Complete Genome Sequence of Pythium oligandrum, Isolated from Rhizosphere Soils of Chinese Angelica sinensis.

Most of the Pythium species are pathogenic to a wide range of economically important crops and, sometimes, can even cause diseases in animals and humans. An exception is that the soil-inhabiting P. oligandrum is an effective biocontrol agent against a diverse suite of pathogens and promotes plant growth. In this work, we sequenced the whole genome of P. oligandrum PO-1, isolated from rhizosphere soils of Chinese Angelica sinensis, using a combination of long-read single-molecule real-time sequencing technology (Pacific Biosciences [PacBio]) and Illumina sequencing. The 2.5-Gb and 5.2-Gb bases were generated respectively. The sequencing depths were 93× with PacBio and 145× with Illumina sequencing. With the PacBio sequencing results further corrected by Illumina sequencing, the genome was assembled into 71 scaffolds with a total size of 39.10 Mb (N50 = 1.45 Mb; L50 = 9)and the longest scaffold is 3.49 Mb. Genome annotation identifies 15,632 protein-coding genes and 0.47 Mb of transposable elements. Our genomic assembly and annotation have been greatly improved compared with the already released three genomes of P. oligandrum. This genomic data will provide valuable information to understand the mechanism underlying its biocontrol potentials and will also facilitate the dissection of genome evolution and environmental adaptation within the genus Pythium. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Hybrid Genome Assembly and Gene Repertoire of the Root Endophyte Clitopilus hobsonii QYL-10 (Entolomataceae, Agaricales, Basidiomycetes).

Clitopilus hobsonii (Entolomataceae, Agaricales, Basidiomycetes) is a common soil saprotroph. There is also evidence that C. hobsonii can act as a root endophyte benefitting tree growth. Here, we report the genome assembly of C. hobsonii QYL-10, isolated from ectomycorrhizal root tips of Quercus lyrata. The genome size is 36.93 Mb, consisting of 13 contigs (N50 = 3.3 Mb) with 49.2% GC content. Of them, 10 contigs approached the length of intact chromosomes, and three had telomeres at one end only. BUSCO analysis reported a completeness score of 98.4%, using Basidiomycota_odb10 lineage data. Combining ab-initio, RNA-seq data, and homology-based predictions, we identified 12,710 protein-coding genes. Approximately, 1.43 Mb of transposable elements (3.88% of the assembly), 36 secondary metabolite biosynthetic gene clusters, and 361 genes encoding putative carbohydrate-active enzymes were identified. This genomic resource will allow functional studies aimed to characterize the symbiotic interactions between C. hobsonii and its host trees and will also provide a valuable foundation for further research on comparative genomics of the Entolomataceae.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The Chromosome-Scale Genome Resource for Two Endophytic Fusarium species, F. culmorum and F. pseudograminearum.

Genus Fusarium (Ascomycota, Hypocreales, Nectriaceae) includes many economically important plant pathogens that cause devastating diseases of a wide range of crops and trees. Interestingly, there is increasing evidence that some Fusarium species also live as endophytes and benefit plant growth and stress tolerance. In this work, we sequence the whole genomes of endophytic F. culmorum and F. pseudograminearum, isolated from a coastal dunegrass (Leymus mollis), using long-read single-molecule real-time sequencing technology. Their genomes are assembled into four chromosomes and a mitochondrial genome with a total assembly size of 40.05 and 42.90 M, respectively. This resource should not only facilitate functional studies designed to better understand what makes the two Fusarium species such successful plant-beneficial fungi but should also reveal their genome evolution and adaptation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Facultative symbiosis with a saprotrophic soil fungus promotes potassium uptake in American sweetgum trees.

Several species of soil free-living saprotrophs can sometimes establish biotrophic symbiosis with plants, but the basic biology of this association remains largely unknown. Here, we investigate the symbiotic interaction between a common soil saprotroph, Clitopilus hobsonii (Agaricomycetes), and the American sweetgum (Liquidambar styraciflua). The colonized root cortical cells were found to contain numerous microsclerotia-like structures. Fungal colonization led to increased plant growth and facilitated potassium uptake, particularly under potassium limitation (0.05 mM K+ ). The expression of plant genes related to potassium uptake was not altered by the symbiosis, but colonized roots contained the transcripts of three fungal genes with homology to K+ transporters (ACU and HAK) and channel (SKC). Heterologously expressed ChACU and ChSKC restored the growth of a yeast K+ -uptake-defective mutant. Upregulation of ChACU transcript under low K+ conditions (0 and 0.05 mM K+ ) compared to control (5 mM K+ ) was demonstrated in planta and in vitro. Colonized plants displayed a larger accumulation of soluble sugars under 0.05 mM K+ than non-colonized plants. The present study suggests reciprocal benefits of this novel tree-fungus symbiosis under potassium limitation mainly through an exchange of additional carbon and potassium between both partners.

