical data were collected over 12 months from patients in one 25-bed medical intensive care unit (ICU) in Chicago, IL and tested for the following MDROs: vancomycin-resistant enterococci; third-generation cephalosporin-resistant Enterobacterales, including extended-spectrum β-lactamase-producing Enterobacterales; and carbapenem-resistant Enterobacterales. MDRO detection by (1) admission and discharge surveillance cultures or (2) clinical cultures were compared to daily surveillance cultures. Samples underwent 16S rRNA gene sequencing to measure the relative abundance of operational taxonomic units (OTUs) corresponding to each MDRO. Compared with daily surveillance cultures, admission/discharge cultures detected 91% of prevalent MDRO colonization and 63% of MDRO acquisitions among medical ICU patients. Few (7%) MDRO carriers were identified by clinical cultures alone. Higher relative abundance of MDRO-associated OTUs and specific antibiotic exposures were independently associated with higher probability of MDRO detection by culture. Admission and discharge surveillance cultures underestimated MDRO acquisitions in an ICU. These limitations should be considered when designing sampling strategies for epidemiologic studies that use culture-based surveillance.

The faecal microbiome of the Pacific banana slug, Ariolimax columbianus, displays seasonal variation

ABSTRACT The Pacific banana slug, Ariolimax columbianus, is the largest land mollusc in North America and occurs in forests ranging from northwestern California to Alaska. We explored the microbial community found within the faeces of 24 slugs from the Oregon Coast Range. Twenty-four slugs were collected in 2019, 12 in the spring and 12 in the fall. These two time points were selected to investigate the composition of microbial populations in wild-caught slugs, also in response to seasonal changes in available plants as food sources. Results from 16S rRNA gene amplicon sequencing indicate that the most prevalent phyla detected from A. columbianus were Proteobacteria (66%) and Bacteriodetes (16%), similar to previous observations from six other species/genera of terrestrial gastropods (Stylommatophora). The most abundant operational taxonomic units across all specimens were Enterobacter sp., Pseudomonas sp. and Flavobacterium sp. Significant seasonal variation was observed for several species of Flavobacteriales, Firmicutes and Proteobacteria, with the majority showing higher abundance in fall. In contrast to Cornu aspersum (previously Helix aspersa, parapatric with A. columbianus) and Geomaculus maculosus, A. columbianus harbours very low levels of Buttiauxella (0.35%). These findings raise questions about the origin, specificity and selection of specific bacteria as components of the intestinal microbiome of terrestrial gastropods.

Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach.

Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.

Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum

BackgroundBacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2.ResultsOur results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere.ConclusionsThe study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.

Identification of keystone taxa in root canals and periapical lesions of post-treatment endodontic infections: Next generation microbiome research.

The aim of this study was to analyse and compare the microbiome present in root canals and periapical lesions of teeth with post-treatment infections, and to identify the presence of keystone taxa in both habitats using next-generation sequencing analysis. Apices and periapical lesions of patients with post-treatment apical periodontitis were surgically extracted. Specimens were cryo-pulverized, bacterial DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced using the Illumina Miseq platform. Bioinformatic analysis was carried out with Mothur software, whilst diversity indices were obtained using operational taxonomic units (OTUs). The diversity indices were compared with the Kruskal-Wallis test, and community composition differences were explored with Permutational Multivariate Analysis of Variance (PERMANOVA). A bacterial functional study was performed with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Co-occurrence network analyses were performed using the Sparse Correlations for Compositional data (SparCC). Eigencentrality, clr-based abundance and ubiquitousness were applied to infer keystone taxa. P values <.05 were considered statistically significant. Thirty-two apices and thirty-nine periapical lesions were sequenced and analysed. A similar alpha-diversity (p < .05) and community composition (p = .91) was observed for apices and lesion samples. The most abundant OTUs identified amongst all samples included Fusobacterium nucleatum, Prevotella loescheii, Streptococcus intermedius, Porphyromonas gingivalis, Parvimonas micra, Synergistetes bacterium, Tannerella forsythia and Peptostreptococcus stomatis. The metabolic pathways with >0.81% abundances included membrane transport, genetic information processing and metabolic pathways. F. nucleatum was identified as a keystone taxon as it showed ubiquitousness, an eigenvector centrality value of 0.83 and a clr-based abundance >4. The microbiome in apices and periapical lesions of post-treatment endodontic infections showed a similar diversity and taxonomic composition. Co-occurrence network analyses at OTU level identified F. nucleatum as a keystone taxon candidate in these infections.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms.

