Integrative analysis of genome and transcriptome reveal the genetic basis of high temperature tolerance in pleurotus giganteus (Berk. Karun & Hyde).

BACKGROUND: Pleurotus giganteus is a commonly cultivated mushroom with notable high temperature resistance, making it significant for the growth of the edible fungi industry in the tropics. Despite its practical importance,, the genetic mechanisms underlying its ability to withstand high temperature tolerance remain elusive. RESULTS: In this study, we performed high-quality genome sequencing of a monokaryon isolated from a thermotolerant strain of P. giganteus. The genome size was found to be 40.11 Mb, comprising 17 contigs and 13,054 protein-coding genes. Notably, some genes related to abiotic stress were identified in genome, such as genes regulating heat shock protein, protein kinase activity and signal transduction. These findings provide valuable insights into the genetic basis of P. giganteus' high temperature resistance. Furthermore, the phylogenetic tree showed that P. giganteus was more closely related to P. citrinopileatus than other Pleurotus species. The divergence time between Pleurotus and Lentinus was estimated as 153.9 Mya, and they have a divergence time with Panus at 168.3 Mya, which proved the taxonomic status of P. giganteus at the genome level. Additionally, a comparative transcriptome analysis was conducted between mycelia treated with 40 °C heat shock for 18 h (HS) and an untreated control group (CK). Among the 2,614 differentially expressed genes (DEGs), 1,303 genes were up-regulated and 1,311 were down-regulated in the HS group. The enrichment analysis showed that several genes related to abiotic stress, including heat shock protein, DnaJ protein homologue, ubiquitin protease, transcription factors, DNA mismatch repair proteins, and zinc finger proteins, were significantly up-regulated in the HS group. These genes may play important roles in the high temperature adaptation of P. giganteus. Six DEGs were selected according to fourfold expression changes and were validated by qRT-PCR, laying a good foundation for further gene function analysis. CONCLUSION: Our study successfully reported a high-quality genome of P. giganteus and identified genes associated with high-temperature tolerance through an integrative analysis of the genome and transcriptome. This study lays a crucial foundation for understanding the high-temperature tolerance mechanism of P. giganteus, providing valuable insights for genetic modification of P. giganteus strains and the development of high-temperature strains for the edible fungus industry, particularly in tropical regions.

Rhizosphere environmental factors regulated the cadmium adsorption by vermicompost: Influence of pH and low-molecular-weight organic acids.

Vermicompost is a promising amendment for immobilization of cadmium (Cd) in soils; however, its effectiveness can be influenced by rhizosphere environment conditions, such as pH and the presence of low-molecular-weight organic acids (LMWOAs). In this study, a batch experiment was conducted to examine the characteristics of Cd adsorption by vermicompost at different pH (pH = 3, 5, and 7) and after the addition of different LMWOAs (oxalic acid; citric acid; malic acid). Furthermore, a series of morphology and structural analyses were conducted to elucidate the mechanisms of observed effects. The results showed that the adsorption capacity of vermicompost for Cd increased as pH increased, and chemisorption dominated the adsorption process. Changes in pH altered adsorption performance by affecting the -OH groups of alcohol/phenol and the -CH2 groups of aliphatics. Further, the addition of oxalic acid promoted Cd adsorption, and the effect was concentration dependent. Modifying the verimicompost surface with more adsorption sites might be the main reason. Conversely, citric acid and malic acid showed the ability to inhibit Cd adsorption by vermicompost. Citric acid caused a blocking effect by covering flocculent substances on the vermicompost surface while reducing surface adsorption sites by dissolving mineral components such as iron oxides. However, the action of malic acid did not appear to be related to changes in morphology or the structure of vermicompost. Overall, the results of this study partially explain the limited effectiveness of Cd immobilization within the rhizosphere by vermicompost, and provide theoretical support for regulating rhizosphere environments to improve the effectiveness of vermicompost immobilization of Cd.

Insight into humification of mushroom residues under addition of Rich-N sources: Comparing key molecular evolution processes using EEM-PARAFAC and 2D-FTIR-COS analysis.

