Higher Relative Abundance Research Articles

Comprehensive analysis reveals the differentiated influential mechanism of biodegradable and non-biodegradable microplastics on core microbial metabolisms and functional genes in an adsorption-biological coupling wastewater treatment system

The effects of different types of microplastics (MPs) on the wastewater treatment efficiency of an adsorption-biological coupling system were investigated. The distribution of the microbial community and metabolic pathways in the coupled system were also analyzed. Biodegradable polybutylene succinate microplastics (PBS MPs) were added to reactor A, while non-biodegradable polystyrene microplastics (PS MPs) was added to reactor B. The average chemical oxygen demand (COD) removal rates in reactor A with 0, 50, and 100 mg/L of MPs were 95.34 %, 89.13 %, and 86.08 %, respectively; the average COD removal rates in reactor B were 96.84 %, 88.43 %, and 87.02 %, respectively. The average total phosphorus (TP) removal rates in reactor A were 74.14 %, 38.94 %, and 36.45 %, respectively, while those in reactor B were 71.73 %, 39.50 %, and 33.09 %, respectively. In the two reactors, Proteobacteria had the highest relative abundance (53 %–62 %), followed by Actinobacteria. PS MPs inhibited the expression of quorum sensing genes by influencing SecA and SecY. Horizontal transfer genes illustrated that both MPs led to up-regulation of reactive oxygen species (ROS)-related functional genes. During glycolysis, the abundances of glucokinase (GLK), pyruvate kinase (PK), and phosphofructokinase (PFK) in reactor A were 0.0179 %, 0.0133 %, and 0.0387 % higher than that in reactor B, respectively. Meanwhile, in nitrogen metabolism, the abundance of key genes such as nasA (A: 40.8 % B: 37.9 %) was greater in reactor A than in reactor B.

Intestinal helminth infections in the African golden wolf (Canis anthus, Cuvier., 1820) population in Bejaia province, northern Algeria

ABSTRACT Forty-seven faecal samples of wolves from Bejaia were examined for intestinal helminths. Five nematodes (Ancylostoma caninum (egg), Strongyloides stercoralis (larvae L1), Toxocara canis (egg), Toxascaris leonina (egg), and Trichuris vulpis (egg)), and one cestode (Dipylidium caninum) were identified. These nematodes were detected with a prevalence of 46.8%, 23.4%, 38.2%, 25.3%, and 2.12%, respectively; and a cestode, with a prevalence of 4.3%. Our results show a high relative abundance of Strongyloides stercoralis larvae L1 (37.5%), followed by eggs of Ancylostoma caninum, whether non-embryonated (16.77%) or embryonated (14.28%). Among the ascarids, Toxocara canis was represented with 18.1%, followed by Toxascaris leonina (8.1%). Finally, Dipylidium caninum and Trichuris vulpis were only poorly represented. This is the first study on helminth parasites in wild golden wolves in Bejaia. The results indicate the presence of six gastrointestinal helminths in the wolf population.

Bacterial microbiome diversity along poultry slaughtering lines: insights from chicken carcasses and environmental sources

Abstract Introduction This study aimed to determine the bacterial diversity of chicken carcasses and their surrounding environment at various stages along a poultry slaughter line. Material and Methods Amplicon sequencing of the 16S rRNA gene was employed to assess the shifts in bacterial community diversity at both phylum and genus levels. Samples were collected from September to November 2021, targeting carcass surfaces at various operational stages (post-defeathering, post-evisceration, post-water chilling, and post-cooling), as well as from the internal environments and air of these units. The study took place in a vertically integrated poultry slaughterhouse in Konya, Turkey. Results Microbial diversity increased after the chilling and storage stages as a result of redistribution of the microorganisms after the physical effect of the slaughtering stages. The final product sample taken after storage had the highest bacterial abundance. The abundance at this stage was found to be strongly correlated with that at other slaughtering stages, as well as with the abundance in chilling water and on the personnel’s hands. The common genera in chicken carcasses during slaughter stages were Macrococcus, Acinetobacter, Enterococcus, Escherichia-Shigella, Psychrobacter, Streptococcus, Lactococcus and Ligilactobacillus. Microbiome data in environmental samples indicated that the genera in highest relative abundance were Bacillus, Anoxybacillus, Acinetobacter and Psychrobacter. In air samples, the storage room had the highest diversity and in this place Bacillus spp. and Staphylococcus spp. were in the majority. Conclusion This study may provide some useful information to pinpoint the critical contamination sources in the poultry slaughtering process.

