Genus Level Research Articles

Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands.

The Antarctic continent hosts exceptional niches, making it an ideal environment for studying polyextremophilic microorganisms. These organisms are uniquely shaped by the geographic niches and variations in soil types. Here we present, a culture-independent approach using DNA metabarcoding to assess the bacterial communities associated with accumulated snow and exposed sediments across different Antarctic islands situated in the Larsemann Hills, Antarctica. The exposed sediments (ES) were found to be more diverse than the accumulated snow (AS) sediments as represented by the alpha diversity metrics. Out of the total 303 amplicon sequence variants (ASVs) found at the genus level, 93 were unique to accumulated snow sediments and 97 were unique to exposed sediments. The bacterial community composition in accumulated snow was dominated by the phylum Actinobacteriota (24.7%). However, Pseudonocardia (11.9%), Crossiella (11%), and Rhodanobacter (9.1%) were the predominant genera. In contrast, in the exposed sediments, Bacteroidota (24.6%) was the most prevalent phylum, with Crossiella (17.1%), Rhodanobacter (11.1%), and Blastocatella (10%) as the most abundant genera. Metagenomic imputations revealed the abundance of gene families responsible for carbon metabolism, coping with environmental stresses through DNA repair mechanisms, and carbon fixation.

Quantifying Aristotelian essences: On some fourteenth-century applications of limit decision problems to the perfection of species

ABSTRACT This paper explores a specific problem within an important philosophical genre of the fourteenth century: the debates over the perfection of species. It investigates how the problem of defining limits for continuous magnitudes – a problem typical of Aristotelian physics – was integrated into these debates at the levels of genera, species, and individuals as these entities began to be conceptualized in quantitative terms. After explaining the emergence of this problem within fourteenth-century metaphysics, the paper examines the contributions of three philosophers – Hugolinus of Orvieto, John of Ripa, and Paul of Venice – who offered varying solutions to the challenge of defining limits between species. It demonstrates that two primary solutions arose, inspired by continuous and discrete mathematical objects. It is shown that whereas Hugolinus of Orvieto advocates for a continuist model, John of Ripa proposes a discrete one. The last part of the paper examines Paul of Venice's hybrid approach, which combines elements from both models, facilitating a more comprehensive treatment of species particularly difficult to analyse, namely geometric figures. The conclusions of this comparative study underscore how profoundly the metaphysical reflections of the Middle Ages contributed to the analysis of the structure of the continuum and the extension of the notion of quantity to various objects.

Melting temperature mapping method using imperfect-match linear long probes

Identifying pathogenic microorganisms as early as possible is critical for selecting the appropriate antimicrobial therapy in infected patients. We previously reported the development of the Tm mapping method for identifying a broad range of pathogenic bacteria within 3 h of blood collection. However, the Tm mapping identification requires an analytical instrument with a tube-to-tube variation of no more than 0.1 °C, so we can only use a few instruments that have such high thermal accuracy. To address the problem, we developed the improved Tm mapping method using imperfect-match linear long quenching probes (IMLL Q-probes). Using IMLL Q-probes, almost all commercially available analytical instruments can be used for the Tm mapping method. Some bacterial species cannot be narrowed down to one species, but they can at least be narrowed down to the genus level. The Tm mapping method using IMLL Q-probes is useful for deciding on antimicrobial therapy in infected patients.

Microbiome structure and function in parallel full-scale aerobic granular sludge and activated sludge processes

Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised microorganisms that are transformed into spherical biofilms, whereas CAS has floccular sludge of lower density. In this study, we investigated the treatment performance and microbiome dynamics of two full-scale AGS reactors and a parallel CAS system at a municipal WWTP in Sweden. Both systems produced low effluent concentrations, with some fluctuations in phosphate and nitrate mainly due to variations in organic substrate availability. The microbial diversity was slightly higher in the AGS, with different dynamics in the microbiome over time. Seasonal periodicity was observed in both sludge types, with a larger shift in the CAS microbiome compared to the AGS. Groups important for reactor function, such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), followed similar trends in both systems, with higher relative abundances of PAOs and GAOs in the AGS. However, microbial composition and dynamics differed between the two systems at the genus level. For instance, among PAOs, Tetrasphaera was more prevalent in the AGS, while Dechloromonas was more common in the CAS. Among NOB, Ca. Nitrotoga had a higher relative abundance in the AGS, while Nitrospira was the main nitrifier in the CAS. Furthermore, network analysis revealed the clustering of the various genera within the guilds to modules with different temporal patterns, suggesting functional redundancy in both AGS and CAS.Key points• Microbial community succession in parallel full-scale aerobic granular sludge (AGS) and conventional activated sludge (CAS) processes.• Higher periodicity in microbial community structure in CAS compared to in AGS.• Similar functional groups between AGS and CAS but different composition and dynamics at genus level.Graphical abstract

Epiphytic and endophytic bacteria on Camellia oleifera phyllosphere: exploring region and cultivar effect

The epiphytic and endophytic bacteria play an important role in the healthy growth of plants. Both plant species and growth environmental influence the bacterial population diversity, yet it is inconclusive whether it is the former or the latter that has a greater impact. To explore the communities of the epiphytic and endophytic microbes in Camellia oleifera, this study assessed three representative C. oleifera cultivars from three areas in Hunan, China by Illumina high-throughput sequencing. The results showed that the diversity and species richness of endophytic microbial community in leaves were significantly higher than those of microbial community in the epiphytic. The diversity and species richness of epiphytic and endophytic microbes are complex when the same cultivar was grown in different areas. The C. oleifera cultivars grown in Youxian had the highest diversity of epiphytic microbial community, but the lowest abundance, while the cultivars grown in Changsha had the highest diversity and species richness of endophytic microbes in leaves. It was concluded that the dominant phylum mainly included Proteobacteria, Actinobacteriota and Firmicutes through the analysis of the epiphytic and endophytic microbial communities of C. oleifera. The species and relative abundances of epiphytic and endophytic microbial community were extremely different at the genus level. The analysis of NMDS map and PERMANOVA shows that the species richness and diversity of microbial communities in epiphytes are greatly influenced by region. However, the community structure of endophytic microorganisms in leaves is influenced by region and cultivated varieties, but the influence of cultivars is more significant. Molecular ecological network analysis showed that the symbiotic interaction of epiphytic microbial community was more complex.

Revealing microbiota characteristics and predicting flavor-producing sub-communities in Nongxiangxing baijiu pit mud through metagenomic analysis and metabolic modeling

The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and quality of baijiu. Herein, we utilize metagenomics and genome-scale metabolic models (GSMMs) to investigate the microbial composition, metabolic functions in PM microbiota, as well as to identify microorganisms and communities linked to flavor compounds. Metagenomic data revealed that the most prevalent assembly of bacteria and archaea was Proteiniphilum, Caproicibacterium, Petrimonas, Lactobacillus, Clostridium, Aminobacterium, Syntrophomonas, Methanobacterium, Methanoculleus, and Methanosarcina. The important enzymes ofPMwere in bothGH and GT familymetabolism. A total of 38 high-quality metagenome-assembled genomes (MAGs) were obtained, including those at the family level (n = 13), genus level (n = 17), and species level (n = 8). GSMMs of the 38 MAGs were then constructed. From the GSMMs, individual and community capabilities respectively were predicted to be able to produce 111 metabolites and 598 metabolites. Twenty-three predicted metabolites were consistent with the metabonomics detected flavors and served as targets. Twelve sub-community of were screened by cross-feeding of 38 GSMMs. Of them, Methanobacterium, Sphaerochaeta, Muricomes intestini, Methanobacteriaceae, Synergistaceae, and Caloramator were core microorganisms for targets in each sub-community. Overall, this study of metagenomic and target-community screening could help our understanding of the metabolite–microbiome association and further bioregulation of baijiu.