Accelerating the humification of organic solid waste is one of the most important issues in composting. This present study aims to study and compare the humification process of different rich-N sources (chicken manure, cattle manure, and urea) addition during the composting of mushroom residues, from macro physicochemical properties to micro humic molecular structure evolution process. The physicochemical elements and humic components were determined for evaluating the compost quality and humification degree as composting proceed. The coupled analysis of excitation-emission matrix with parallel factor analysis (EEM-PARAFAC) and two-dimensional correlation with Fourier transform infrared spectrum (2D-FTIR-COS) were used to characterize the functional molecular structure evolution of dissolved organic matter during humification process. The results indicated that the rank order for humification level were the treatments of chicken manure (HM), urea (UM), cattle manure (CM), and single mushroom residue treatment (CK), with their humification index of 22.18%, 22.05%, 18.47%, and 16.52%, respectively. Humic substance, humic acid, and fulvic acid were obtained the highest in HM treatment with contents of 35.41 ± 0.86%, 23.32 ± 1.57%, and 10.97 ± 0.52%, respectively. The rich-N source addition enhanced the degradation of protein-like and polysaccharides-like substances in dissolved organic matter, thus accelerating the humification process of mushroom residues. The key structure evolution of dissolved organic matter in the HM treatment, in which the CO and CC stretching of quinone, amide, or ketone, and the C-O stretching of polysaccharides may be responsible for the faster formation of humus compared to the other nitrogen treatments. In this study, redundancy analysis indicated that the total nitrogen (TN) and nitrate nitrogen (NO3--N) may be the potential indicators for determining the humification level as composting proceed. The result provides significant insight into the humification mechanism of mushroom residue under different types of nitrogen sources at the molecular level, and will be reference for improving the composting technique in practical field.

Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting.

Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and ß-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.

Effect of moisture content, aeration rate, and C/N on maturity and gaseous emissions during kitchen waste rapid composting.

To determine factors affecting compost maturity and gaseous emissions during the rapid composting of kitchen waste, an orthogonal test was conducted with three factors: moisture content (MC) (55%, 60%, 65%), aeration rate (AR) (0.3,0.6 and 0.9 L·kg-1DM·min-1) and C/N ratio (21, 24, 27). The results showed that the importance of factors affecting compost maturity was: C/N > AR > MC, optimal conditions were: C/N of 24, AR of 0.3 L·kg-1DM·min-1and MC of 65%. For gaseous emissions, the sequence of essential factors affecting NH3 emissions was: C/N > MC > AR, and the optimal parameters for NH3 reduction were: C/N of 27, MC of 65%, and AR of L·kg-1DM·min-1. The important factors affecting N2O and H2S emissions are both: MC > C/N > AR, while their best parameters were different. The optimal parameters for N2O emission reduction were MC of 60%, AR of 0.3 L·kg-1DM·min-1 and C/N of 24, while these for H2S were MC of 55%, AR of 0.3 L·kg-1DM·min-1 and C/N of 21. The C/N mainly affected the compost maturity and AR further affected the maturity and pollutant gas emissions by influencing the temperature and O2 content. Considering comprehensively the maturity and gaseous reduction, the optimal control parameters were: MC of 60%-65%, AR of L·kg-1DM·min-1, and C/N of 24-27.

Synergistically mitigating nitric oxide emission by co-applications of biochar and nitrification inhibitor in a tropical agricultural soil.