Molecular transformation of heavy oil during slurry phase hydrocracking process: influences of operational conditions

The influences of reaction temperature, duration, pressure, and catalyst concentration on the molecular transformation of residual slurry phase hydrocracking process were investigated. The molecular composition of the heteroatom compounds in the residue feedstock and its upgrading products were characterized using high-resolution Orbitrap mass spectrometry coupled with multiple ionization methods. The simultaneous promotion of cracking and hydrogenation reactions was observed with increasing of the reaction temperature and time. Specifically, there was a significant increase in the cracking degree of alkyl side chain, while the removal of low-condensation sulfur compounds such as sulfides and benzothiophenes was enhanced. In particular, the cracking reactions were more significantly facilitated by high temperatures, while an appropriately extended reaction time can result in the complete elimination of the aforementioned sulfur compounds with a lower degree of condensation. Under conditions of low hydrogen pressure and catalyst concentration, the products still exhibit a high relative abundance of easily convertible compounds such as sulfoxides, indicating a significant deficiency in the effectiveness of hydrogenation. The hydrogen pressure exhibits an optimal value, beyond which further increments have no effect on the composition and performance of the liquid product but can increase the yield of the liquid product. At significantly high catalyst concentration, the effect of desulfurization and deoxidation slightly diminishes, while the aromatic saturation of highly condensed compounds was notably enhanced. This hydrogenation saturation effect cannot be attained through manipulation of other operational parameters, thereby potentially benefiting subsequent product processing and utilization. This present study demonstrates a profound comprehension of the molecular-level residue slurry phase hydrocracking process, offering not only specific guide for process design and optimization but also valuable fundamental data for constructing reaction models at the molecular level.

Enhanced nitrogen removal from low C/N municipal wastewater through nitrification, partial denitrification and anammox via a step-feed strategy: Synergistic contribution by bacteria in biofilm and floc sludge

Energy-efficient nitrogen removal from carbon-limited municipal wastewater poses challenges. This study developed a novel partial denitrification and anammox (PD/A) process using a step-feed strategy in a single-stage integrated fixed-biofilm activated sludge (IFAS) system operated under sequencing batch mode. Despite relatively low temperatures (15.9–21.6 °C), biological nitrogen removal efficiency reached 80.5 % without the addition of external carbon sources. With the total inorganic nitrogen (TIN) of 48.9 ± 1.2 mg N/L, and C/N of 4.0 in influent, the TIN in effluent achieved 9.6 ± 1.5 mg N/L. Anammox bacteria (AnAOB) activity in the biofilm was 27.96 mg N/(g VSS·d), which was threefold greater than in floc sludge. Candidatus Brocadia (AnAOB) presented a high relative abundance in biofilm (0.53 %), whereas denitrifying bacteria including Thauera and Candidatus Competibacter were mainly retained in floc sludge. Overall, the coupling of step-feed strategy and IFAS offers novel insights into the efficient nitrogen removal from low C/N domestic sewage for retrofitting of municipal wastewater treatment plants, not only saving the energy consumption for aeration, but also fully utilizing carbon sources and ammonium in the influent for the PD/A process.

Habitat quality effects on the abundance of a coral-dwelling fish across spatial scales.