Monolithic integrated cyclic 64-channel AWG with MZI filters and arrayed vertical reflecting mirrors for WDM-PON application.

The paper introduces a silica-on-silicon monolithic integrated cyclic arrayed waveguide grating (AWG) with Mach-Zehnder interference (MZI) filters and arrayed vertical reflecting mirrors in silicon to realize effective and stable optical transmission between waveguides and photodiodes. The cyclic AWG acts as both multiplexer over the L-band for upstream traffic and demultiplexer over the C-band for downstream traffic. The integrated chip, including AWG, MZI filters, and arrayed reflecting mirrors, has been made successfully with a 6.0 dB insertion loss, which is less than the discrete devices. At the same time, the arrayed reflecting mirrors are more stable than separate reflectors.

Integrated athermal arrayed-waveguide grating multiplexer and demultiplexer with all-metal compensating rod for broadband temperature application.

In this paper, a unique device that can act as both multiplexer and demultiplexer is proposed with two all-metal compensating rods that makes the compensated chip almost the same spectrum profile as the original one. In this way a flat-top athermal arrayed-waveguide grating module of 100-GHz×40-ch is successfully fabricated. A small center wavelength shift of ±25 pm is achieved for the ultra-wide temperature range from -40°C to 85°C with the low insertion loss change of less than ±0.14 dB.

Microwave photonic bandstop filter with wide tunability and adjustable bandwidth.

A microwave photonic bandstop filter is proposed and experimentally demonstrated in this work. The filter exhibits promising performance combination of reconfigurability, frequency tunability, and bandwidth adjustment. The phase modulation on two orthogonal polarization states produces a bandpass and a lowpass MPF, respectively. The key concept of destructive interference between the bandpass and lowpass MPF enables the reconfiguration of MPF from bandpass to bandstop. By adjusting the wavelength of two orthogonally polarized optical carriers and the bandwidth of an optical bandpass filter, the bandstop filter is tunable in terms of center frequency and bandwidth.

Endophytic Diaporthe from Southeast China are genetically diverse based on multi-locus phylogeny analyses.

Species of Diaporthe (anamorph Phomopsis) comprise a diverse and widely distributed group of phytopathogens, saprophytes and endophytes. However, the degree of genetic diversity of endophytic Diaporthe has not yet been fully investigated. In this paper, a survey of endophytes from 28 plants in southeast China yielded 116 Diaporthe isolates, out of which 64 haplotypes were determined using DnaSP ver. 5.1 based on alignment result of internal transcribed spacer of ribosomal nucleotide sequences (ITS rDNA). Many haplotypes turned out to be quite different from known species and displayed high diversity. Among them, 14 strains from 5 discriminating terminal clades were selected to go through further analysis according to partial sequence of translation elongation factor 1-α (tef1-α) and again they got separated from others. The following multi-gene phylogenetic analysis based on ITS rDNA, tef1-α, ß tubulin and calmodulin grouped eight most discrepant strains into three distinctive clusters, cluster 1 (Rc001, Eu004 and Eu009), cluster 2 (ZJWCF252, Sjm001 and Ac001) and cluster 3 (Pcs013 and Sfp005) respectively with high support values. These clusters above represent three potentially novel species. This research provides strong evidence of high biodiversity and novelty of Diaporthe endophytes from southeast China, which is thus important not only for better resolving the taxonomy in this genus, but also for further utilization due to their multiple application.

Phosphorus/nitrogen sensing and signaling in diverse root-fungus symbioses.

Establishing mutualistic relationships between plants and fungi is crucial for overcoming nutrient deficiencies in plants. This review highlights the intricate nutrient sensing and uptake mechanisms used by plants in response to phosphate and nitrogen starvation, as well as their interactions with plant immunity. The coordination of transport systems in both host plants and fungal partners ensures efficient nutrient uptake and assimilation, contributing to the long-term maintenance of these mutualistic associations. It is also essential to understand the distinct responses of fungal partners to external nutrient levels and forms, as they significantly impact the outcomes of symbiotic interactions. Our review also highlights the importance of evolutionarily younger and newly discovered root-fungus associations, such as endophytic associations, which offer potential benefits for improving plant nutrition. Mechanistic insights into the complex dynamics of phosphorus and nitrogen sensing within diverse root-fungus associations can facilitate the identification of molecular targets for engineering symbiotic systems and developing plant phenotypes with enhanced nutrient use efficiency. Ultimately, this knowledge can inform tailored fertilizer management practices to optimize plant nutrition.