Shotgun metagenomic investigation of foodborne pathogens and antimicrobial resistance genes in artisanal fermented meat products from the Mediterranean area

In this pilot study, we compared the metagenomic profiles of different types of artisanal fermented meat products collected in Italy, Greece, Portugal, and Morocco to investigate their taxonomic profile, also in relation to the presence of foodborne pathogens and antimicrobial resistance genes. In addition, technical replicates of the same biological sample were tested to estimate the reproducibility of shotgun metagenomics. The taxonomic analysis showed a high level of variability between different fermented meat products at both the phylum and genus levels. Staphylococcus aureus was identified with the highest abundance in Italian fermented meat; Escherichia coli in fermented meat from Morocco; Salmonella enterica in fermented meat from Greece; Klebsiella pneumoniae and Yersinia enterocolitica in fermented meat from Portugal. The fungi Aspergillus, Neosartoria, Emericella, Penicillum and Debaryomyces showed a negative correlation with Lactococcus, Enterococcus, Streptococcus, Leuconostoc and Lactobacillus. The resistome analysis indicated that genes conferring resistance to aminoglycoside, macrolide, and tetracycline were widely spread in all the samples. Our results showed that the reproducibility between technical replicates tested by shotgun metagenomic was very high under the same conditions of analysis (either DNA extraction, library preparation, sequencing analysis, and bioinformatic analysis), considering both the degree of overlapping and the pairwise correlation.

Microbial Diversity and Community Structure of Chinese Fresh Beef during Cold Storage and Their Correlations with Off-Flavors

To investigate the diversity and dynamics of microorganisms in Chinese fresh beef (CFB) without acid discharge treatment during cold storage, high-throughput sequencing was employed to analyze the CFB refrigerated for 0, 3, 7, and 10 days. The results showed that the community richness of the fungi and bacteria decreased significantly. However, the diversity decreased in the early stage and increased in the later stage. At the phylum level, Ascomycota (74.1–94.1%) and Firmicutes (77.3–96.8%) were the absolutely dominant fungal and bacterial phyla. The relative abundance of both fungal and bacterial phyla displayed a trend of increasing and then decreasing. At the genus level, Candida (29.3–52.5%) and Lactococcus (19.8–59.3%) were, respectively, the dominant fungal and bacterial genera. The relative abundance of Candida showed a trend of increasing and then decreasing, while Lactococcus possessed the opposite trend. KEGG metabolic pathways analysis suggested that carbohydrate metabolism, membrane transport, and amino acid metabolism were the major metabolic pathways of bacteria. Bugbase prediction indicated the major microbial phenotype of bacteria in CFB during cold storage was Gram-positive (17.2–31.6%). Correlation analysis suggested that Lactococcus, Citrobacter, Proteus, and Rhodotorula might be the main microorganisms promoting the production of off-flavor substances in CFB. This study provides a theoretical basis for the preservation of Chinese fresh beef.

Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary

Abstract Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal–spatial dataset, from a subtropical hypereutrophic estuary. Screening 54 water samples across brackish to marine sites revealed that nutrient concentrations and salinity best explained spatial community variations, whereas temperature and dissolved oxygen likely drive seasonal shifts. By combining short and long read sequencing data, we recovered 2459 metagenome-assembled genomes (MAGs), proposed new taxon names for previously uncharacterised lineages, and created an extensive, habitat specific genome reference database. Community profiling based on this genome reference database revealed a diverse prokaryotic community comprising 61 bacterial and 18 archaeal phyla, and resulted in an improved taxonomic resolution at lower ranks down to genus level. We found that the vast majority (61 out of 73) of abundant genus level taxa (>1% average) represented unnamed and novel lineages, and that all genera could be clearly separated into brackish and marine ecotypes with inferred habitat specific functions. Applying supervised machine learning and metabolic reconstruction, we identified several microbial indicator taxa responding directly or indirectly to elevated nitrate and total phosphorus concentrations. In conclusion, our analysis highlights the importance of improved taxonomic resolution, sheds light on the role of previously uncharacterised lineages in estuarine nutrient cycling, and identifies microbial indicators for nutrient levels crucial in estuary health assessments.