Agricultural soils are the hotspots of nitric oxide (NO) emissions, which are related to atmospheric pollution and greenhouse effect. Biochar application has been recommended as an important countermeasure, however, its mitigation efficiency is limited as biochar, under certain conditions, can stimulate soil nitrification. Therefore, biochar co-applied with nitrification inhibitor could optimize the mitigation potential of biochar. Herein, a laboratory-scale experiment was conducted to investigate the effects of co-application of biochar and nitrification inhibitor on NO emission, nitrogen cycling function and bacterial community in a tropical vegetable soil. Results showed that a single application of biochar or nitrification inhibitor significantly decreased NO emissions, and this mitigation effectiveness was amplified by their co-applications. Soil NO2--N intensity, along with abundances of AOB-amoA and nirK were significantly and positively correlated with cumulative NO emissions. The stimulated activity of ammonia monooxygenase and growths of AOB and total comammox Nitrospira by biochar were weakened by nitrification inhibitor, implying decreased nitrification-driven NO production. The nitric oxide reductase activity and related qnorB abundance in nitrification inhibitor-added soils were increased by biochar, indicating promoted NO consumption during denitrification. The nirK abundance and NO2--N intensity were decreased more by co-applications of biochar or nitrification inhibitor. Moreover, both biochar and nitrification inhibitor changed bacterial ß-diversity, and their co-application synergistically enriched Armatimonadetes and Verrucomicrobia abundances and decreased WPS-2 abundance. This study highlights that co-applications of biochar and nitrification inhibitor can make their respective advantages complementary to each other, thereby achieving a larger mitigation of NO emissions from agricultural soils in tropical regions.

Extensimonas perlucida sp. nov., a Novel Bacterium Isolated from Sludge.

A bacterium, designated HX2-24 T, was isolated from activated sludge treating pesticide-manufacturing wastewater. Colonies of the strain on nutrient agar were circular, transparent, and colorless. Strain HX2-24 T shared 98.1% 16S rRNA gene sequence similarity with Extensimonas vulgaris S4T, and less than 97% similarities with other type strains. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a clade with E. vulgaris S4T. The major cellular fatty acids were C16:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C17:0 cyclo, the major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), aminophospholipid (APL), glycophospholipid (GPL), and aminoglycolipid (AGL). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between HX2-24 T and E. vulgaris S4T were 92% and 41%, respectively. The G + C content of strain HX2-24 T was 64.4 mol%. Thus, based on the phenotypic, chemotaxonomic, and genotypic characteristics, strain HX2-24 T represents a novel species in the genus Extensimonas, for which the name Extensimonas perlucida HX2-24 T sp. nov. is proposed. The type strain is HX2-24 T (= KCTC 72472 T = CCTCC AB 2019178 T).

Remediation effectiveness of vermicompost for a potentially toxic metal-contaminated tropical acidic soil in China.

Potentially toxic metal (PTM) contamination coupled with soil acidification has posed a severe threat to agricultural sustainability of tropical region in the world. In this study, a vermicopomst (VC) produced from vermicomposting cattle manure under tropical environment was applied to remediating a tropical acidic soil in Hainan, China. The effectiveness of VC in reducing available PTMs in soils was evaluated by incubation experiments with a Cd, Cr or Ni spiked soil and a Cd contaminated field soil. The dynamic changes of soil physical, chemical and biological properties after VC amendment were determined to understand the mechanisms of PTM immobilization. The results showed that VC amendment significantly reduced 0.01M CaCl2 extractable amounts of Cd, Ni and Cr in the spiked soils, and CaCl2 extractable Cd was reduced by 49.3% when VC was amended to the Cd contaminated field soil. Thermodynamic studies showed that VC had a high adsorption capacity for Cd, Ni and Cr, with the maximum adsorption (obtained from the Langmuir model) of 33.45, 26.17, and 20.88 mg/g, respectively. The reduction in CaCl2 extractable metals after VC amendment was consistent with the order of maximum adsorption of VC for Cd, Ni, and Cr. Vermicompost amendment increased soil pH by 0.7 to 1.5 units, which is positively related with VC rate, but negatively with the decrease in extractable metals. These results indicates that adsorption of metals onto VC and an increase in soil pH after VC amendment are likely responsible for the decreased availability of Cd, Ni, and Cr in the contaminated soil. In addition, the addition of stable organic substances and subsequent formation of water-stable aggregates may be also beneficial for immobilizing PTMs and improving tropical soil quality.

Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil.

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)).

Differences in the uptake and translocation of differentially charged microplastics by the taproot and lateral root of mangroves.

The interception of microplastics (MPs) by mangrove roots plays an indispensable role in reducing the environmental risks of MPs. However, there remains limited research on the fate of the intercepted MPs. Hereby, the uptake and subsequent translocation of 0.2 µm and 2 µm PS MPs with different coating charge by the typical salt-secreting mangrove plants (Aegiceras corniculatum) were investigated. Compared to amino-functionalized PS with positive charge (PS-NH2), the visualized results indicated that the efficient uptake of carboxy-functionalized PS with negative charge (PS-COOH) was more dependent on taproots. But for the lateral roots, it only allowed the entry of PS-NH2 instead of PS-COOH. The specific uptake pathways of PS-NH2 on the lateral roots could attribute to the release of H+ and organic acids by root hairs, as well as the relative higher Zeta potential. After entering the Aegiceras corniculatum roots, the translocation of PS MPs was restricted by their particle sizes. Furthermore, the release of PS MPs from Aegiceras corniculatum leaf surfaces through the salt glands and stomata was observed. And the decline in the photochemical efficiency of leaves under PS MPs exposure also indirectly proved the foliar emission of PS MPs. Our study improved the understanding of the environmental behaviors and risks of the retained MPs in mangroves.

Accelerating the humification of mushroom waste by regulating nitrogen sources composition: Deciphering mechanism from bioavailability and molecular perspective.

Regulating nitrogen source composition is efficient approach to accelerate the spent mushroom substrate (SMS) composting process. However, currently, most traditional composting study only focuses on total C/N ratio of initial composting material. Rarely research concerns the effect of carbon or nitrogen components at different degradable level and their corresponding decomposed-substances on humification process. This study deciphers and compares the mechanism of mixed manure-N sources on SMS humification from bioavailability and molecular perspective. Two different biodegradable manure-N sources, cattle manure (CM) and Hainan chicken manure (CH), were added into the SMS composting with the different CM:CH ratio of 1:0, 3:1, 1:1, 1:3, and 0:1, respectively. The physicochemical properties and humic substances were determined to evaluate the compost quality. Coupling analysis of spectroscopy, fluorescence, and humic intermediate precursors were conducted to characterizing molecular formation process of humic acid (HA). The results indicated that regulating the carbon-nitrogen nutrient biodegradability of composting material by adding mixed nitrogen sources is an effective strategy to accelerate the SMS humification process. The C1H3 (CM:CH ratio of 1:3) and CH treatments obtained great physicochemical properties and the highest growth rate of HA (31.96% and 27.02%, respectively). The rapid reaction of polysaccharide, ketone, quinone, and amide in DOM (LCP1) might be the key for the fast humification in C1H3 and CH. The polyphenol, reducing sugar and amino acid originated from the labile-carbon-proportion I (LCP1) and recalcitrant-carbon-proportion (RCP), labile-carbon-proportion II (LCP2) and RCP, and labile-nitrogen-proportion I (LNP1), respectively, were the main driving intermediate precursors for the formation of HA. This study deciphers the SMS humification mechanism at molecular level and provides a strategy in accelerating-regulating the composting process. which will be beneficial for enhancing the disposing efficiency of SMS, producing high-quality organic fertilizer, and even popularizing to the similar types of organic waste in practical field.

Residual effects of chlorinated organic pollutants on microbial community and natural redox processes in coastal wetlands.

Chlorinated organic pollutants (COPs) are common in flooded environments. To examine the residual status and effects of COPs on flooded environments, a survey of 7 coastal wetlands in Zhejiang, East China was conducted. Total COP concentrations detected from 95.69 to 412.76 ng g-1 dw. Gamma-HCH and o,p'-DDT posed the greatest risk with exceedance rates of 100% according to sediment quality guidelines. Samples with higher COP pollution had higher microbial diversity, more complex microbial networks, more deterministic community assembly processes and lower microbiome stability, indicating an improved soil function for balance cycle of substances, especially for COP degradation. Further analysis using quantitative real-time PCR suggested COP-dechlorination interacted with natural redox processes, especially sulfate reduction and methanogenesis. The positive correlation between CH4 and pentachlorobenzene indicated a potential increase in greenhouse gas emissions caused by COP pollution. Correlation between dsr gene and COPs demonstrated the ability of sulfate-reducing bacteria to degrade COPs. Particularly, facultative OHRB such as sulfate-reducing bacteria hold significant importance in the process of COP-dechlorination. This finding provides a reference for COP pollution remediation. Collectively, our study offers new insight into the residual effect of COPs in coastal wetlands and contributes to an improved understanding of bioremediation strategies for COP pollution.

Effect of biodegradable PBAT microplastics on the C and N accumulation of functional organic pools in tropical latosol.

Microplastics (MPs) pollution is becoming an emerging global stressor for soil ecosystems. However, studies on the impacts of biodegradable MPs on soil C sequestration have been mainly based on bulk C quantity, without considering the storage form of C, its persistency and N demand. To address this issue, the common poly (butylene adipate-co-terephthalate) (PBAT) was used as the model, and its effects on soil functional organic pools, including mineral-associated (MAOM), particulate (POM) and dissolved organic matter (DOM), were investigated from the novel coupled perspective of C and N stocks. After adding PBAT-MPs, the contents of soil POM-C, DOM-C, and MAOM-C were increased by 546.9 %-697.8 %, 54.2 %-90.3 %, and 13.7 %-18.9 %, respectively. Accordingly, the total C increased by 116.0 %-191.1 %. Structural equation modeling showed that soil C pools were regulated by PBAT input and microbial metabolism associated with C and N enzymes. Specifically, PBAT debris could be disguised as soil C to promote POM formation, which was the main pathway for C accumulation. Inversely, the MAOM-C and DOM-C formation was attributed to the PBAT microbial product and the selective consumption in DOM-N. Random forest model confirmed that N-activated (e.g., Nitrospirae) and PBAT-degrading bacteria (e.g., Gemmatinadetes) were important taxa for soil C accumulation, and the key enzymes were rhizopus oryzae lipas, invertase, and ammonia monooxygenase. The soil N accumulation was mainly related to the oligotrophic taxa (e.g., Chloroflexi and Ascomycota) associated with aggregate formation, decreasing the DOM-N by 46.9 %-84.3 %, but did not significantly change the total N storage and other N pools. Collectively, the findings highlight the urgency to control the nutrient imbalance risk of labile N loss and recalcitrant C enrichment in POM to avoid the depressed turnover rate of organic matter in MPs-polluted soil.

Microbial resistance and resilience to drought and rewetting modulate soil N2O emissions with different fertilizers.

Future climate models indicate an enhanced severity of regional drought and frequent rewetting events, which may cause cascading impacts on soil nitrogen cycle and nitrous oxide (N2O) emissions, but the underlying microbial mechanism remains largely unknown. Here we report an incubation study that examined the impacts of soil moisture status and nitrification inhibitor (DCD) on the N2O-producers and N2O-reducers following the application of urea and composted swine manure in an acid soil. The soil moisture treatments included 100 % water-holding capacity (WHC) (wetting, 35.3 % gravimetric soil water content), 40 % WHC (drought, 7 % gravimetric soil water content), and 40 % to 100 % WHC (rewetting). The results showed that N2O emissions were significantly decreased under drought conditions and were significantly increased after rewetting. The resistance of ammonia-oxidizing bacteria and nosZII, which was inhibited by urea or manure application, modulated N2O emissions under drought conditions. The resilience of the functional guilds modulated their dominant role in N2O emissions with rewetting. Ammonia-oxidizing bacteria, nirS-type denitrifying bacteria and nosZI showed significant resilience in response to rewetting. Significant negative relationships were observed between N2O emissions and nosZII clade under wetting condition and between N2O emissions and nosZI clade after rewetting. Our results highlighted the importance of microbial resistance and resilience in modulating N2O emissions, which help to better understand the dominant way of N2O emissions, and consequently make efficient mitigation strategies under the global climate change.

Plant-derived biochar amendment for compost maturity improvement and gaseous emission reduction in food waste composting: Insight from bacterial community and functions.

