The mid-domain effect in flowering phenology.

The timing of flowering is an important driver of species distribution and community assembly patterns. However, we still have much to learn about the factors that shape flowering diversity (i.e.

Evaluating the relative importance of predictors in Generalized Additive Models using the R package.

Generalized Additive Models (GAMs) are widely employed in ecological research, serving as a powerful tool for ecologists to explore complex nonlinear relationships between a response variable and predictors. Nevertheless, evaluating the relative importance of predictors with concurvity (analogous to collinearity) on response variables in GAMs remains a challenge. To address this challenge, we developed an R package named .

The evolutionary adaptation of wood-decay macrofungi to host gymnosperms differs from that to host angiosperms.

Wood-decay macrofungi play a vital role in forest ecosystems by promoting nutrient cycling and soil structure, and their evolution is closely related to their host plants. This study investigates the potential evolutionary adaptation of wood-decay macrofungi to their host plants, focusing on whether these relationships differ between gymnosperms and angiosperms. While previous research has suggested non-random associations between specific fungi and plant deadwood, direct evidence of evolutionary adaptation has been lacking.

Preparation of bacterial fertilizer from biogas residue after anaerobic co-digestion of kitchen waste and residual sludge.

Azotobacter chroococcum and Bacillus subtilis were selected as fermentation strains, and biogas residue after anaerobic digestion of kitchen waste and residual sludge was used as fermentation substrate. A single factor optimization test was used to optimize the solid-state fermentation parameters of biogas residue with the number of viable bacteria and the number of spores as indexes. The results showed that the optimum inoculation conditions involved the following: 55% initial moisture content, 15% initial inoculation amount, 30 ℃, and 1:1 initial inoculation ratio for 13 days.

 (Aspleniaceae), a distinct new fern species from northern Guangdong, China, based on morphological data and molecular phylogeny.

A new spleenwort species, , was found and described from Danxia landform region in Guangdong, China. The new species has close resemblance to Ching ex S.H.

Transmission characteristics in Tuberculosis by WGS: nationwide cross-sectional surveillance in China.

China, with the third largest share of global tuberculosis cases, faces a substantial challenge in its healthcare system as a result of the high burden of multidrug-resistant and rifampicin-resistant tuberculosis (MDR/RR-TB). This study employs a genomic epidemiological approach to assess recent tuberculosis transmissions between individuals, identifying potential risk factors and discerning the role of transmitted resistant isolates in the emergence of drug-resistant tuberculosis in China. We conducted a population-based retrospective study on 5052 (MTB) isolates from 70 surveillance sites using whole genome sequencing (WGS).

Endemic medicinal plant distribution correlated with stable climate, precipitation, and cultural diversity.

Medicinal plants provide crucial ecosystem services, especially in developing countries such as China, which harbors diverse endemic medicinal plant species with substantial cultural and economic value. Accordingly, understanding the patterns and drivers of medicinal plant distribution is critical. However, few studies have investigated the patterns and drivers of endemic medicinal plants distribution in China.

Geographical patterns and determinants in plant reproductive phenology duration.

Biodiversity is and always has been an important issue in ecological research. Biodiversity can reflect niche partitioning among species at several spatial and temporal scales and is generally highest in the tropics. One theory to explain it is that low-latitude tropical ecosystems are dominated by species that are generally only distributed over a narrow area.

Engineering Outer Membrane Vesicles to Increase Extracellular Electron Transfer of .

Outer membrane vesicles (OMVs) of Gram-negative bacteria play an essential role in cellular physiology. The underlying regulatory mechanism of OMV formation and its impact on extracellular electron transfer (EET) in the model exoelectrogen MR-1 remain unclear and have not been reported. To explore the regulatory mechanism of OMV formation, we used the CRISPR-dCas9 gene repression technology to reduce the crosslink between the peptidoglycan (PG) layer and the outer membrane, thus promoting the OMV formation.

Improved targeting of the 16S rDNA nanopore sequencing method enables rapid pathogen identification in bacterial pneumonia in children.

Objectives: To develop a rapid and low-cost method for 16S rDNA nanopore sequencing.