Microhabitat associated fishes are expected to be negatively affected by coral reef degradation, given that many species are coral dwellers. However, the factors underlying this negative impact and the spatial scale(s) at which it occurs are poorly understood. We explored how habitat quality metrics and host preferences influence fish abundance across multiple spatial scales, using the functionally important cleaner fish Elacatinus evelynae as a study species. We surveyed fish at 10 sites in Curaçao that varied in coral cover and health. At the microhabitat scale, we found that E. evelynae group size increases on large, healthy corals and on some coral host species, namely Montastraea cavernosa. We also found that, although E. evelynae can occupy at least 10 coral host species, it selectively inhabits just three corals: M. cavernosa, Colpophyllia natans, and Diploria labrynthiformis. Scaling up to explore goby abundance along 30-m transects, we did not find a clear relationship between live coral cover and goby abundance. However, goby abundance was substantially higher at one location with elevated coral cover and a high relative abundance of E. evelynae host species. Collectively, these results confirm that E. evelynae abundance is impacted by reef health. They also indicate that the species' long-term persistence may depend on both the maintenance of healthy coral hosts and the gobies' plasticity in host preferences on changing reefscapes. Cryptobenthic fishes such as E. evelynae play a vital role in the ecosystem and understanding drivers of their abundance is important as reefs face increased degradation.

Advancing fluorescence tracing with 3D-2D spectral conversion: A mixed culture on microbial degradation mechanisms of DOM from a large-scale watershed

Fluorescence tracing, known for its precision, rapid application, and cost-effectiveness, faces challenges due to the microbial degradation of dissolved organic matter (DOM) in aquatic environments, altering its original spectral fingerprint. This study conducted a 15-day microcosm experiment to examine the effects of biodegradation on the spectral properties of DOM from various sources: livestock excrement (EXC), urban sewage (URB), industrial wastewater (IND), and riparian topsoil (tDOM). Our findings show that while the spectral structures of DOM from different sources change during 15 days of microbial degradation, these changes do not overlap or interfere with each other. However, distinguishing between tDOM and URB in the presence of both IND and EXC is only possible at high resolution. Spectral index calculations revealed significant fluctuations and interference in FI and BIX indices among samples from different sources due to microbial degradation. In contrast, the HIX index exhibited independent fluctuations and remained a reliable spectral index for tracing. LEfSe (Linear discriminant analysis Effect Size) identified characteristic bio-indicators (CBI) for each DOM source. The CBI for tDOM and URB differed significantly; tDOM showed a marked CBI only within the first four days of microbial degradation, with a sharp decline in abundance thereafter, while URB's CBI remained abundant for 12 days. Similarly, IND's CBI maintained high relative abundance for the first 12 days. EXC's CBI was unique, showing a distinct and stable community only after six days of degradation, likely due to its high bioavailability and initial rapid microbial utilization. This study addresses the temporal variability in spectral tracing techniques caused by pollutant biodegradation. We developed a combined spectral-biological tracing technique using the “three-dimensional to two-dimensional” method along with bio-indicators, enhancing the accuracy and timeliness of spectral tracing.

Wild-caught adult black flies (Diptera: Simuliidae) from various ecological landscapes in Malaysia

Most studies on black flies focus on the taxonomy and ecology of their aquatic stages. Despite posing a public health threat, the adults remain poorly studied in many countries, including Malaysia. The present study represents the first investigation of the distribution of wild-caught black flies from various ecological landscapes and climatic conditions in Malaysia. CO2-baited Malaise traps were set randomly at 41 sampling sites across Peninsular Malaysia from 2020 to 2023. In total, 532 black flies belonging to 14 species of four subgenera were captured. To ensure taxonomic rigor, specimens were identified to species morphologically and molecularly. The subgenus Gomphostilbia was the most abundant (71.43 %), followed by Simulium (14.28 %) and Davieselleum and Nevermannia each representing 7.14 % of the total captures. These species represented 14.74 % of the total species recorded from Malaysia. The most frequently collected species were Simulium roslihashimi (24.39 %), followed by S. aureohirtum, S. vanluni, and S. (Gomphostilbia) sp. 1 with 7.32 % each. The highest relative abundance was found for S. vanluni (86.09 %) and S. roslihashimi (7.14 %). Most species were found at elevation below 300 m (78.57 %); fewer were at elevation higher than 1,000 m (21.43 %). Two principal components accounted for 85.3 % of the total intersite variance. Simulium roslihashimi was found at almost every site, with a maximum relative humidity of 90 %. Simulium aureohirtum and S. vanluni were found at sites with relative humidity up to 73 %, but S. aureohirtum was found at higher temperatures (31 °C) compared with S. roslihashimi (28 °C) and S. vanluni (29 °C). The present study establishes the groundwork for further studies of wild adults in Malaysia and identifies the need to use more traps over the range of seasons and environmental conditions, particularly near breeding sites.