SEM and LM insights: Spore morphology and its taxonomic significance in Sino Himalayan, Malesian, and European elements of Pteridaceae.

The Pteridaceae family, known for its taxonomic complexity, presents challenges in identification due to high variability among its species. This study investigates the spore morphology employing both SEM and LM techniques in 10 Pteridaceae taxa phytogeographicaly Sino-Himalayan, Malesian, and European elements in Pakistan. The taxa include Adiantum capillus-veneris, A. incisum, A. venustum, Aleuritopteris bicolor, Oeosporangium nitidulum, O. pteridioides, Onychium cryptogrammoides, O. vermae, Pteris cretica, and P. vittata. The objective is to assess their taxonomic relevance and develop a spore-based taxonomic key. Findings indicate differences in spore shape, sizes, exospore thickness, and in surface ornamentation highlighting the potential for taxonomic differentiation. Spores are trilete, and notable differences are observed in the dimension of spores in both distal and proximal sides. Equatorial dimensions vary between 35 and 50 μm, while the polar diameter ranges from 29 to 50 μm. SEM revealed different spore ornamentation types that show several useful characteristics establishing valuable taxonomic variations. The studied Adiantum taxa feature a perispore with tubercules and a micro-granulose surface. The spores of examined Oeosporangium and Aleuritopteris taxa shows cristate sculptures with variable ornamentations. Both species of Onychium have tuberculate-pleated tubercles with sinuous folds on both distal and proximal sides. The surface ornamentation among examined Pteris taxa show variability. PCA analysis indicated that spore quantitative data identified distinct groups, underscoring taxonomic significance. Nevertheless, there was variation observed in surface ornamentation and spore shape, indicating the potential for discrimination among taxa. RESEARCH HIGHLIGHTS: Spore morphology of 10 Pteridaceae taxa has been investigated through LM and SEM. Investigated species shows differences in spore shape, sizes, exospore thickness, and in surface ornamentation. Ornamentation on the perispore provides several valuable characteristics, establishing useful taxonomic distinctions. Spore morphological analysis is effective at the generic level, with minor distinctions discernible at the species level.

Highly effective removal of nitrate from saline wastewater by glucose-enhanced sulfur autotrophic system

The denitrification performance of the elemental sulfur autotrophic denitrification (S0AD) system requires improvements to broaden its applicability for treating nitrate (NO3−-N) wastewater contaminated with high salinity. Therefore, this work investigated the denitrification performance and mechanism of the glucose-enhanced (C:N ratio = 1) S0AD system with saline wastewater (0–15 g/L). The results showed that by adding glucose, our research successfully constructed the elemental sulfur autotrophic/heterotrophic denitrification (HS0AD) system, which showed a stable NO3−-N removal efficiency above 95 % and lower effluent sulfate generation. The NO3−-N removal efficiency of the HS0AD system was over 95.62 % with wastewater containing different salinity levels. With increasing salinity, the glucose utilization efficiency increased from 65.23 % to 74.35 %. Microbial community analysis showed that adding glucose promoted the growth of the Proteobacteria phylum and stimulated its activity under salt stress. High salinity (≥10 g/L) reduced the microbial diversity at the genus level. However, the growth of salt-tolerant denitrifying bacteria (Thiobacillus and Vitellibacter) still enabled efficient denitrification performance with the system. These microorganisms can resist high salinity stresses by releasing proteins. All results indicated that the glucose-enhanced system shows great nitrate removal potential, even under salt stress. These conclusions provide a theoretical basis for applying a synergistic system to treat saline wastewater contaminated with NO3−-N.