Methods: This was a prospective study on a 16S rDNA nanopore sequencing method. We developed this nanopore barcoding 16S sequencing method by adding barcodes to the 16S primer to reduce the reagent cost and simplify the experimental procedure.

Corrigendum: Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing.

[This corrects the article DOI: 10.3389/fmicb.2022.

Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing.

Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy.

Soil nutrients and plant diversity affect ectomycorrhizal fungal community structure and functional traits across three subalpine coniferous forests.

The symbiotic relationship between ectomycorrhizal fungi (EMF) and the roots of host plants is significantly important in regulating the health and stability of ecosystems, especially of those such as the climate warming affected subalpine forest ecosystems. Therefore, from the coniferous forest systems located in the Southern Qinghai-Tibetan Plateau, root tips from three forest tree species: , , were collected to look for the local causes of EMF community composition and diversity patterns. The EMF colonization rate, diversity and taxonomic community structure were determined by morphotyping and sanger sequencing of the fungal ITS gene from the root tip samples.

Inorganic Nitrogen-Containing Aerosol Deposition Caused "Excessive Photosynthesis" of Herbs, Resulting in Increased Nitrogen Demand.

The amount of atmospheric nitrogen-containing aerosols has increased dramatically due to the globally rising levels of nitrogen from fertilization and atmospheric deposition. Although the balance of carbon and nitrogen in plants is a crucial component of physiological and biochemical indexes and plays a key role in adaptive regulation, our understanding of how nitrogen-containing aerosols affect this remains limited; in particular, regarding the associated mechanisms. Using a fumigation particle generator, we generated ammonium nitrate solution (in four concentrations of 0, 15, 30, 60 kg N hm year) into droplets, in 90% of which the diameters were less than 2.

Nanopore sequencing technology and its application in plant virus diagnostics.

Plant viruses threaten crop yield and quality; thus, efficient and accurate pathogen diagnostics are critical for crop disease management and control. Recent advances in sequencing technology have revolutionized plant virus research. Metagenomics sequencing technology, represented by next-generation sequencing (NGS), has greatly enhanced the development of virus diagnostics research because of its high sensitivity, high throughput and non-sequence dependence.

Extensive sharing of chloroplast haplotypes among East Asian Cerris oaks: The imprints of shared ancestral polymorphism and introgression.

Shared ancestral polymorphism and introgression are two main causes of chloroplast DNA (cpDNA) haplotype sharing among closely related angiosperms. In this study, we explored the roles of these two processes in shaping the phylogeographic patterns of East Asian Cerris oaks by examining the geographic distributions of randomly and locally distributed shared haplotypes, which coincide with the expectations of shared ancestry and introgression, respectively. We sequenced 1340 bp of non-coding cpDNA from ( = 418) and ( = 183) and compiled previously published sequence data of ( = 439).

Identification of the first case of Penicillium marneffei infection in Shaanxi province by nanopore sequencing.

Introduction: Penicillium marneffei is one of the most common opportunistic infectious fungi associated with AIDS (Acquired Immunodeficiency Syndrome). It is prevalent in Southeast Asia and southern China (such as Guangdong), but rare in inland provinces of China. Penicillium marneffei infections are often misdiagnosed.

Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a pandemic and is threatening human health globally. The rapid genome sequencing and bioinformatic analysis of SARS-CoV-2 have become a helpful tool in the battle against the COVID-19. Here, we report the genetic characteristics, variations and phylogenetic analysis of SARS-CoV-2 sequenced from 42 clinical specimens.

Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships.

Background: Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships.

Results: We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes.

Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China.

Background And Aims: Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa.

Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation.

The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies. However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China.

Long-Term Nitrogen Deposition Alters Ectomycorrhizal Community Composition and Function in a Poplar Plantation.

The continuous upsurge in soil nitrogen (N) enrichment has had strong impacts on the structure and function of ecosystems. Elucidating how plant ectomycorrhizal fungi (EMF) mutualists respond to this additional N will facilitate the rapid development and implementation of more broadly applicable management and remediation strategies. For this study, we investigated the responses of EMF communities to increased N, and how other abiotic environmental factors impacted them.