Occurrence of tyre-derived particles in size-segregated aerosol in the urban area of Venice

Benzothiazoles (BTHs), commonly used in various industrial applications, have emerged as significant contaminants due to their widespread usage and potential adverse effects on ecosystems and human health. The aim of this study is to quantify and, for the first time, to characterize the particle size distribution of eight BTHs across twelve fractions of atmospheric aerosol representative of the urban boundary layer. Samples were collected from August to October 2023 in the urban area of Venice, located in the Po Valley, known for its poor air quality. Instrumental analysis was achieved via an UHPLC system coupled with a triple quadrupole mass spectrometer.All target compounds were present in the samples analyzed and most of them tended to distribute mainly in the fine fraction of aerosol (<1.8 μm). An exception is given by BTH-SO3H, which presents a bimodal distribution with maxima centered in the coarse fraction; this may imply a different source compared to other BTHs. BTH-SH is the most abundant benzothiazole derivative, suggesting tyre debris as the main source since it is the main compound used in vulcanizing accelerators in rubber manufacture. Given its mutagenic properties, its high relative abundance could be of concern for human health. Resultsof this work provide valuable insights into the distribution of BTHs in urban aerosols, laying the groundwork for future research aimed at better understanding their sources and environmental pathways, fate and impacts.

Enhancing pediatric attention-deficit hyperactivity disorder treatment: exploring the gut microbiota effects of French maritime pine bark extract and methylphenidate intervention.

The pathogenesis of Attention-Deficit Hyperactivity Disorder (ADHD) is thought to be multifactorial, with a potential role for the bidirectional communication between the gut microbiome and brain development and function. Since the "golden-standard" medication therapy with methylphenidate (MPH) is linked to multiple adverse effects, there is a need for alternative treatment options such as dietary polyphenols. These secondary plant metabolites exert antioxidant and anti-inflammatory effects, but much less is known about their impact on the gut microbiota. Since polyphenols are believed to modulate gut microbial composition, interventions might be advantageous in ADHD therapy. Therefore, intervention studies with polyphenols in ADHD therapy investigating the gut microbial composition are highly relevant. Besides the primary research questions addressed previously, this study explored a potential prebiotic effect of the polyphenol-rich French Maritime Pine Bark Extract (PBE) compared to MPH and a placebo in pediatric ADHD patients by studying their impact on the gut microbiota via amplicon sequencing of the full length 16S rRNA gene ribosomal subunit (V1-V9). One interesting finding was the high relative abundance of Bifidobacteria among all patients in our study cohort. Moreover, our study has identified that treatment (placebo, MPH and PBE) explains 3.94% of the variation in distribution of microbial taxa (adjusted p-value of 0.011). Our small sample size (placebo: n = 10; PBE: n = 13 and MPH: n = 14) did not allow to observe clear prebiotic effects in the patients treated with PBE. Notwithstanding this limitation, subtle changes were noticeable and some limited compositional changes could be observed. doi: 10.1186/S13063-017-1879-6.

Dynamic changes in the gut microbiota composition during adalimumab therapy in patients with ulcerative colitis: implications for treatment response prediction and therapeutic targets

BackgroundWhile significant research exists on gut microbiota changes after anti-tumor necrosis factor-alpha (anti TNF-α) therapy for ulcerative colitis, little is known about the longitudinal changes related to the effects of anti TNF-α. This study aimed to investigate the dynamics of gut microbiome changes during anti TNF-α (adalimumab) therapy in patients with ulcerative colitis (UC).ResultsThe microbiota composition was affected by the disease severity and extent in patients with UC. Regardless of clinical remission status at each time point, patients with UC exhibited microbial community distinctions from healthy controls. Distinct amplicon sequence variants (ASVs) differences were identified throughout the course of Adalimumab (ADA) treatment at each time point. A notable reduction in gut microbiome dissimilarity was observed only in remitters. Remitters demonstrated a decrease in the relative abundances of Burkholderia-Caballeronia-Paraburkholderia and Staphylococcus as the treatment progressed. Additionally, there was an observed increase in the relative abundances of Bifidobacterium and Dorea. Given the distribution of the 48 ASVs with high or low relative abundances in the pre-treatment samples according to clinical remission at week 8, a clinical remission at week 8 with a sensitivity and specificity of 72.4% and 84.3%, respectively, was predicted on the receiver operating characteristic curve (area under the curve, 0.851).ConclusionsThe gut microbiota undergoes diverse changes according to the treatment response during ADA treatment. These changes provide insights into predicting treatment responses to ADA and offer new therapeutic targets for UC.

Achieving nitrite shunt using in-situ free ammonia enriched by natural zeolite: Pilot-scale mainstream anammox with flexible nitritation strategy

The mainstream partial nitritation/anammox (PN/A) process represents a significant innovation in decarbonizing municipal wastewater treatment. However, its implementation is considerably hampered by the challenge of stable nitrite supply. In this study, a pilot-scale PN/A system receiving real sewage (20 m3) was operated at room temperature for nearly one year. Remarkable PN performance with relatively high nitrite accumulation ratio of 75.04 ± 10.05 % was obtained via in-situ free ammonia (FA) strategy. The ammonium concentration enriched in the zeolite increased significantly by 548.8 times compared to that in the aqueous phase by ion exchange. This substantial increase robustly inhibited nitrite-oxidizing bacteria (NOB), resulting in high relative abundance ratio of ammonia-oxidizing bacteria (AOB) to NOB of 37.93 ± 12.61 in the zeolite biofilm, compared to 10.22 ± 1.67 in suspended floc sludge. The significant differences in FA concentrations between zeolite biofilm and suspended floc sludge resulted in distinct spatial distribution disparities of AOB and NOB, which were central to achieving stable nitrite accumulation without complex multiple selective pressures. Consequently, compliant effluent with total nitrogen of 10.91 ± 4.23 mg N/L was achieved at 10.4-31.1 °C without external carbon source addition. The biocarriers in the anammox process played a key role in enhancing functional genes and electron flow, supporting anammox-dominated nitrogen removal. This study presents a flexible and adaptable strategy for mainstream nitrite shunting, highlighting its potential for large-scale implementation of mainstream anammox treatment.

Candidatus Midichloria mitochondrii can be vertically transmitted in Hyalomma anatolicum

In this study, a tick intracellular symbiont, Candidatus Midichloria mitochondrii, was detected in Hyalomma anatolicum from Xinjiang, China. Morphological identification and cytochrome oxidase subunit I sequence alignment were used for molecular identification of the tick species. PCR detection further revealed the presence of endosymbiont C. M. mitochondrii in the tick. Specific primers were designed for Groel and 16S rRNA genes of C. M. mitochondrii for PCR amplification and phylogenetic analysis. To further investigate the vertical transmission characteristics of C. M. mitochondrii, specific primers were designed based on the FabⅠ gene fragment to detect C. M. mitochondrii in different developmental stages and organs of the tick using qPCR. Of the 336 tick specimens collected from the field, 266 samples were identified as H. anatolicum on the basis of morphological characteristics. The gene fragment alignment results of COI confirmed that these ticks were H. anatolicum. The phylogenetic analysis showed that Groel gene of C. M. mitochondrii clustered with Midichloria strains detected in Ixodes ricinus ticks from Italy and Ixodes holocyclus ticks from Australia, with 100% sequence similarity. Furthermore, the 16S rRNA gene of C. M. mitochondrii clusters with the strains isolated from Hyalomma rufipes ticks in Italy, exhibiting the highest degree of homology. qPCR results showed that C. M. mitochondrii was present at all developmental stages of H. anatolicum, with the highest relative abundance in eggs, and lower relative abundance in nymphs and unfed males. With female tick blood feeding, the relative abundance of C. M. mitochondrii increased, and a particularly high relative abundance was detected in the ovaries of engorged female ticks. This study provides information for studying the survival adaptability of H. anatolicum, and provides data for further investigation of the mechanisms regulating tick endosymbionts in ticks, enriching the reference materials for comprehensive prevention and control of tick-borne diseases.

De novo anaerobic granulation with varying organic substrates: granule growth and microbial community responses

Anaerobic granulation from dispersed inoculum is recognized as a slow process. However, studies under saline conditions have shown that adding complex proteinaceous substrates can accelerate this process. To explore whether this holds true also under non-saline conditions, we conducted a 262-days experiment with four lab-scale upflow anaerobic sludge blanket reactors inoculated with digested sewage sludge. Each reactor received a synthetic feed containing varying amount of carbohydrate/protein substrate: glucose (RGlu), acetate/tryptone (RAc+Try), glucose/tryptone (RGlu+Try), and glucose/starch (RGlu+Sta). Development of granules with different influent composition was monitored with macroscopy, analysis of the extracellular polymeric substances, and microbial diversity. Granulation was faster in reactors RGlu+Try and RGlu+Sta. Increasing granule diameters positively correlated with the occurrence of bacteria from Muribaculaceae and Lachnospiraceae families, suggesting their involvement in de novo granulation. Granules of RGlu+Try also had high relative abundances of both fermenting bacteria (e.g. Lactococcus, Streptococcus, Trichococcus) and bacteria involved in the oxidation of volatile fatty acids (Smithella, Acetobacteroides). The results of this study provide a basis for strategies to enhance the sludge granulation rate in practice when granular inoculum is not available. Specifically, supplementing small amounts of waste protein during reactor start-up can be effective.

Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series.

Nucleocytoplasmic Large DNA Viruses (NCLDVs, also called giant viruses) are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding 'rules' underpinning their community dynamics over time. We leveraged a five-year monthly metagenomic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize these populations' temporal dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and non-seasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic with a strong seasonal signal. The Imitervirales group had highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is a key driver of the temporal niche of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. Finally, we identified distinct functional content and possible host interactions of two major NCLDV orders-including connections of Imitervirales with primary producers like the diatom Chaetoceros and widespread marine grazers like Paraphysomonas and Spirotrichea ciliates. Together, our results reveal key insights on season-specific effect of phylogenetically distinct giant virus communities on marine protist metabolism, biogeochemical fluxes and carbon cycling.

Impact of additives on syntrophic propionate and acetate enrichments under high-ammonia conditions