The alterations of oral, airway and intestine microbiota in chronic obstructive pulmonary disease: a systematic review and meta-analysis

BackgroundIncreasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease’s status and severity, and distinct microbial ecological variations exist between COPD and healthy control (HC). This systematic review and meta-analysis aimed to summarize microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota of different stages of COPD and HC to make comparisons.MethodsA comprehensive systematic literature search was conducted in PubMed, Embase, the Web of Science, and the Cochrane Library databases to identify relevant English articles on the oral, airway, and intestine microbiota in COPD published between 2003 and 8 May 2023. Information on microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota was collected for comparison between different stages of COPD and HC.ResultsA total of 20 studies were included in this review, involving a total of 337 HC participants, 511 COPD patients, and 154 AECOPD patients. We observed that no significant differences in alpha diversity between the participant groups, but beta diversity was significantly different in half of the included studies. Compared to HC, Prevotella, Streptococcus, Actinomyces, and Veillonella of oral microbiota in SCOPD were reduced at the genus level. Most studies supported that Haemophilus, Lactobacillus, and Pseudomonas were increased, but Veillonella, Prevotella, Actinomyces, Porphyromonas, and Atopobium were decreased at the genus level in the airway microbiota of SCOPD. However, the abundance of Haemophilus, Lactobacillus and Pseudomonas genera exhibited an increase, whereas Actinomyces and Porphyromonas showed a decrease in the airway microbiota of AECOPD compared to HC. And Lachnospira of intestine microbiota in SCOPD was reduced at the genus level.ConclusionThe majority of published research findings supported that COPD exhibited decreased alpha diversity compared to HC. However, our meta-analysis does not confirm it. In order to further investigate the characteristics and mechanisms of microbiome in the oral-airway- intestine axis of COPD patients, larger-scale and more rigorous studies are needed.Systematic review registrationPROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023418726.

Arbuscular Mycorrhizal Fungi Diversity in Sophora japonica Rhizosphere at Different Altitudes and Lithologies

Arbuscular mycorrhizal fungi play a key role in mediating soil–plant relationships within karst ecosystems. Sophora japonica, a medicinal plant with anti-inflammatory and antitumor properties, is widely cultivated in karst areas of Guangxi, China. We considered limestone, dolomite, and sandstone at altitudes ranging from 100 to 800 m and employed Illumina sequencing to evaluate AMF diversity and identify the factors driving S. japonica rhizosphere AMF community changes. We showed that the increase in altitude increased S. japonica AMF colonization and the Shannon index. The colonization of limestone plots was higher than that of other lithology. In total, 3,096,236 sequences and 5767 OTUs were identified in S. japonica rhizosphere soil. Among these, 270 OTUs were defined at the genus level and divided into 7 genera and 35 species. Moreover, available nitrogen, soil organic matter, and available calcium content had a coupling effect and positive influence on AMF colonization and Shannon and Chao1 indices. Conversely, available phosphorus, available potassium, and available magnesium negatively affected AMF Shannon and Chao1 indices. Lithology, altitude, pH, and available phosphorus are important factors that affect the dynamics of AMF in the S. japonica rhizosphere.

Effects of soil microbial ecology on ginsenoside accumulation in Panax ginseng across different cultivation years

The quality of ginseng is greatly influenced by ecological factors, especially soil factors. However, there are few reports on the association between the physicochemical properties of ginseng rhizosphere soil, enzyme activity, microbial bacterial community, and ginsenoside content accumulation in ginseng planted at different ages. In order to investigate the relationship between the soil microbial ecology of ginseng and the content of ginsenosides, this study compared the differences in the rhizosphere soil microecological environment and ginsenoside accumulation between ginseng planted for one, two, and three years, using soil without ginseng cultivation as a control. The results showed that monomer saponins Ro, Re, Rf, Rb1, and total ginsenoside content increased significantly (P < 0.05), while monomer saponins Rb2, Rd, Rh2, and Rg3 content decreased significantly in three-year-old ginseng, (P < 0.05). And soil pH, soil bulk weight and soil enzyme activity in ginseng rhizosphere soils altered the abundance and diversity of rhizosphere soil bacterial community. Redundancy analysis and Pearson correlation analysis revealed that soil pH, soil bulk density, soil urease, and protease were the primary factors influencing the bacterial community in the soil around roots of one, two, three years old ginseng. Co-occurrence network visualization analysis indicated that seven bacterial communities, Planctomycetota, Methylomirabilota, Verrucomicrobiota and Acidobacteriota at the phylum level, Vicinamibacterales_unclassified, Vicinamibacteraceae_unclassified and Candidatus_Udaeobacter at the genus level, had a significant effect on the synthesis of ginsenosides. In summary, soil urease, pH, and soil bulk density in agricultural soils can regulate soil physicochemical properties, soil enzymatic activities, and soil bacterial community abundance. These factors are key drivers of the ginseng soil microbial ecology in ginseng cultivation. These studies will provide a scientific basis for subsequent optimization of soil improvement techniques for cultivated ginseng in farmland by improving the soil microbial ecology.

Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing

This study aimed to evaluate the blood bacterial microbiota in healthy and febrile cats. High-quality sequencing reads from the 16S rRNA gene variable region V3-V4 were obtained from genomic blood DNA belonging to 145 healthy cats, and 140 febrile cats. Comparisons between the blood microbiota of healthy and febrile cats revealed dominant presence of Actinobacteria, followed by Firmicutes and Proteobacteria, and a lower relative abundance of Bacteroidetes. Upon lower taxonomic levels, the bacterial composition was significantly different between healthy and febrile cats. The families Faecalibacterium and Kineothrix (Firmicutes), and Phyllobacterium (Proteobacteria) experienced increased abundance in febrile samples. Whereas Thioprofundum (Proteobacteria) demonstrated a significant decrease in abundance in febrile. The bacterial composition and beta diversity within febrile cats was different according to the affected body system (Oral/GI, systemic, skin, and respiratory) at both family and genus levels. Sex and age were not significant factors affecting the blood microbiota of febrile cats nor healthy ones. Age was different between young adult and mature adult healthy cats. Alpha diversity was unaffected by any factors. Overall, the findings suggest that age, health status and nature of disease are significant factors affecting blood microbiota diversity and composition in cats, but sex is not.

Description of a pathogenic strain of Aeromonas dhakensis isolated from Ancherythroculter nigrocauda in an inland region of China.

Aeromonas dhakensis is reported as an emerging pathogenic species within the genus Aeromonas and is widely distributed in tropical coastal areas. This study provided a detailed description and characterization of a strain of A. dhakensis (202108B1) isolated from diseased Ancherythroculter nigrocauda in an inland region of China. Biochemical tests identified the isolate at the genus level, and the further molecular analysis of concatenated housekeeping gene sequences revealed that the strain belonged to the species A. dhakensis. The isolated A. dhakensis strain was resistant to five antibiotics, namely, penicillin, ampicillin, clindamycin, cephalexin and imipenem, while it was susceptible or showed intermediate resistance to most of the other fifteen tested antibiotics. The isolated strain of A. dhakensis caused acute haemorrhagic septicaemia and tissue damage in artificially infected A. nigrocauda, with a median lethal dose of 7.76×104 CFU/fish. The genome size of strain 202108B1 was 5043286 bp, including one chromosome and four plasmids. This is the first detailed report of the occurrence of infection caused by an A. dhakensis strain causing infection in an aquaculture system in inland China, providing important epidemiological data on this potential pathogenic species.

A multi-locus phylogeny for the Diamesinae (Chironomidae: Diptera) provides new insights into evolution of an amphitropical clade

Abstract Diamesinae is a subfamily of Chironomidae, whose species live in cold lotic or oligotrophic lentic habitats with global distribution excepting Antarctica. The cool stenothermic ecology of nearly all diamesines produces a typical amphitropical pattern of absence at tropical latitudes, except at high elevation. Recent attention has focused on the species discovery, while evolutionary relationships at the generic and tribal level have remained inadequately understood. Current classification implies analogous evolutionary diversification in each hemisphere (boreal and austral). To test this concept, we used six genetic markers (18S, 28S, CAD1, COI-5p, COI-3p and COII) and fossil calibrations to produce a well-supported and resolved time-calibrated phylogeny of the subfamily. Austral and boreal diamesines indeed are reciprocally monophyletic lineages, with estimated Jurassic divergence (130-196, 164 Ma). The boreal Protanypodini, previously understood to be a tribe within Diamesinae, is excluded and elevated here to subfamily rank as Protanypodinae stat. nov. Ancestral austral diamesines probably originated in South America and successively reached New Zealand, Australia and South Africa during the Cretaceous-Paleogene. The Holarctic tribes Diamesini and Boreoheptagyiini probably originated in the Eastern Palaearctic with further dispersal/vicariance into the Western Palaearctic, Nearctic, East, and very likely dispersed southwards to montane East Africa and Borneo.

