TOR-mediated Ypt1 phosphorylation regulates autophagy initiation complex assembly.

The regulation of autophagy initiation is a key step in autophagosome biogenesis. However, our understanding of the molecular mechanisms underlying the stepwise assembly of ATG proteins during this process remains incomplete. The Rab GTPase Ypt1/Rab1 is recognized as an essential autophagy regulator. Here, we identify Atg23 and Atg17 as binding partners of Ypt1, with their direct interaction proving crucial for the stepwise assembly of autophagy initiation complexes. Disruption of Ypt1-Atg23 binding results in significantly reduced Atg9 interactions with Atg11, Atg13, and Atg17, thus preventing the recruitment of Atg9 vesicles to the phagophore assembly site (PAS). Likewise, Ypt1-Atg17 binding contributes to the PAS recruitment of Ypt1 and Atg1. Importantly, we found that Ypt1 is phosphorylated by TOR at the Ser174 residue. Converting this residue to alanine blocks Ypt1 phosphorylation by TOR and enhances autophagy. Conversely, the Ypt1S174D phosphorylation mimic impairs both PAS recruitment and activation of Atg1, thus inhibiting subsequent autophagy. Thus, we propose TOR-mediated Ypt1 as a multifunctional assembly factor that controls autophagy initiation via its regulation of the stepwise assembly of ATG proteins.

Two distinct regulatory pathways govern Cct2-Atg8 binding in the process of solid aggrephagy.

CCT2 serves as an aggrephagy receptor that plays a crucial role in the clearance of solid aggregates, yet the underlying molecular mechanisms by which CCT2 regulates solid aggrephagy are not fully understood. Here we report that the binding of Cct2 to Atg8 is governed by two distinct regulatory mechanisms: Atg1-mediated Cct2 phosphorylation and the interaction between Cct2 and Atg11. Atg1 phosphorylates Cct2 at Ser412 and Ser470, and disruption of these phosphorylation sites impairs solid aggrephagy by hindering Cct2-Atg8 binding. Additionally, we observe that Atg11, an adaptor protein involved in selective autophagy, directly associates with Cct2 through its CC4 domain. Deficiency in this interaction significantly weakens the association of Cct2 with Atg8. The requirement of Atg1-mediated Cct2 phosphorylation and of Atg11 for CCT2-LC3C binding and subsequent aggrephagy is conserved in mammalian cells. These findings provide insights into the crucial roles of Atg1-mediated Cct2 phosphorylation and Atg11-Cct2 binding as key mediators governing the interaction between Cct2 and Atg8 during the process of solid aggrephagy.

Mec1 regulates PAS recruitment of Atg13 via direct binding with Atg13 during glucose starvation-induced autophagy.

Mec1 is a DNA damage sensor, which performs an essential role in the DNA damage response pathway and glucose starvation-induced autophagy. However, the functions of Mec1 in autophagy remain unclear. In response to glucose starvation, Mec1 forms puncta, which are recruited to mitochondria through the adaptor protein Ggc1. Here, we show that Mec1 puncta also contact the phagophore assembly site (PAS) via direct binding with Atg13. Functional analysis of the Atg13-Mec1 interaction revealed two previously unrecognized protein regions, the Mec1-Binding Region (MBR) on Atg13 and the Atg13-Binding Region (ABR) on Mec1, which mediate their mutual association under glucose starvation conditions. Disruption of the MBR or ABR impairs the recruitment of Mec1 puncta and Atg13 to the PAS, consequently blocking glucose starvation-induced autophagy. Additionally, the MBR and ABR regions are also crucial for DNA damage-induced autophagy. We thus propose that Mec1 regulates glucose starvation-induced autophagy by controlling Atg13 recruitment to the PAS.

A selective colorimetric and efficient removal strategy for mercury(II) in aquatic systems using mesoporous Fe3O4-loaded silver probes.