High ammonia concentrations in anaerobic degradation systems cause volatile fatty acid accumulation and reduced methane yield, which often derive from restricted activity of syntrophic acid-oxidising bacteria and hydrogenotrophic methanogens. Inclusion of additives that facilitate the electron transfer or increase cell proximity of syntrophic species by flocculation can be a suitable strategy to counteract these problems, but its actual impact on syntrophic interactions has yet to be determined. In this study, microbial cultivation and molecular and microscopic analysis were performed to evaluate the impact of conductive (graphene, iron oxide) and non-conductive (zeolite) additives on the degradation rate of acetate and propionate to methane by highly enriched ammonia-tolerant syntrophic cultures derived from a biogas process. All additives had a low impact on the lag phase but resulted in a higher rate of acetate (except graphene) and propionate degradation. The syntrophic bacteria ‘Candidatus Syntrophopropionicum ammoniitolerans’, Syntrophaceticus schinkii and a novel hydrogenotrophic methanogen were found in higher relative abundance and higher gene copy numbers in flocculating communities than in planktonic communities in the cultures, indicating benefits to syntrophs of living in close proximity to their cooperating partner. Microscopy and element analysis showed precipitation of phosphates and biofilm formation in all batches except on the graphene batches, possibly enhancing the rate of acetate and propionate degradation. Overall, the concordance of responses observed in both acetate- and propionate-fed cultures highlight the suitability of the addition of iron oxide or zeolites to enhance acid conversion to methane in high-ammonia biogas processes.Key points• All additives promoted acetate (except graphene) and propionate degradation.• A preference for floc formation by ammonia-tolerant syntrophs was revealed.• Microbes colonised the surfaces of iron oxide and zeolite, but not graphene.Graphical

Integrative analysis of microbiome and metabolome revealed the effect of microbial inoculant on microbial community diversity and function in rhizospheric soil under tobacco monoculture.

Over-application of chemical fertilizers and continuous cropping obstacles seriously restrict the sustainable development of tobacco production. Localized fertilization of beneficial microbes has potential advantages in achieving higher productivity, but the underlying biological mechanisms of interactions between rhizospheric microorganisms and the related metabolic cycle remain poorly characterized. Here, an integrative analysis of microbiomes with non-targeted metabolomics was performed on 30 soil samples of rhizosphere, root surrounding, and bulk soils from flue-cured tobacco under continuous and non-continuous monocropping systems. The analysis was conducted using UPLC-MS/MS platforms and high-throughput amplicon sequencing targeting the bacterial 16S rRNA gene and fungal ITS gene. The microbial inoculant consisted of Bacillus subtilis, B. velezensis, and B. licheniformis at the ratio of 1:1:1 in effective microbial counts, improved the cured leaf yield and disease resistance of tobacco, and enhanced nicotine and nitrogen contents of tobacco leaves. The bacterial taxa Rhizobium, Pseudomonas, Sphingomonadaceae, and Burkholderiaceae of the phylum Proteobacteria accumulated in high relative abundance and were identified as biomarkers following the application of the microbial inoculant. Under continuous monocropping, metabolomics demonstrated that the application of the microbial inoculant significantly affected the soil metabolite spectrum, and the differential metabolites were significantly enriched to the synthesis and degradation of nicotine (nicotinate and nicotinamide metabolism and biosynthesis of alkaloids derived from nicotinic acid). In addition, microbes were closely related to the accumulation of metabolites through correlation analysis. The interactions between plant roots and rhizospheric microorganisms provide valuable information for understanding how these beneficial microbes affect complex biological processes and the adaption capacity of plants to environments.IMPORTANCEThis study elaborated on how the microbial fertilizer significantly changed overall community structures and metabolite spectrum of rhizospheric microbes, which provide insights into the process of rhizosphere microbial remolding in response to continuous monocropping. we verified the hypothesis that the application of the microbial inoculant in continuous cropping would lead to the selection of distinct microbiota communities by establishing models to correlate biomarkers. Through correlation analysis of the microbiome and metabolome, we proved that rhizospheric microbes were closely related to the accumulation of metabolites, including the synthesis and degradation of nicotine. The interactions between plant roots and rhizospheric microorganisms provide valuable information for understanding how these beneficial microbes affect complex biological processes and the adaption capacity of plants to environments.

Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire.

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.

Individuality and generality of intratumoral microbiome in the three most prevalent gynecological malignancies: an observational study.

Growing evidence have indicated the crucial role of intratumor microbiome in a variety of solid tumor. However, the intratumoral microbiome in gynecological malignancies is largely unknown. In the present study, a total of 90 Han patients, including 30 patients with cancer in cervix, ovary, and endometrium each were enrolled, the composition of intratumoral microbiome was assessed by 16S rDNA amplicon high throughput sequencing. We found that the diversity and metabolic potential of intratumoral microbiome in all three cancer types were very similar. Furthermore, all three cancer types shared a few taxa that collectively take up high relative abundance and positive rate, including Pseudomonas sp., Comamonadaceae gen. sp., Bradyrhizobium sp., Saccharomonospora sp., Cutibacterium acnes, Rubrobacter sp., Dialister micraerophilus, and Escherichia coli. Additionally, Haemophilus parainfluenzae and Paracoccus sp. in cervical cancer, Pelomonas sp. in ovarian cancer, and Enterococcus faecalis in endometrial cancer were identified by LDA to be a representative bacterial strain. In addition, in cervical cancer patients, alpha-fetoprotein (AFP) (correlation coefficient = -0.3714) was negatively correlated (r = 0.4, 95% CI: 0.03 to 0.7) with Rubrobacter sp. and CA199 (correlation coefficient = 0.3955) was positively associated (r = 0.4, 95% CI: 0.03 to 0.7) with Saccharomonospora sp.. In ovarian cancer patients, CA125 (correlation coefficient = -0.4451) was negatively correlated (r = -0.4, 95% CI: -0.7 to -0.09) with Porphyromonas sp.. In endometrial cancer patients, CEA (correlation coefficient = -0.3868) was negatively correlated (r = -0.4, 95% CI: -0.7 to -0.02) with Cutibacterium acnes. This study promoted our understanding of the intratumoral microbiome in gynecological malignancies.IMPORTANCEIn this study, we found the compositional spectrum of tumor microbes among gynecological malignancies were largely similar by sharing a few taxa and differentiated by substantial species owned uniquely. Certain species, mostly unreported, were identified to be associated with clinical characteristics. This study prompted our understanding of gynecological malignancies and offered evidence for tumor microbes affecting tumor biology among cancers in the female reproductive system.

Actualistic taphonomy of microvertebrates ingested by the barn owl (Tyto alba) in a forested area. Implications for the fossil record

Rodents are common prey of nocturnal raptor birds, which ingest whole individuals and subsequently expel partially digested remains as regurgitated pellets. This generates accumulations of skeletal elements that may become part of the fossil record. Inferring which predator was responsible of any given fossil microvertebrate assemblage allows assessing potential biases and making paleoecological inferences. Neotaphonomic studies allow modelling the particularities characterizing different raptors under different environmental conditions. Based on them, it is possible to suggest the predator involved in fossil microvertebrate assemblages by considering the taxonomic and anatomical abundance, the degree of digestive corrosion and that of breakage of skeletal remains. Yet, no detailed neotaphonomic studies on raptors had been made so far in NW Argentina, and other studies in South America have been made mainly in open and arid environments. This has forced paleontological studies to use analogues that might not be fully relevant. Here we present an actualistic study on rodent skeletal remains (NISP = 7540) recovered from modern pellets produced by the barn owl (Tyto alba), recovered at Villa Padre Monti (Tucumán, Argentina), a Yungas forest area partially affected by the presence of crops. The aim is to characterize the taphonomic traces of T. alba under these environmental conditions. The assemblage is composed of at least five species of Cricetidae rodents and a varied representation of skeletal elements, especially of the post-cranium; it has a high relative anatomical abundance (58.7%). Skeletal breakage levels are low, especially in the mandibles and post-cranium. Digestive corrosion is predominantly absent (62.1%) to light, although some elements with high degrees of digestive corrosion were found, even in the extreme digestion category. These results generally compare well with other taphonomic studies on the barn owl, and add data to the known variability of modern accumulations by this Strigiformes. They are thus expected to have an impact on the interpretations of fossil faunas.