Effects of tefluthrin and guadipyr on the midgut bacteria of adult Apis mellifera

The objective of this study is to assess the potential impact of tefluthrin and guadipyr on the gut microbial composition and metabolism in adult Apis mellifera ligustica, thereby elucidating the underlying mechanisms of insecticide action and its practical implications for bee protection. In this investigation, A. mellifera were subjected to one of three dietary conditions: (1) control sugar water, (2) tefluthrin-infused sugar water, or (3) guadipyr-infused sugar water. After a 10-day exposure period, genomic DNA from the gut bacteria was extracted. High-throughput sequencing was employed to evaluate the potential influence of tefluthrin and guadipyr treatments on the diversity and abundance of gut bacteria. Among the A. mellifera specimens, a total of twenty species of gut bacteria were identified, spanning across five phyla, six classes, eleven orders, eleven families, and fifteen genera. The dominant phyla within the gut bacterial community were Proteobacteria and Bacteroidetes. In comparison to the control group, both the tefluthrin-treated and deltamethrin-treated groups exhibited alterations in the composition of their gut bacterial flora. At the phylum level, there was a significant decrease in the relative abundance of Cyanobacteria (P < 0.05). On the genus level, the tefluthrin group displayed a significant increase in the relative abundance of Bartonella and Serratia (P < 0.05). In the guadipyr-treated group, the relative abundance of Gilliamella and Frischella increased significantly (P < 0.05), while the relative abundance of norank_o_Chloroplast and Enterobacter decreased significantly (P < 0.05). Further analysis of cluster of orthologous genes predicted functional changes in gut microbial metabolism following tefluthrin exposure but no significant changes after guadipyr exposure. Consequently, exposure to tefluthrin and guadipyr can induce shifts in both the composition and metabolic activity of the gut bacteria in A. mellifera. Notably, the impact of tefluthrin on the gut bacteria of A. mellifera appears to be more pronounced compared to that of guadipyr.

A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.

Describing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S rRNA short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina) in 26 HNC tumour tissues. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. We observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.131, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in relative abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (75% vs. 18.8%). FL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing.

Aquatic vegetation mapping with UAS-cameras considering phenotypes

Aquatic vegetation species at the genus level in an oxbow lake were identified in Hungary based on a multispectral Uncrewed Aerial System (UAS) survey within an elongated oxbow lake area of the Tisza River under continental climate. Seven and 13 classes were discriminated using three different classification methods (Support Vector Machine [SVM], Random Forest [RF], and Multivariate Adaptive Regression Splines [MARS]) using different input data in ten combinations: original spectral bands, spectral indices, Digital Surface Model (DSM), and Haralick texture indices. We achieved a high (97.1%) overall accuracies (OAs) by applying the SVM classifier, but the RF performed only <1% worse, as it was represented in the first places of the classification rank before the MARS. The highest classification accuracies (>84% OA) were obtained using the most important variables derived by the Recursive Feature Elimination (RFE) method. The best classification required DSM as an input variable. The poorest classification performance belonged to the model that used only texture indices or spectral indices. On the class level, Stratiotes aloides exhibit the lowest degree of separability compared to the other classes. Accordingly, we recommend using supplementary input data for the classifications besides the original spectral bands, for example, DSM, spectral, and texture indices, as these variables significantly improve the classification accuracies in the proper combinations of the input variables.