A new magnetic resonance imaging-based PUMCH classification system for congenital cervical malformations: devising a standardised diagnosis pathway.

OBJECTIVES: To develop an innovative magnetic resonance imaging (MRI)-based PUMCH (Peking Union Medical College Hospital) classification system aimed at standardising the diagnosis of congenital cervical malformations (CCMs) by identifying their distinctive MRI features. METHODS: Seventy-nine consecutive patients with CCM underwent pre-treatment pelvic MRI; three experienced gynaecological radiologists retrospectively analysed these images. Qualitative assessments included Rock et al's classification; PUMCH classification; haematometra; cervical signal features; ovarian endometriosis; haematosalpinx; and uterine, vaginal, urinary, and musculoskeletal malformations. Quantitative assessments involved the uterine volume, sagittal cervical length, and maximum ovarian cross-sectional area. The surgical treatment types were also recorded. Statistical methods were used to incorporate differences in clinical features and surgical methods into our classification. RESULTS: Morphologically, CCMs were categorised into three types: type I (53%) was characterised by the presence of a cervix with visible cervical canals; type II (23%) featured an existing cervix with concealed cervical canals; and type III (24%) indicated cervical aplasia, which involves a blind end in the lower part of the uterine corpus. Haematometra was significantly more prevalent in patients with type I CCM than in those with type II (p < 0.001). There were three cervical signal patterns: no signal (27%), no evident layer differentiation (21%), and multi-layer differentiation with haematocele (52%). Most patients (94%) had complete vaginal atresia. Type I CCM patients had a higher likelihood of regaining normal uterovaginal anatomy compared to types II and III. CONCLUSIONS: Our proposed PUMCH classification system has a high potential for enhancing the efficiency of clinical diagnosis among patients with CCM. CRITICAL RELEVANCE STATEMENT: The proposed new PUMCH classification promised to elevate the conventional diagnostic trajectory for congenital cervical malformations, offering a valuable framework to refine the selection and planning of surgical interventions, thereby enhancing overall clinical efficacy. KEY POINTS: Effective classification of congenital cervical malformations is desirable to optimise the diagnostic process. We presented a PUMCH classification of congenital cervical malformations using pelvic MRI. The new classification significantly aids clinical triage for congenital cervical malformations.

Intraspecific diploidization of a halophyte root fungus drives heterosis.

How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.

Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte.

Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a âˆ¼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.

Differed biotic interactions influenced by anthropogenic disturbances among trophic levels in fragmented wetlands.

Environmental changes derived from various human activities have largely disturbed the structure and functioning of various biological communities. However, little is known on how such disturbance impacts species interactions in biological communities. This study aims to elucidate the variation of species interactions across multiple trophic levels and further determine crucial factor(s) in regulating observed variation. We collected plankton samples from Sanjiang Wetlands in Northeastern China and used random matrix theory (MRT)-based approach to construct species interaction networks for bacterioplanktons, protozoans, and metazoans, respectively. We found that biotic interactions were more complex at lower trophic levels. Network key species (e.g., module hubs and connectors) were detected only in the bacterioplankton network. More inter- and intra-module connections, particularly negative connections, were detected in the bacterioplankton network. Across all three trophic levels, the element sodium (Na) was the most important factor influencing the network structure, while at each trophic level, physicochemical factors, nutrients, and organic pollutants were identified as crucial determinants but their relative importance differed. In particular, no correlation was detected between the metazoan network and any environmental factor. After separating protozoan and metazoan communities into subgroups in relatively poor and good water environments, we found community interaction networks were more complex in good conditions than in poor conditions. A simple network structure (e.g., no inter-module connectors or intra-module hubs, and less competitive links) and less association with environmental factors in the higher trophic levels clearly illustrate that metazoan and protozoan communities in the fragmented wetlands are unstable and vulnerable. Therefore, further environmental changes may greatly influence species interactions in these communities. Collectively, our findings provide new insights into dynamics of influence of environmental changes on biotic interactions in aquatic biological communities, highlighting the necessity to use a multi-trophic strategy when assessing negative effects of environmental changes in aquatic ecosystems.

Long non-coding RNA NNT-AS1 positively regulates NPM1 expression to affect the proliferation of estrogen-mediated endometrial carcinoma by interacting.