Mesoporous Fe3O4-loaded silver nanocomposites (Fe3O4@Ag) were simply fabricated as bi-functional nanozymes for the catalysis-based detection and removal of Hg2+ ions. It was found that the as-prepared magnetic Fe3O4@Ag could display peroxidase-like catalysis activity that could be rationally enhanced in the presence of Hg2+ ions. To our surprise, the shell of the Ag element may decrease the catalysis of the Fe3O4 to some degree. However, the Ag particles could serve as the probes for specifically recognizing Hg2+ ions and trigger increased catalysis through the formation of Ag-Hg alloys, with a decreased signal background. A high-throughput colorimetric analytical method was thereby developed based on the Fe3O4@Ag catalysis for probing Hg2+ ions in the muscles of fish by using 96-well plates, at linear Hg2+ concentrations ranging from 0.010 to 2.5 mg kg-1. Moreover, the developed colorimetric analytical method was applied to evaluate Hg2+ levels in muscle samples of different kinds of fish. Unexpectedly, an obvious difference of Hg2+ levels in muscles of four kinds of fish was discovered, with the order of snakehead (Ophicephalus argus) > largemouth bass (Micropterus salmoides) > crucian carp (Carassius auratus) > silver carp (Hypophthalmichthys molitrix), where the carnivorous fish showed higher Hg2+ levels than the omnivorous or plant-based ones. Moreover, the as-fabricated Fe3O4@Ag adsorbents with their large specific surface area and high environmental robustness could exhibit efficient Hg2+ adsorption with capacities of up to 397.60 mg g-1. A removal efficiency of 99.40% can also be expected for Hg2+ ions from wastewater, with the magnet-aided recycling of Fe3O4@Ag adsorbents. Such an Fe3O4@Ag-based colorimetric analysis and removal strategy for Hg2+ ions should find wide applications in the fields of aquatic food safety, environmental monitoring, and clinical diagnostics of Hg-poisoning diseases.

First worldwide report of Exserohilum rostratum causing leaf spot on strawberry (Fragaria × ananassa Duch.).

During April 2022, leaf spot was observed on strawberry (Fragaria × ananassa Duch.) with a disease incidence of approximately 45% among 100 plants. Strawberry was cultivated in a nursery at Huzhou University (30.87゜N, 120.13゜E), Zhejiang Province, China. In the strawberry greenhouse, the average temperature was 15-18 degrees, 40%-60% humidity. Early symptoms appeared as dark brown or black spotted necrotic lesions, which expanded from 2 to 6 mm in diameter. Dark brown spots with yellow halos occupied half of the leaf area and eventually developed leaf blight with large yellow halos. To isolate the causal agent, 0.5 cm x 0.5 cm fragments were cut from three symptomatic leaves, and were surface sterilized with 75% ethanol for 30 s and then rinsed three times with sterilized water. The airdried leaf fragments were placed on PDA with 50 µg/ml ampicillin and incubated in the dark at 25℃ for two days. Isolates were obtained by transferring hyphal plugs of 1 mm in diameter onto PDA. The colony morphology was circular and dark brown on the upperside and black on the underside, with cottony mycelium and an large amount of gray aerial mycelium. Conidia were large, light olive-brown to dark olive-brown and light olive-black and septate. The typical conidia were oval or rod-shaped, rarely curved, and dark septa defined the basal and apical cells. In the two typical forms of conidia, the average size of oval conidia was approximately 18.77 × 54.92 µm (11.99 to 26.97 × 35.13 to 74.59 µm, n = 20), and the average size of the rod-shaped conidia was approximately 14.80 × 103.24 µm (11.24 to 24.64 × 73.11 to 131.51 µm, n = 20). The morphological characteristics matched well with previous descriptions of Exserohilum rostratum (Sharma et al. 2014; Liu et al. 2021). The identity of C1-L and C1-S from symptomatic tissues was confirmed by means of multi-locus gene sequencing. Genomic DNA was extracted from the mycelium using the CTAB (cetyltrimethylammonium bromide) method (Griffith & Shaw 1998). Molecular identification was conducted by sequencing the internal transcribed spacer (ITS) rDNA region, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, partial actin (ACT) gene, and partial beta-tubulin 2 (TUB2), using the primers ITS1/ITS4 (White et al. 1990), GDF/GDR (Templeton et al. 1992), ACT512F/ACT783R (Carbone and Kohn 1999), T1 (O'Donnell and Cigelnik 1997) and Bt2b (Glass and Donaldson, 1995). The obtained sequences of C1-L and C1-S were the same. Moreover, the sequences have been deposited in GenBank under accession numbers ON982516 (ITS), ON996915 (GAPDH), ON996916 (ACT), and ON996917 (TUB2). The results of Basic Local Alignment Search Tool (BLAST) analysis revealed that the ITS, GAPDH, and ACT had 100% identity with the sequences of E. rostratum (GenBank Accession No. LT837834, LT883550, and LT837672, respectively), the TUB2 had 99.61% similarity with BLAST sequences of E. rostratum (LT899391). These morphological characteristics and molecular analyses allowed the identification of the pathogen as E. rostratum. Koch's postulates were performed with five healthy detached strawberry leaves with three inoculations per leaf of the 'Akihime' strawberry variety. Surface-sterilized leaves were wounded with an aseptic needle, and inoculated with 2 mm diameter mycelial plugs from 5-day-old cultures of E. rostratum. Control leaves were also wounded with the aseptic needle, and inoculated with a sterile PDA agar plug. The leaves were incubated at 25℃ in Petri plates with petioles wrapped in moist sterile cotton. The diseased symptoms included black spots on the epidermis of the wounded leaves within 5, 10, and 20 days after inoculation. Mock-inoculated controls remained asymptomatic, and three biological repetitions were conducted. The fungus reisolated from the diseased leaves was confirmed as E. rostratum by sequencing. Abundant reports have shown that E. rostratum can infect many economically important crops such as maize, rice, and pineapple (Sun et al. 2021; Kabore et al. 2022; Luo et al. 2012). To the best of our knowledge, this is the first report of E. rostratum on strawberry in China and worldwide.

Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B.

BACKGROUND: Chrysanthemum virus B (CVB), a key member of the genus Carlavirus, family Betaflexiviridae, causes severe viral diseases in chrysanthemum (Chrysanthemum morifolium) plants worldwide. However, information on the mechanisms underlying the response of chrysanthemum plants to CVB is scant. METHODS: Here, an integrated next-generation sequencing and comparative transcriptomic analysis of chrysanthemum leaves was conducted to explore the molecular response mechanisms of plants to a Chinese isolate of CVB (CVB-CN) at the molecular level. RESULTS: In total, 4934 significant differentially expressed genes (SDEGs) were identified to respond to CVB-CN, of which 4097 were upregulated and 837 were downregulated. Gene ontology and functional classification showed that the majority of upregulated SDEGs were categorized into gene cohorts involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, and ribosome metabolism. Enrichment analysis demonstrated that ethylene pathway-related genes were significantly upregulated following CVB-CN infection, indicating a strong promotion of ethylene biosynthesis and signaling. Furthermore, disruption of the ethylene pathway in Nicotiana benthamiana, a model plant, using virus-induced gene silencing technology rendered them more susceptible to cysteine-rich protein of CVB-CN induced hypersensitive response, suggesting a crucial role of this pathway in response to CVB-CN infection. CONCLUSION: This study provides evidence that ethylene pathway has an essential role of plant in response to CVB and offers valuable insights into the defense mechanisms of chrysanthemum against Carlavirus.

First report of Colletotrichum fructicola causing anthracnose on cherry (Prunus avium) in China.