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Community structure and association network of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

The Bering-Chukchi shelf is one of the world's most productive areas and characterized by high benthic biomass. Sedimentary microbial communities play a crucial role in the remineralization of organic matter and associated biogeochemical cycles, reflecting both short-term changes in the environment and more consistent long-term environmental characteristics in a given habitat. In order to get a better understanding of the community structure of sediment-associated prokaryotes, surface sediments were collected from 26 stations in the Bering-Chukchi shelf and adjacent northern deep seas in this study. Prokaryote community structures were analyzed by metabarcoding of the 16S rRNA gene, and potential interactions among prokaryotic groups were analyzed by co-occurrence networks. Relationships between the prokaryote community and environmental factors were assessed. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the dominant bacterial classes, contributing 35.0, 18.9, and 17.3% of the bacterial reads, respectively. The phototrophic cyanobacteria accounted for 2.7% of the DNA reads and occurred more abundantly in the Bering-Chukchi shelf. Prokaryotic community assemblages were different in the northern deep seas compared to the Bering-Chukchi shelf, represented by the lowered diversity and the increased abundant operational Taxonomic Units (OTU), suggesting that the abundant taxa may play more important roles in the northern deep seas. Correlation analysis showed that latitude, water depth, and nutrients were important factors affecting the prokaryote community structure. Abundant OTUs were distributed widely in the study area. The complex association networks indicated a stable microbial community structure in the study area. The high positive interactions (81.8-97.7%) in this study suggested that symbiotic and/or cooperative relationships accounted for a dominant proportion of the microbial networks. However, the dominant taxa were generally located at the edge of the co-occurrence networks rather than in the major modules. Most of the keystone OTUs were intermediately abundant OTUs with relative reads between 0.01 and 1%, suggesting that taxa with moderate biomass might have considerable impacts on the structure and function of the microbial community. This study enriched the understanding of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity.

A more detailed understanding of the mechanisms underlying the formation of microbial communities is essential for the efficient management of microbial ecosystems. The stable states of microbial communities are commonly perceived as static and, thus, have not been extensively examined. The present study investigated stabilizing mechanisms, minority functions, and the reliability of quantitative ana-lyses, emphasizing a metabolic network perspective. A bacterial community, formed by batch transferred cultures supplied with phenol as the sole carbon and energy source and paddy soil as the inoculum, was analyzed using a principal coordinate ana-lysis (PCoA), mathematical models, and quantitative parameters defined as growth activity, community-changing activity, community-forming activity, vulnerable force, and resilience force depending on changes in the abundance of operational taxonomic units (OTUs) using 16S rRNA gene amplicon sequences. PCoA showed succession states until the 3rd transferred cultures and stable states from the 5th to 10th transferred cultures. Quantitative parameters indicated that the bacterial community was dynamic irrespective of the succession and stable states. Three activities fluctuated under stable states. Vulnerable and resilience forces were detected under the succession and stable states, respectively. Mathematical models indicated the construction of metabolic networks, suggesting the stabilizing mechanism of the community structure. Thirteen OTUs coexisted during stable states, and were recognized as core OTUs consisting of majorities, middle-class, and minorities. The abundance of the middle-class changed, whereas that of the others did not, which indicated that core OTUs maintained metabolic networks. Some extremely low abundance OTUs were consistently exchanged, suggesting a role for scavengers. These results indicate that stable states were formed by dynamic metabolic networks with members functioning to achieve robustness and plasticity.

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.

Composition and diversity of culturable cyanobacteria in sediment samples from the upper layers of two tropical reservoirs

Benthic cyanobacteria research in high mountain reservoirs remains limited, mainly due to their complexity and knowledge gaps that persist in relation to their ecology in tropical regions. This study aimed to explore the composition, diversity, and toxic potential of cyanobacterial in the upper sediment of two Colombian reservoirs. Our investigation involved multiple methodologies, such as germination experiments, that allowed us to assess the presence and viability of cyanobacteria in upper sediment samples, while the competitive ELISA assay allowed for the quantification of toxins within the cultures. The molecular analysis of Operational Taxonomic Units (OTUs) from subsamples of sediment cultures focused on evaluating cyanobacterial diversity and richness among prokaryotic phyla, and the Phylogenetic analysis of culturable cyanobacteria. Chlorophyll-a measurements confirmed the presence of viable populations in sediment cultures, while microscopic identification demonstrated the growth capacity of cyanobacteria from the orders Nostocales, Chroococcales, Oscillatoriales, and Synechococcales under controlled laboratory conditions. Despite low microcystin levels in culture, the prior detection of mcy genes in direct sediment samples suggests a possible toxic potential of cyanobacterial inhabiting the upper sediments. Community analysis, based on the OTUs abundance, revealed a notably diverse microbial community in both reservoir sediments, with a higher relative abundance of cyanobacteria compared to other prokaryotic phyla. These findings support the hypothesis that surface sediments play a fundamental role as a repository for cyanobacteria that may pose inherent risks to ecosystem health. In conclusion, this research underscores the necessity of further studies to achieve a holistic comprehension of benthic cyanobacteria dynamics in high-mountain tropical reservoirs.