This study assessed the impact of different plant-derived biochar (cornstalk, rice husk, and sawdust) on bacterial community and functions for compost maturity and gaseous emissions during the composting of food waste. Results showed that all biochar strengthened organic biotransformation and caused a higher germination index on day 12 (over 100%), especially for rice husk biochar to enhance the growth of Thermobifida related to aerobic chemoheterotrophy. Rice husk biochar also achieved a relatively higher reduction efficiency of methane (85.8%) and ammonia (82.7%) emissions since its greater porous structure. Besides, the growth of Pseudomonas, Pusillimonas, and Desulfitibacter was restricted to constrict nitrate reduction, nitrite respiration, and sulfate respiration by optimized temperature and air permeability, thus reducing nitrous oxide and hydrogen sulfide emissions by 48.0-57.3% by biochar addition. Therefore, rice husk biochar experienced the optimal potential for maturity increment and gaseous emissions mitigation.

Comamonas jiangduensis sp. nov., a biosurfactant-producing bacterium isolated from agricultural soil.

A novel biosurfactant-producing strain, designated YW1(T), was isolated from agricultural soil. Its taxonomic position was investigated using a polyphasic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YW1(T) was a member of the genus Comamonas, and showed highest sequence similarities to Comamonas aquatica LMG 2370(T) (98.5%), Comamonas kerstersii LMG 3475(T) (97.7%) and Comamonas terrigena LMG 1253(T) (97.7%). Furthermore, DNA-DNA hybridization experiments against these three strains gave results that were clearly lower than 70% DNA-DNA similarity, and consequently confirmed that this new strain does not belong to a previously described species of the genus Comamonas. The major respiratory quinone was ubiquinone-8. The major fatty acids (>5%) were C16:0 (30.1%), summed feature 3 (C16:1ω6c and/or C16:1ω7c; 25.4%), summed feature 8 (C18:1ω6c and/or C18:1ω7c; 15.3%), C17:0 cyclo (7.4%) and C14:0 (5.8%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipids and unknown lipids. Based on the phylogenetic analysis, DNA-DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain YW1(T) was clearly distinguishable from all species of the genus Comamonas with validly published names and should be classified as a representative of a novel species of the genus Comamonas, for which the name Comamonas jiangduensis sp. nov. is proposed. The type strain is YW1(T) (=CCTCC AB 2012033(T)=KACC 16697(T)).

Olivibacter jilunii sp. nov., isolated from DDT-contaminated soil.

Bacterial strain 14-2A(T), isolated from a long-term DDT-contaminated soil in China, was characterized by using a polyphasic approach to clarify its taxonomic position. Strain 14-2A(T) was found to be Gram-negative, aerobic, non-spore-forming, non-motile, non-flagellated and rod-shaped. The new isolate was able to grow at 4-42 °C, pH 6.0-9.0 and with 0-5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the family Sphingobacteriaceae. The 16S rRNA gene sequence of strain 14-2A(T) showed the highest similarity with Olivibacter oleidegradans TBF2/20.2(T) (99.4 %), followed by Pseudosphingobacterium domesticum DC-186(T) (93.8 %), Olivibacter ginsengisoli Gsoil 060(T) (93.6 %), Olivibacter terrae Jip13(T) (93.1 %), Olivibacter soli Gsoil 034(T) (92.8 %) and Olivibacter sitiensis AW-6(T) (89.6 %). The DNA-DNA hybridization value between strains 14-2A(T) and O. oleidegradans TBF2/20.2(T) was 34.45±2.11 %. Strain 14-2A(T) contained phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminophospholipid and phosphatidylinositol mannoside as the major polar lipids. The DNA G+C content was 41.2 mol%. MK-7 is the major isoprenoid quinone. Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH are the major fatty acids. The phenotypic and chemotaxonomic data confirmed the affiliation of strain 14-2A(T) to the genus Olivibacter. On the basis of the phylogenetic and phenotypic characteristics, and chemotaxonomic data, strain 14-2A(T) is considered to represent a novel species of the genus Olivibacter, for which the name Olivibacter jilunii sp. nov. is proposed; the type strain is 14-2A(T) ( = KCTC 23098(T) = CCTCC AB 2010105(T)).