Cherry (Prunus avium) has become an important economical fruit in China. In October 2020, a leaf spot disease was found on cherry in the orchard of Taizhou Academy of Agriculture Sciences, Zhejiang, China. The symptoms appeared as small, water-soaked spots on the leaves, which later became larger, dark brown, and necrotic lesions of 1 cm to 3 cm in width, 4 cm to 8 cm in length. Disease incidences of approximately 60% of the leaves were observed by sampling five locations. To isolate the causing agent, small fragments from five target symptomatic leaves were surface-sterilized with 1.0% sodium hypochlorite solution for 1 min and then rinsed three times with sterilized water. Afterwards the leaf fragments were air-dried, plated onto potato dextrose agar (PDA) medium, and incubated at 25 ℃ in the dark for 2 days. The pure cultures were obtained by transferring hyphal plug of 2 mm in diameter onto PDA, which followed single spore isolation. The colony morphology showed light to dark gray, cottony mycelium, with the underside of the culture became brownish after 7 days. Conidia (n = 28) were hyaline, smooth-walled, cylindrical, aseptate, broadly rounded ends, and average size around 3.84 × 12.82 µm (2.99 to 4.87 × 10.27 to 15.68 µm). Appressoria (n = 27) were mostly brown, ovoid and slightly irregular in shape, and average size around 8.04 × 9.68 µm (6.29 to 9.67 × 9.32 to 12.06 µm). Perithecia average size is 106.25 µm, textura angularis, thick-walled. Asci 26.35-49.18 × 5.00-12.03 µm (average size 37.44 × 7.80 µm, n = 17), unitunicate, thin-walled, clavate or cymbiform. Ascospores 13.69-20.93 × 3.86-6.69 µm (average size 16.00 × 5.42 µm, n = 30), one-celled, hyaline, one or two large guttulate at the centre, slightly rounded ends. The morphological characteristics matched well with previous descriptions of Colletotrichum species of C. gloeosporioides species complex, including C. fructicola (Prihastuti et al. 2009; Fu et al. 2019). The identity of two representative isolates (cf2-3 and cf4-4) from different leaves was confirmed by means of multi-locus gene sequencing. To this end, genomic DNA was extracted by the Plant Direct PCR kit (Vazyme Biotech Co., Ltd, China). Molecular identification was conducted by sequencing the internal transcribed spacer (ITS) rDNA region, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, partial actin (ACT) gene, partial beta-tubulin 2 gene (TUB2), and partial chitin synthase gene (CHS). The obtained sequences have been deposited in GenBank under accession numbers MW581851 and MW581852 (ITS), MW590586 and MW590587 (GAPDH), MW616561 and MW616562 (ACT), MW729380 and MW729381 (TUB2), MW729378 and MW729379 (CHS). The results of Basic Local Alignment Search Tool (BLAST) analysis revealed that the ITS, GAPDH, ACT, TUB2 and CHS sequences of both isolates matched with 100% identity to Colletotrichum fructicola culture collection sequences in GenBank database (JX010165, JX009998, JX009491, JX010405, and JX009866 respectively). These morphological characteristics and molecular analyses allowed the identification of the pathogen as C. fructicola. Koch's postulates were performed with healthy detached cherry leaves of cultivar namely 'HongMi' from Taizhou Academy of Agriculture Sciences. Surface-sterilized leaves were inoculated with five-day-old cultures of C. fructicola mycelial discs of 2 mm in diameter after being wounded with a needle or non-wounded. Control leaves were inoculated with discs of same size PDA agar. Treated leaves were incubated at 25 ℃ in the dark at high relative humidity. Anthracnose symptoms appeared within 3 days both on non-wounded and wounded inoculation approaches. Mock-inoculated controls remained asymptomatic. Biological repetitions were carried out three times. The fungus was reisolated from infected leaves and confirmed as C. fructicola following the methods described above. Until recently, it has been found that C. fructicola can infect tea, apple, pear, Pouteria campechiana in China (Fu et al. 2014; Li et al. 2013; Shi et al. 2018; Yang et al. 2020). To the best of our knowledge, this is the first report of C. fructicola on cherry in China.

Agromyces kandeliae sp. nov., isolated from rhizosphere soil of Kandelia candel in a mangrove.

A novel, Gram-stain-positive, aerobic, non-spore-forming, non-motile and irregular rod-shaped bacterium designated Q22T was isolated from the rhizosphere soil of mangrove plant, Kandelia candel collected in Zhangzhou, Fujian province, China. Strain Q22T was able to grow at 10-40 °C (optimum 30 °C), pH 5.5-9.0 (optimum 7.0-8.0) and with 0-5.0% (w/v) NaCl (optimum 1.0 %). The genomic DNA G+C content was 71.9%. The average nucleotide identity, and in silico DNA-DNA hybridization values between strain Q22T and the reference strains were 79.7-88.9% and 22.6-37.4%, respectively. The predominant isoprenoid quinone was MK-12 and the major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The major polar lipids of strain Q22T were diphosphatidylglycerol, phosphatidylglycerol, one glycolipid and three unidentified lipids. The strain Q22T contained 2,4-diaminobutyric acid, alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and genotypic features, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q22T represents a novel species of the genus Agromyces, for which the name Agromyces kandeliae sp. nov. is proposed. The type strain is Q22T (=MCCC 1K03340T= KCTC 39961T).

Screening of tea saponin-degrading strain to degrade the residual tea saponin in tea seed cake.