Wound healing of experimental equine skin wounds and concurrent microbiota in wound dressings following topical propylene glycol gel treatment.

Topical wound treatments rely on carrier formulations with little to no biological impact. The potential for a common vehicle, a propylene glycol (PG) gel, to affect wound healing measures including microbiota is not known. Microbiome characterization, based on next generation sequencing methods is typically performed on tissue or directly obtained wound fluid samples. The utility for primary wound dressings to characterize equine wound microbiota in the context of topical treatments is currently unknown. This investigation reports the topical effect of an 80% PG based gel on wound healing and microbiota in wound dressings. Experiments were performed in six mature horses utilizing a surgical, distal limb wound model, histology of sequential wound biopsies, photographic wound measurements and microbiota profiling via 16s rRNA sequencing of wound dressing samples. Experimental wounds were surveyed for 42 days and either treated (Day 7, 14, 21 and 28; at 0.03 ml/cm2) or unexposed to the PG gel. Wound surface area, relative and absolute microbial abundances, diversity indices and histologic parameters were analyzed in the context of the experimental group (treatment; control) using qualitative or quantitative methods depending on data characteristics. Compared to controls, treatment slowed the wound healing rate (17.17 ± 4.27 vs. 18.56 ± 6.3 mm2/day), delayed the temporal decline of polymorphonucleated cells in wound beds and operational taxonomic units (OTU) in wound dressings and lowered alpha-diversity indices for microbiota in primary wound dressing. Relative abundances of OTUs were in line with those previously reported for equine wounds. Clinical outcomes 42 days post wounding were considered similar irrespective of PG gel exposure. Results highlight the potential for vehicle exposure to alter relevant wound outcome measures, imposing the need for stringent experimental control measures. Primary wound dressings may represent an alternate sample source for characterization of the wound microbiome alleviating the need for additional interventions. Further studies are warranted to contrast the microbiome in wound dressings against that present on wound surfaces to conclude on the validity of this approach.

Effects of nanocarbon and nano‐calcium carbonate on soil enzyme activities and soil microbial community in wheat (Triticum aestivum L.) rhizosphere soil

AbstractBackgroundNanofertilisers can enhance the efficiency of nutrient utilization in crop production. Nevertheless, it is unclear how soil microbial and enzyme activities are affected by the application of nanofertilisers to wheat inter‐root soil.AimsThe study aims to investigate the influences of nanocarbon (NC) and nano‐calcium carbonate (NCC) on soil enzyme activities and microbial community in the open field setting.MethodsThe effects of nanofertilisers on soil wheat rhizosphere soil were studied through the evaluation of soil microbial quantity, enzyme activity, and microbial diversity.ResultsThe findings revealed that the combined utilization of nanofertilizers and compound fertilizers (CF) led to an augmentation in the diversity of the soil microbial community. When comparing the effects of 100% composite nanofertilizers (100% CF + 50% NC + 50% NCC) with the control (CK) (100% CF), it was observed that the activities of urease (EC 3.5.1.5), catalase (EC 1.11.1.6), alkaline phosphatase (EC 3.1.3.1), sucrase (EC.3.2.1.26), as well as the number of fungi, actinomycetes, and bacteria, increased by 22.4%, 7.7%, 17.8%, 9.3%, 35.9%, 27.7%, and 26.0%, respectively. Similarly, the employment of 70% composite nanofertilizers (70% CF + 35% NC + 35% NCC) also resulted in an enhancement of these aforementioned indicators. The magnitude of increase over the 100% CF was 19.0%, 6.6%, 13.6%, 6.2%, 26.8%, 21.3%, and 23.5%, respectively. Notably, there was no significant difference observed between 100% CF + 50% NC + 50 % NCC and 70% CF + 35% NC + 35% NCC within the 0–35 d after anthesis. Furthermore, both 100% CF + 50% NC + 50% NCC and 70% CF + 35% NC + 35% NCC contributed to an improvement in the species uniformity and operational taxonomic unit abundance of wheat rhizosphere microorganisms, while also increasing the abundance of Proteobacteria and Actinobacteria compared to the CK. The relative abundance of Bacteroidetes and Actinobacteria was found to be elevated in the nanomaterials‐treated groups, both at 0–7 d and 14–21 d after anthesis, and positively correlated with soil enzyme activities and soil microbial populations.ConclusionsThese results indicate that the application of composite nanofertilizers can enhance the soil microenvironment in wheat fields, particularly under reduced fertilization conditions.