The role of pores in micro-zone distribution of Cd in a tropical paddy soil: Results from X-ray computed tomography combined energy dispersive spectroscopy analysis.

Accurate description of Cd micro-zone distribution and accumulation is the prerequisite for revealing Cd transfer and transformation processes. However, to date, the role of soil pores in the Cd micro-zone distribution characteristics in undisturbed soil is still unclear. In this study, the obvious heterogeneous distribution of Cd in and around the soil pores at the cross-sectional surface of the tropical undisturbed topsoil was visualized by the combination of X-ray micro-computed tomography and scanning electron microscope-energy dispersive spectroscopy. For both the air space and water-holding pores, the micro-zone distribution characteristics of Cd around the pores were dominated by pore sizes. For macropores and mesopores, Cd preferred to distribute in the micro-zone within 167.5-335 µm from pores. But for micropores, the highest content percentage of Cd was exhibited in the micro-zone within 67-167.5 µm from pores. The random forest model revealed that the occurrence of Fe (13.83%) and P (13.59%) contributed most to Cd micro-zone distribution around air space pores. While for water-holding pores, Fe occurrence (18.30%) contributed more significantly than P (11.92%) to Cd micro-zone distribution. Our study provided new insights into Cd retention mechanism, which is help for accessing Cd migration and transformation.

An unrecognized entry pathway of submicrometre plastics into crop root: The split of hole in protective layer.

Threats to food safety caused by the continuous accumulation of plastic particles in the terrestrial environment is currently a worldwide concern. To date, descriptions of how plastic particles pass the external biological barrier of crop root have been vague. Here, we demonstrated that submicrometre polystyrene particles passed unimpededly the external biological barrier of maize through the split of holes in the protective layer. We identified plastic particles induced the apical epidermal cells of root tips become round, thereby expanding the intercellular space. It further pulled apart the protective layer between the epidermal cells, and eventually formed the entry pathway for plastic particles. The enhancement of oxidative stress level induced by plastic particles was the main reason for the deformation of the apical epidermal cells (increased roundness values: 15.5%), comparing to the control. Our findings further indicated that the presence of cadmium was conducive to the "holes" formation. Our results highlighted the critical insights into the fracture mechanisms of plastic particles for the external biological barriers of crop roots, providing a strong incentive to access the risk of plastic particles in agriculture security.

Implications of vermicompost on antibiotic resistance in tropical agricultural soils - A study in Hainan Island, China.

The contamination of antibiotic resistance genes (ARGs) associated with animal manure fertilization have attracted a global concern. Vermicompost has been widely popularized as an eco-friendly alternative to recycle animal manure on Hainan Island, China. However, the effects of vermicompost application on ARG spread and environmental fate in tropical agricultural soils remains undefined. Herein, the spatial prevalence and vertical behavior of ARGs in the soil profiles of vermicompost-applied agricultural regions were explored by a large-scale survey across Hainan Island. The results showed that although vermicompost application marginally enhanced the load of ARG pollution in the soil in Hainan, the ARGs derived from vermicompost did not eventually accumulate in the soil profile. The increase rate of ARGs in 40-60 cm soil layer was only 0.0015 % compared with that of unfertilized soil. Interestingly, vermicompost application reduced the abundance of high-risk ARGs, such as blaNDM and blaampC, by approximately one order of magnitude. Vermicompost was also observed to increase the abundance of beneficial bacteria, like Clostridium, and decrease those of Acidobacteriae, Planctomycetes and Verrucomicrobiae, which caused changes in the potential host bacteria of soil ARGs. Mobile genetic elements were further proven to be an essential factor that regulated the vertical dynamics of ARGs in vermicomposted soil, with a direct influence coefficient of 0.9975. This study demonstrated that the controllable risk associated with vermicompost application provided useful information to effectively reduce the threat of ARGs and promote the development of sustainable agriculture on Hainan Island.