Although tea seed cake (TSC) possesses high nutritional value, its high content of tea saponin (TS) limits its potential as feed. This study aimed to degrade TS in TSC by saponin-degrading strain and used a multistrains fermentation method to improve its nutritional value and palatability. Three saponin-degrading strains were isolated from Oleum Camelliae mill soil and identified as Citrobacter sp. FCTS301, Pantoea sp. FCTS302, and Enterobacter sp. FCTS303. Single-factor experiment showed that Citrobacter sp. FCTS301 had the highest degradation rate of TS. Response surface analysis for Citrobacter sp. FCTS301 indicated that the optimum culture conditions were as follows: initial pH of 7.2, culture temperature of 34.2 °C, inoculation amount of 7.3%, the agitation rate of 150 rpm, and the TS concentration of 10.0 g/L. Under these conditions, the maximum degradation rate was 82.6%. The fermentation process of TSC was obtained by a multistrains fermentation experiment. Considering the protein content, crude fiber degradation rate, and TS degradation rate of each group, the optimum inoculum amount of strains included Citrobacter sp. FCTS301, Aspergillus oryzae NCUF414, Saccharomyces cersvisiae NCUF306.5, and Lactobacillus plantarum NCUF201.1(5%, 0.5%, 1.0%, and 1.5%). After TS was degraded efficiently, fermented TSC can be presumed a potential feed raw material.

The roles of jasmonate signalling in nitrogen uptake and allocation in rice (Oryza sativa L.).

Herbivore damage by chewing insects activates jasmonate (JA) signalling that can elicit systemic defense responses in rice. Few details are known, however, concerning the mechanism, whereby JA signalling modulates nutrient status in rice in response to herbivory. (15 NH4 )2 SO4 labelling experiments, proteomic surveys, and RT-qPCR analyses were used to identify the roles of JA signalling in nitrogen (N) uptake and allocation in rice plants. Exogenous applications of methyl jasmonate (MeJA) to rice seedlings led to significantly reduced N uptake in roots and reduced translocation of recently-absorbed 15 N from roots to leaves, likely occurring as a result of down-regulation of glutamine synthetase cytosolic isozyme 1-2 and ferredoxin-nitrite reductase. Shoot MeJA treatment resulted in a remobilization of endogenous unlabelled 14 N from leaves to roots, and root MeJA treatment also increased 14 N accumulation in roots but did not affect 14 N accumulation in leaves of rice. Additionally, proteomic and RT-qPCR experiments showed that JA-mediated plastid disassembly and dehydrogenases GDH2 up-regulation contribute to N release in leaves to support production of defensive proteins/compounds under N-limited condition. Collectively, our results indicate that JA signalling mediates large-scale systemic changes in N uptake and allocation in rice plants.

Enhancement of marinacarboline A biosynthesis by optimizing the riboflavin supplement in marine derived Nocardiopsis flavescens CGMCC 4.5723.

OBJECTIVES: To improve the bioproductivity of secondary metabolites of marine derived Nocardiopsis flavescens CGMCC 4.5723 by enhancing its riboflavin supplement. RESULTS: The NfRibA, type II guanosine triphosphate (GTP) cyclohydrolase (GCH II) of Nocardiopsis flavescens CGMCC 4.5723, was biochemically identified and showed that NfRibA could efficiently catalyze the first step of riboflavin biosynthesis to hydrolyze GTP into 2, 5-diamino-6-ribosylamino-4(3H)-pyrimidinedione 5'-phosphate (DARPP) with Km value of 160.11 ± 26.81 µM in vitro. The overexpression of NfribA could obviously increase riboflavin bioproduction to the titers of 0.41 ± 0.19 mg/l by comparing with the wild type counterpart. Consequently, this rise of riboflavin bioproduction did not disturb the expression of genes involved in marinacarboline A biosynthesis, but could significantly enhance its bioproduction with the titer of 5.5 ± 0.17 mg/l through comparing with wild type control. CONCLUSIONS: Optimization of riboflavin supplement could be a new promising strategy in actinomycetic marinacarboline A exploitation.

Suppressing a plant-parasitic nematode with fungivorous behavior by fungal transformation of a Bt cry gene.

BACKGROUND: Pine wilt disease, caused by the pinewood nematode Bursaphelenchus xylophilus (PWN), is an important destructive disease of pine forests worldwide. In addition to behaving as a plant-parasitic nematode that feeds on epithelial cells of pines, this pest relies on fungal associates for completing its life cycle inside pine trees. Manipulating microbial symbionts to block pest transmission has exhibited an exciting prospect in recent years; however, transforming the fungal mutualists to toxin delivery agents for suppressing PWN growth has received little attention. RESULTS: In the present study, a nematicidal gene cry5Ba3, originally from a soil Bacillus thuringiensis (Bt) strain, was codon-preferred as cry5Ba3Φ and integrated into the genome of a fungus eaten by PWN, Botrytis cinerea, using Agrobacterium tumefaciens-mediated transformation. Supplementing wild-type B. cinerea extract with that from the cry5Ba3Φ transformant significantly suppressed PWN growth; moreover, the nematodes lost fitness significantly when feeding on the mycelia of the cry5Ba3Φ transformant. N-terminal deletion of Cry5Ba3Φ protein weakened the nematicidal activity more dramatically than did the C-terminal deletion, indicating that domain I (endotoxin-N) plays a more important role in its nematicidal function than domain III (endotoxin-C), which is similar to certain insecticidal Cry proteins. CONCLUSIONS: Transformation of Bt nematicidal cry genes in fungi can alter the fungivorous performance of B. xylophilus and reduce nematode fitness. This finding provides a new prospect of developing strategies for breaking the life cycle of this pest in pines and controlling pine wilt disease.

An effective method for the detoxification of cyanide-rich wastewater by Bacillus sp. CN-22.

The biodetoxification of cyanide-rich wastewater has become increasingly popular because of its cost-effectiveness and environmental friendliness. Therefore, we have developed an effective method, optimised by response surface methodology, for detoxifying cyanide-rich wastewater using Bacillus sp. CN-22, which was newly isolated from a cyanide-contaminated electroplating sludge and could tolerate a CN⁻ concentration of 700 mg L⁻¹. The concentration of CN⁻ in the treated wastewater decreased from 200 to 6.62 mg L⁻¹ after cultivation with 2.38 % inocula for 72 h on the medium, consisting of 0.05 % KH2PO4, 0.15 % K2HPO4, 1.0 mM MgCl2, 1.0 mM FeCl3, 0.1 % NH4Cl, and 0.1 % glycerol. The CN⁻ degradability of 96.69 % is similar to the predicted value of 96.82 %. The optimal cultivation conditions were controlled as follows: initial pH, 10.3; temperature, 31 °C; and rotary speed, 193 rpm. The maintenance of higher pH in the overall treatment procedures may avoid the production of volatile HCN and the risk associated with cyanide detoxification. Additionally, the bacterial strain Bacillus sp. CN-22, with its potent cyanide-degrading activity at the initial CN⁻ concentration of 200 mg L⁻¹, may be employed to effectively treat cyanide-rich wastewater, especially electroplating effluent.

Depth-related coupling relation between methane-oxidizing bacteria (MOBs) and sulfate-reducing bacteria (SRBs) in a marine sediment core from the Dongsha region, the South China Sea.

The vertical distributions of methane-oxidizing bacteria (MOBs) and sulfate-reducing bacteria (SRBs) in the marine sediment core of DH-CL14 from the Dongsha region, the South China Sea, were investigated. To enumerate MOBs and SRBs, their specific genes of pmoA and apsA were quantified by a culture-independent molecular biological technique, real-time polymerase chain reaction (RT-PCR). The result shows that the pmoA gene copies per gram of sediments reached the maximum of 1,118,679 at the depth of 140-160 cm. Overall considering the detection precision, sample amount, measurement cost, and sensitivity to the seepage of methane from the oil/gas reservoirs or gas hydrates, we suggest that the depth of 140-160 cm may be the optimal sampling position for the marine microbial exploration of oils, gases, and gas hydrates in the Dongsha region. The data of the pmoA and apsA gene copies exhibit an evident coupling relation between MOBs and SRBs as illustrated in their vertical distributions in this sediment core, which may well be interpreted by a high sulfate concentration inhibiting methane production and further leading to the reduction of MOBs. In comparison with the numbers of the pmoA and apsA copies at the same sediment depth, we find out that there were two methane-oxidizing mechanisms of aerobic and anaerobic oxidation in this sediment core, i.e., the aerobic oxidation with free oxygen dominantly occurred above the depth of 210-230 cm, while the anaerobic oxidation with the other electron acceptors such as sulfates and manganese-iron oxides happened below the depth of 210-230 cm.

Construction of the flagellin F mutant of Vibrio parahaemolyticus and its toxic effects on silver pomfret (Pampus argenteus) cells.

Vibrio parahaemolyticus causes diseases in aquatic organisms, leading to substantial financial losses to the aquaculture industry; its flagellin F (flaF) protein triggers severe inflammation in host cells. To enhance the understanding of the function of flaF in V. parahaemolyticus infection, in this study, a flaF-deficient mutant was constructed by employing two-step homologous recombination. The flaF-deficient mutant induced a significantly lower toll-like receptor 5 (TLR5) expression and apoptosis in fish intestinal epithelial cells than the wild-type V. parahaemolyticus. Furthermore, fluorescence labelling and microscopy analysis of TLR5 showed that V. parahaemolyticus and its mutant strain significantly enhanced TLR5 expression. Additionally, the findings suggest that flaF deletion did not significantly affect the expression of myeloid differentiation factor 88 (MyD88) and interleukin-8 (IL-8) induced by V.parahaemolyticus. In summary, V. parahaemolyticus induced a TLR5-dependent inflammatory response and apoptosis through MyD88, which was observed to be influenced by flaF deletion. In this study, we obtained stable mutants of V. parahaemolyticus via target gene deletion-which is a rapid and effective approach-and compared the induction of inflammatory response and apoptosis by V. parahaemolyticus and its mutant strain, providing novel perspectives for functional gene research in V. parahaemolyticus.

Ca2+-triggered Atg11-Bmh1/2-Snf1 complex assembly initiates autophagy upon glucose starvation.

Autophagy is essential for maintaining glucose homeostasis. However, the mechanism by which cells sense and respond to glucose starvation to induce autophagy remains incomplete. Here, we show that calcium serves as a fundamental triggering signal that connects environmental sensing to the formation of the autophagy initiation complex during glucose starvation. Mechanistically, glucose starvation instigates the release of vacuolar calcium into the cytoplasm, thus triggering the activation of Rck2 kinase. In turn, Rck2-mediated Atg11 phosphorylation enhances Atg11 interactions with Bmh1/2 bound to the Snf1-Sip1-Snf4 complex, leading to recruitment of vacuolar membrane-localized Snf1 to the PAS and subsequent Atg1 activation, thereby initiating autophagy. We also identified Glc7, a protein phosphatase-1, as a critical regulator of the association between Bmh1/2 and the Snf1 complex. We thus propose that calcium-triggered Atg11-Bmh1/2-Snf1 complex assembly initiates autophagy by controlling Snf1-mediated Atg1 activation in response to glucose starvation.

The role of flagellin F in Vibrio Parahaemolyticus-induced intestinal immunity and functional domain identification.

The marine pathogen Vibrio parahaemolyticus has caused huge economic losses to aquaculture. Flagellin is a key bacterial virulence factor that induces an inflammatory response via activation of Toll-like receptor 5 (TLR5) signaling. Herein, to explore the inflammatory activity of V. parahaemolyticus flagellins (flaA, flaB, flaC, flaD, flaE, and flaF), we investigated their ability to induce apoptosis in a fish cell line. All six flagellins induced severe apoptosis. Moreover, treatment with V. parahaemolyticus flagellins increased TLR5 and myeloid differentiation factor 88 (MyD88) expression and the production of TNF-α and IL-8 significantly. This indicated that flagellins might induce a TLR5-meditated immune response via an MyD88-dependent pathway. FlaF exhibited the strongest immunostimulatory effect; therefore, the interaction between TLR5 and flaF was screened using the yeast two-hybrid system. A significant interaction between the two proteins was observed, indicating that flaF binds directly to TLR5. Finally, the amino acids that participate in the TLR5-flaF interaction were identified using molecular simulation, which indicated three binding sites. These results deepen our understanding of the immunogenic properties of flagellins from V. parahaemolyticus, which could be used for vaccine development in the future.

A microdots array-based fluoremetric assay with superwettability profile for simultaneous and separate analysis of iron and copper in red wine.

A microdots array-based fluoremetric method with superwettability profile has been developed for the simultaneous and separate detection of Fe3+ and Cu2+ ions in red wine samples. A wettable micropores array was initially designed with high density by using polyacrylic acid (PAA) and hexadecyltrimethoxysilane (HDS), followed by the NaOH etching route. Zinc metal organic frameworks (Zn-MOFs) were fabricated as the fluorescent probes to be immobilized into the micropores array to obtain the fluoremetric microdots array platform. It was found that the fluorescence of Zn-MOFs probes could decrease significantly in the presence of Fe3+ and/or Cu2+ ions towards their simultaneous analysis. Yet, the specific responses to Fe3+ ions could be expected if using histidine to chelate Cu2+ ions. Moreover, the developed Zn-MOFs-based microdots array with superwettability profile can enable the accumulation of targeting ions from the complicated samples without any tedious pre-processing. Also, the cross-contamination of different samples droplets can be largely avoided so as to facilitate the analysis of multiple samples. Subsequently, the feasibility of simultaneous and separate detection of Fe3+ and Cu2+ ions in red wine samples was demonstrated. Such a design of microdots array-based detection platform may promise the wide applications in analyzing Fe3+ and/or Cu2+ ions in the fields of food safety, environmental monitoring, and medical diseases diagnostics.

Global-scale no-tillage impacts on soil aggregates and associated carbon and nitrogen concentrations in croplands: A meta-analysis.

No-tillage treatment, including no-tillage with straw retention (NTS) and without (NT), has been widely used as an efficient and sustainable alternative to conventional tillage with straw retention (CTS) and without (CT) and greatly affects soil physical quality and organic matter dynamics in cropland ecosystems. Although some studies have reported the effects of NTS on soil aggregate stability and soil organic carbon (SOC) concentration, the underlying mechanisms of how soil aggregates, aggregate-associated SOC and total nitrogen (TN) respond to no-tillage remain unclear. Through a global meta-analysis of 91 studies in cropland ecosystems, we evaluated the effects of no-tillage on soil aggregates and their associated SOC and TN concentrations. On average, no-tillage treatment significantly decreased the proportions of microaggregates (MA) by 21.4 % (95 % CI, -25.5 to -17.3 %) and silt+clay size particles (SIC) by 24.1 (95 % CI, -30.9 to -17.0 %), and increased the proportions of large macroaggregate (LA) by 49.5 % (95 % CI, 36.7-63.0 %) and small macroaggregate (SA) by 6.1 % (95 % CI, 2.0-10.9 %) compared to those in conventional tillage. The SOC concentrations for all three aggregate sizes increased significantly with no tillage: for LA by 28.2 % (95 % CI, 18.8-39.5 %), SA by 18.0 % (95 % CI, 12.8-23.3 %), and MA by 9.1 % (95 % CI, 2.6-16.8 %). TN also increased significantly for all sizes with no tillage, with LA by 13.6 % (95 % CI, 8.6-17.6 %), SA by 11.0 % (95 % CI, 5.0-17.0 %), MA by 11.7 % (95 % CI, 7.0-16.4 %), and SIC by 7.6 % (95 % CI, 2.4-13.8 %). The magnitude of the no-tillage treatment effect on soil aggregation, aggregate-associated SOC and TN varied with the environmental and experimental conditions. The positive effect on the proportions of LA occurred with initial soil organic matter (SOM) content >10 g kg-1, whereas SOM <10 g kg-1 did not change significantly. Additionally, the effect size of NTS compared with CTS was lower than that of NT compared with CT. These findings suggest that NTS may promote physically protective SOC accumulation through the formation of macroaggregates by reducing disturbance destruction and increasing plant-derived binding agents. The findings highlight that no-tillage may enhance the formation of soil aggregates and the associated SOC and TN concentrations in global cropland ecosystems.

Integrated comparative transcriptome and weighted gene co-expression network analysis provide valuable insights into the response mechanisms of crayfish (Procambarus clarkii) to copper stress.

One of the significant limitations of aquaculture worldwide is the prevalence of divalent copper (Cu). Crayfish (Procambarus clarkii) are economically important freshwater species adapted to a variety of environmental stimuli, including heavy metal stresses; however, large-scale transcriptomic data of the hepatopancreas of crayfish in response to Cu stress are still scarce. Here, integrated comparative transcriptome and weighted gene co-expression network analyses were initially applied to investigate gene expression profiles of the hepatopancreas of crayfish subjected to Cu stress for different periods. As a result, 4662 significant differentially expressed genes (DEGs) were identified following Cu stress. Bioinformatics analyses revealed that the "focal adhesion" pathway was one of the most significantly upregulated response pathways following Cu stress, and seven DEGs mapped to this pathway were identified as hub genes. Furthermore, the seven hub genes were examined by quantitative PCR, and each was found to have a substantial increase in transcript abundance, suggesting a critical role of the "focal adhesion" pathway in the response of crayfish to Cu stress. Our transcriptomic data can be a good resource for the functional transcriptomics of crayfish, and these results may provide valuable insights into the molecular response mechanisms underlying crayfish to Cu stress.