Objective: This study aims to investigate the mechanism of long non-coding RNA NNT-AS1 in the proliferation of estrogen-mediated endometrial carcinoma (EC). Materials and methods: NNT-AS1, miR-30c, and Nucleophosmin 1 (NPM1) expressions were measured by quantitative real-time PCR and Western blotting. Cell Counting Kit-8 assay and 5-Ethynyl-2'-deoxyuridine (EdU) assay were used to detect the viability and proliferation of Ishikawa and HEC-1-A cells, respectively. RNA immunoprecipitation assay was used to confirm the interaction between NNT-AS1 and miR-30c. Luciferase reporter assay was performed to confirm the interaction between miR-30c and NPM1. Results: NNT-AS1 and NPM1 expressions in EC tissues and cell lines were higher than in benign endometrium and normal endometrial epithelial cells (EECs). miR-30c expression in EC tissues and cell lines was lower than in benign endometrium and normal EECs. NNT-AS1 interacted with miR-30c, and miR-30c negatively regulated NPM1 expression. Overexpression of NNT-AS1 increased NPM1 expression in EC cells, while overexpression of miR-30c reversed the effect. NNT-AS1 interference inhibited the mRNA level of NPM1, while the miR-30c inhibitor reversed the result. Estradiol (E2) promoted the proliferation of EC cells, small interfering RNA (siRNA) against NNT-AS1 inhibited EC cell proliferation, miR-30c inhibitor promoted cell proliferation, and NPM1 siRNA inhibited cell proliferation. E2 increased tumor volume, and NNT-AS1 interference reduced tumor volume in vivo. Conclusion: NNT-AS1 promoted the proliferation of estrogen-mediated EC by regulating miR-30c/NPM1.

A facultative ectomycorrhizal association is triggered by organic nitrogen.

Increasing nitrogen (N) deposition often tends to negatively impact the functions of belowground ectomycorrhizal networks, although the exact molecular mechanisms underlying this trait are still unclear. Here, we assess how the root-associated fungus Clitopilus hobsonii establishes an ectomycorrhiza-like association with its host tree Populus tomentosa and how this interaction is favored by organic N over mineral N. The establishment of a functional symbiosis in the presence of organic N promotes plant growth and the transfer of 15N from the fungus to above ground plant tissues. Genomic traits and in planta transcriptional signatures suggest that C. hobsonii may have a dual lifestyle with saprotrophic and mutualistic traits. For example, several genes involved in the digestion of cellulose and hemicellulose are highly expressed during the interaction, whereas the expression of multiple copies of pectin-digesting genes is tightly controlled. Conversely, the nutritional mutualism is dampened in the presence of ammonium (NH4+) or nitrate (NO3-). Increasing levels of NH4+ led to a higher expression of pectin-digesting genes and a continuous increase in hydrogen peroxide production in roots, whereas the presence of NO3- resulted in toxin production. In summary, our results suggest that C. hobsonii is a facultative ectomycorrhizal fungus. Access to various forms of N acts as an on/off switch for mutualism caused by large-scale fungal physiological remodeling. Furthermore, the abundance of pectin-degrading enzymes with distinct expression patterns during functional divergence after exposure to NH4+ or organic N is likely to be central to the transition from parasitism to mutualism.

Case report: Two PD-L1 positive unresectable advanced pancreatic carcinoma patients with microsatellite stability achieved R0 resection after PD-1 antibody plus chemotherapy as a successful downstaging therapy: A report of two cases.

Background: Nonobvious early symptoms are a prominent characteristic of pancreatic cancer, resulting in only 20% of patients having resectable tumors at the time of diagnosis. The optimal management of unresectable advanced pancreatic cancer (UAPC) remains an open research question. In this study, the tumors shrank significantly after PD-1 antibody combined with chemotherapy in two UAPC patients, and both have achieved R0 (pathologically negative margin) resection and survival to date. Case presentation: Case 1: A 53-year-old man was diagnosed with pancreatic adenocarcinoma (Stage III). He received six cycles of PD-1 antibody plus chemotherapy as the first-line treatment. The tumor was reduced from 11.8×8.8 cm to "0" (the pancreatic head was normal as shown by enhanced computed tomography, ECT) after preoperative neoadjuvant therapy (PNT) and the adverse effects were tolerable. The patient underwent radical surgery and achieved R0 resection. Case 2: A 43-year-old man diagnosed with pancreatic adenocarcinoma with liver metastasis (Stage IV) received three cycles of PD-1 antibody combined with chemotherapy. The tumor was reduced from 5.2×3.9 cm to 2.4×2.3 cm with no side effects. The patient also underwent radical surgery and achieved R0 resection. Conclusion: PD-1 antibody plus a chemotherapy regimen resulted in a surprising curative effect and safety in two patients with UAPC, which may portend an improvement in pancreatic carcinoma treatment. We may have a way for UAPC patients to obtain radical treatment and gain long-term survival. Two PD-L1 positive UAPC patients with microsatellite stability (MSS) enlighten us to have a more comprehensive understanding of the prediction of immunotherapy.

Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism.

Comparative and pan-genomic analyses of the endophytic fungus Pezicula neosporulosa (Helotiales, Ascomycota) from needles of the relict fir, Abies beshanzuensis, showed expansions of carbohydrate metabolism and secondary metabolite biosynthetic genes characteristic for unrelated plant-beneficial helotialean, such as dark septate endophytes and ericoid mycorrhizal fungi. The current species within the relatively young Pliocene genus Pezicula are predominantly saprotrophic, while P. neosporulosa lacks such features. To understand the genomic background of this putatively convergent evolution, we performed population analyses of 77 P. neosporulosa isolates. This revealed a mosaic structure of a dozen non-recombining and highly genetically polymorphic subpopulations with a unique mating system structure. We found that one idiomorph of a probably duplicated mat1-2 gene was found in putatively heterothallic isolates, while the other co-occurred with mat1-1 locus suggesting homothallic reproduction for these strains. Moreover, 24 and 81 genes implicated in plant cell-wall degradation and secondary metabolite biosynthesis, respectively, showed signatures of the balancing selection. These findings highlight the evolutionary pattern of the two gene families for allowing the fungus a rapid adaptation towards endophytism and facilitating diverse symbiotic interactions.

Near-Chromosome-Level Genome Assembly of the Dark Septate Endophyte Laburnicola rhizohalophila: A Model for Investigating Root-Fungus Symbiosis.

The novel DSE Laburnicola rhizohalophila (Pleosporales, Ascomycota) is frequently found in the halophytic seepweed (Suaeda salsa). In this article, we report a near-chromosome-level hybrid assembly of this fungus using a combination of short-read Illumina data to polish assemblies generated from long-read Nanopore data. The reference genome for L. rhizohalophila was assembled into 26 scaffolds with a total length of 64.0 Mb and a N50 length of 3.15 Mb. Of them, 17 scaffolds approached the length of intact chromosomes, and 5 had telomeres at one end only. A total of 10,891 gene models were predicted. Intriguingly, 27.5 Mb of repeat sequences that accounted for 42.97% of the genome was identified, and long terminal repeat retrotransposons were the most frequent known transposable elements, indicating that transposable element proliferation contributes to its increased genome size. BUSCO analyses using the Fungi_odb10 data set showed that 95.0% of genes were complete. In addition, 292 carbohydrate active enzymes, 33 secondary metabolite clusters, and 84 putative effectors were identified in silico. The resulting high-quality assembly and genome features are not only an important resource for further research on understanding the mechanism of root-fungi symbiotic interactions but will also contribute to comparative analyses of genome biology and evolution within Pleosporalean species.

Soil microbiome-mediated salinity tolerance in poplar plantlets is source-dependent.

Soil salinization is a global environmental problem and one of the most common land degradation processes. To effectively utilize saline lands, it is crucial to improve plant growth and stress tolerance, particularly through the microbiome intervention strategy. However, less is known about the interactions of microbes with trees than those with crops or herbaceous plants. Here, we examined how natural soil microbes affected the performance of salt-sensitive Populus deltoides × P. euramericana 'Nanlin895' (NL895) under salt stress. Gnotobiotic NL895 plantlets were inoculated with soil microbiome extracted from no-salt (NS; soluble salt: 0.71 g/kg), low-salt (LS; 5.14 g/kg), and high-salt (HS; 23.07 g/kg) lands, and then exposed to salt treatments. Compared to control, 33.8%, 18.0%, and 29.9% of the aboveground biomass was increased by NS, LS, and HS inoculation, respectively. The salt injury index was lower in LS and HS than in NS treatments. Rhizosphere microbial communities of all treatments were taxonomically and functionally different across multiple stages, while the variation extent was larger in bacterial than in fungal communities. FUNGuild and PICRUSt2 analysis demonstrated the changes of fungal trophic modes and bacterial metabolic pathways, respectively. In summary, our findings revealed the stronger potential of NS than LS and HS inoculants in growth promotion, while weaker strength than LS and HS inoculants in enhancing salt tolerance of NL895 plantlets. This source-dependent effect should be considered in future microbiome engineering, aiming at harnessing soil microbes to create predictable plant phenotypes.

Phylogenetic Relationships, Speciation, and Origin of Armillaria in the Northern Hemisphere: A Lesson Based on rRNA and Elongation Factor 1-Alpha.

Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56-33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence.