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Some plant-associated microorganisms could improve host plants biotic and abiotic stress tolerance. Imperata cylindrica is a dominant pioneer plant in some abandoned mine lands with higher concentrations of heavy metal (HM). To discover the specific microbiome of I. cylindrica in this extreme environment and evaluate its role, the microbiome of I. cylindrica’s seeds and rhizosphere soils from HM heavily contaminated (H) and lightly contaminated (L) sites were studied. It was found that HM-contamination significantly reduced the richness of endophytic bacteria in seeds, but increased the abundance of resistant species, such as Massilia sp. and Duganella sp. Spearman’s rank correlation coefficient analysis showed that both Massilia sp. and Duganella sp. showed a significant positive correlation with Zn concentration, indicating that it may have a strong tolerance to Zn. A comparison of the microbiome of rhizosphere soils (RS) and adjacent bare soils (BS) of site H showed that I. cylindrica colonization significantly increased the diversity of fungi in rhizosphere soil and the abundance of Ascomycota associated with soil nutrient cycling. Spearman’s rank correlation coefficient analysis showed that Ascomycota was positively correlated with the total nitrogen. Combined with the fact that the total nitrogen content of RS was significantly higher than that of BS, we suppose that Ascomycota may enhance the nitrogen fixation of I. cylindrica, thereby promoting its growth in such an extreme environment. In conclusion, the concentration of HM and nutrient contents in the soil significantly affected the microbial community of rhizosphere soils and seeds of I. cylindrica, in turn, the different microbiomes further affected soil HM concentration and nutrient contents. The survival of I. cylindrica in HM severely contaminated environment may mainly be through recruiting more microorganisms that can enhance its nutrition supply.

Metal-induced oxidative stress in contaminated soils affects plant growth. In the present study, we evaluated the role of seed endophyte FXZ2 on Dysphania ambrosioides Zn/Cd tolerance and accumulation. A series of pot experiments were conducted under variable Zn (500, 1,000, and 1,500 mg kg–1) and Cd (5, 15, 30, and 60 mg kg–1). The results demonstrated that FXZ2-inoculation significantly enhanced the growth of D. ambrosioides and improved its chlorophyll and GSH content. In the rhizosphere, FXZ2 inoculation changed the chemical speciation of Zn/Cd and thus affected their uptake and accumulation in host plants. The exchangeable and carbonate-bound fractions (F1 + F2) of Zn decreased in the rhizosphere of FXZ2-inoculated plants (E+) as compared to non-inoculated plants (E-) under Zn stress (500 and 1,000 mg kg–1), correspondingly, Zn in the shoots of E+ decreased (p < 0.05). However, at Cd stress (30 and 60 mg kg–1), the F1 + F2 fractions of Cd in E+ rhizospheric soils increased; subsequently, Cd in the shoots of E+ increased (p < 0.05). FXZ2 could exogenously secrete phytohormones IAA, GA, and JA. The study suggests that seed endophyte FXZ2 can increase Zn/Cd tolerance of host plant by altering Zn/Cd speciation in rhizospheric soils, as well as exogenous production of phytohormones to promote growth, lowering oxidative damage while enhancing antioxidant properties. For Zn/Cd accumulation, it has opposite effects: Zn uptake in E+ plants was significantly (p < 0.05) decreased, while Cd accumulation in E+ plants was significantly (p < 0.05) increased. Thus, FXZ2 has excellent application prospects in Cd phytoextraction and decreasing Zn toxicity in agriculturally important crops.

Phytoremediation is a promising remediation method of heavy metal (HM)–contaminated soils. However, lower HM tolerance of metal accumulator inhibits its practical application and effects. The current study was aimed to illustrate the role of fungal seed endophyte (FZT214) in improving Dysphania ambrosioides Cd tolerance during different developmental stages under various Cd stresses (5, 15, 30 mg kg–1) by pot experiments. The results showed that FZT214 significantly (p < 0.05) improved the host plant’s growth at the flowering and fruiting stage in most of the treatment, while at the growing stage the increase was less (p > 0.05). The seed yield was also improved (p < 0.05) in the FZT214-inoculated plants (E+) and induced early flowering was observed. Moreover, the inoculation also positively affected total chlorophyll content, antioxidant process, and lipid peroxidation in most of the treatments throughout three developmental stages. Not all but in most cases, IAA and GA were more in E+ plants while JA was more in the E− plants (non-inoculated plants) during three developmental stages. The results suggested that the colonization of FZT214 to the D. ambrosioides might trigger multiple and comprehensive protective strategies against Cd stress, which mainly include activation of the dilution effects, induced biochemical changes to overcome damage from Cd toxicity, and alteration of the endogenous phytohormones. FZT214 can find competent application in the future to improve the growth of other crop plants.

IntroductionHuman adenovirus (HAdV) is a common pathogen in children with acute respiratory infections (ARIs). The aim was to describe the epidemiology, molecular, and clinical characteristics of HAdV among children hospitalized with ARIs in Wenzhou in southeastern China.MethodologyFrom January 2018 to December 2019, nasopharyngeal swab or sputum specimens were prospectively collected from hospitalized children with ARIs. HAdV was detected using direct immunofluorescence. We used a multiplex PCR assay combined with capillary electrophoresis targeting the hexon gene’s hypervariable region to identify HAdV types 1, 2, 3, 4, 5, 7, 14, 21, 37, 40, 41, and 55. We analyzed the epidemiological, molecular, and clinical data according to the HAdV type.ResultsHAdVs were detected in 1,059 (3.5%) of the total of 30,543 children tested. A total of 947 cases with monotype HAdV identified by the PCR assay were included in the analysis. HAdV-3 (415/947, 43.8%), HAdV-7 (318/947, 33.6%), HAdV-2 (108/947, 11.4%), and HAdV-1 (70/947, 7.4%) were the predominant types. Of the 550 (58.1%) cases detected from December 2018 to August 2019, HAdV-3, and HAdV-7 were the main types. The main diagnoses included 358 cases of pneumonia, 232 cases of tonsillitis, 198 cases of bronchitis, and 159 cases of upper respiratory tract infection (URTI). Among children with pneumonia the main types were HAdV-7 (51.1%), HAdV-3 (36.9%), and HAdV-1 (2.2%). Among children with bronchitis, the main types were HAdV-3 (48.0%), HAdV-7 (28.3%), and HAdV-2 (10.6%). Among children with URTIs, the main types were HAdV-3 (49.7%), HAdV-7 (22.6%), and HAdV-2 (13.2%). Among children with tonsillitis, the main types were HAdV-3 (47.4%), HAdV-2 (22.4%), and HAdV-7 (18.5%). In total, 101 (55.2%) patients required supplemental oxygen, 15 (8.2%) required critical care, and 1 child (0.5%) with HAdV-7 pneumonia died.ConclusionHAdV-3 -7, -2, and -1 were the predominant types identified in hospitalized children with ARIs in Wenzhou. From December 2018 to August 2019, there were outbreaks of HAdV-3 and -7. There were significant differences in HAdV types among children with pneumonia, tonsillitis, bronchitis, and URTI. HAdV-7 can cause more severe pneumonia in children than HAdV-3.

The mechanisms of adaptive resistance of Escherichia coli to aminoglycosides remain unclear. Our RNA-Seq study found that expression of yhjX was markedly upregulated during initial exposure to subinhibitory concentrations of gentamicin. The expression of yhjX was then downregulated dramatically during a second exposure to gentamicin compared to the first exposure. YhjX encodes a putative transporter of the major facilitator superfamily, which is known to be the sole target of the YpdA/YpdB two-component system, the expression of which is highly and specifically induced by pyruvate. To investigate the effect of yhjX on the adaptive resistance of E. coli, in the present study, we constructed yhjX deletion and complemented strains of E. coli ATCC25922. Changes in extracellular pyruvate levels of wide-type and yhjX mutant were measured to determine whether YhjX functions as a pyruvate transporter. The results showed that yhjX deletion improved the growth of E. coli in medium containing subinhibitory concentrations of gentamicin. The yhjX deletion mutant did not exhibit adaptive resistance to subinhibitory concentrations of gentamicin. YhjX might not function as a pyruvate efflux pump in E. coli but was associated with the decrease following a sharp increase in the extracellular pyruvate level. Our findings indicate that yhjX regulates the growth of E. coli in the presence of a subinhibitory concentration of gentamicin and mediates the adaptive resistance to gentamicin.

With the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.

Powdery mildew (PM) is one of the most devastating and wide spread fungal diseases of rose, which seriously decrease its productivity and commercial value. In the present study, the endophytic fungal communities of two wild Rosa varieties (Rosa multiflora Thunb and R. multiflora var. carnea Redouté and Thory) with different PM susceptibilities were studied through Illumina MiSeq sequencer. A total of 14,000,424 raw reads were obtained from 60 samples, and 6,862,953 tags were produced after merging paired-end reads. 4462 distinct OTUs were generated at a 97% similarity level. It was found that only 34.2% of OTUs shared between two plant varieties. All of the OTUs were assigned into four fungal phyla, 17 classes, 43 orders, 86 families, 157 genera, and 208 species. Members of Ascomycota were found to be the most common fungal endophytes (EF) among all plant samples (93.7% relative abundance), followed by Basidiomycota (4.7% relative abundance), while Zygomycota and Glomeromycota were found to be rare and incidental. At each developmental stage of plants, the diversity and community structure of EF between two Rosa varieties showed significant differences. Both PCoA plots and PERMANOVA analyses indicated that developmental stage was the major factor contributing to the difference between the Rosa varieties (R2 = 0.348, p < 0.001). In addition, plant varieties and tissues were also important factors contributing to the difference (R2 = 0.031, p < 0.05; R2 = 0.029, p < 0.05). Moreover, Neofusicoccum, Rhodosporidium, and Podosphaera, etc., were found to be significantly different between two Rosa varieties, and some of the endophytes may play a role in PM resistance. These finding are encouraging to testify the potential use of these fungi in the biocontrol of PM in future studies.

Metal-induced oxidative stress in contaminated soils affects plant growth. In the present study, we evaluated the role of seed endophyte FXZ2 on Dysphania ambrosioides Zn/Cd tolerance and accumulation. A series of pot experiments were conducted under variable Zn (500, 1,000, and 1,500 mg kg-1) and Cd (5, 15, 30, and 60 mg kg-1). The results demonstrated that FXZ2-inoculation significantly enhanced the growth of D. ambrosioides and improved its chlorophyll and GSH content. In the rhizosphere, FXZ2 inoculation changed the chemical speciation of Zn/Cd and thus affected their uptake and accumulation in host plants. The exchangeable and carbonatebound fractions (F1 + F2) of Zn decreased in the rhizosphere of FXZ2-inoculated plants (E+) as compared to non-inoculated plants (E-) under Zn stress (500 and 1,000 mg kg-1), correspondingly, Zn in the shoots of E+ decreased (p < 0.05). However, at Cd stress (30 and 60 mg kg-1), the F1 + F2 fractions of Cd in E+ rhizospheric soils increased; subsequently, Cd in the shoots of E+ increased (p < 0.05). FXZ2 could exogenously secrete phytohormones IAA, GA, and JA. The study suggests that seed endophyte FXZ2 can increase Zn/Cd tolerance of host plant by altering Zn/Cd speciation in rhizospheric soils, as well as exogenous production of phytohormones to promote growth, lowering oxidative damage while enhancing antioxidant properties. For Zn/Cd accumulation, it has opposite effects: Zn uptake in E+ plants was significantly (p < 0.05) decreased, while Cd accumulation in E+ plants was significantly (p < 0.05) increased. Thus, FXZ2 has excellent application prospects in Cd phytoextraction and decreasing Zn toxicity in agriculturally important crops. [ABSTRACT FROM AUTHOR]

Diversifying cultivation management, including different crop rotation patterns and soil amendment, are effective strategies for alleviating the obstacles of continuous cropping in peanut (Arachis hypogaea L.). However, the peanut yield enhancement effect and temporal changes in soil chemical properties and microbial activities in response to differential multi-year crop rotation patterns and soil amendment remain unclear. In the present study, a multi-year localization experiment with the consecutive application of five different cultivation managements (including rotation with different crops under the presence or absence of external quicklime as soil amendment) was conducted to investigate the dynamic changes in peanut nutrient uptake and yield status, soil chemical property, microbial community composition and function. Peanut continuous cropping led to a reduction in peanut yield, while green manure-peanut rotation and wheat-maize-peanut rotation increased peanut yield by 40.59 and 81.95%, respectively. A combination of quicklime application increased yield by a further 28.76 and 24.34%. Alterations in cultivation management also strongly affected the soil pH, nutrient content, and composition and function of the microbial community. The fungal community was more sensitive than the bacterial community to cultivation pattern shift. Variation in bacterial community was mainly attributed to soil organic carbon, pH and calcium content, while variation in fungal community was more closely related to soil phosphorus content. Wheat-maize-peanut rotation combined with quicklime application effectively modifies the soil acidification environment, improves the soil fertility, reshapes the composition of beneficial and harmful microbial communities, thereby improving soil health, promoting peanut development, and alleviating peanut continuous cropping obstacles. We concluded that wheat-maize-peanut rotation in combination with quicklime application was the effective practice to improve the soil fertility and change the composition of potentially beneficial and pathogenic microbial communities in the soil, which is strongly beneficial for building a healthy soil micro-ecology, promoting the growth and development of peanut, and reducing the harm caused by continuous cropping obstacles to peanut.

Endophytes are critical for plant growth and health. Tea is an economically important crop in China. However, little is known about the distribution pattern and potential functions of endophytic communities in tea trees. In this study, two genotypes (BXZ and MF) cultivated under the same conditions were selected, and endophytic bacteria and fungi were analyzed through 16S rRNA and ITS high-throughput sequencing technologies, respectively. For endophytic bacteria, root tissues harbored the most diverse endophytes, followed by stems and old leaves, and new leaves possessed the lowest diversity. In contrast, old leave tissues harbored more diverse endophytic fungi than did root and stem tissues. Most of the dominant endophytes showed obvious cultivar and tissue preferences. Tissue type played a more important role in shaping community structure than did cultivar. Nevertheless, some endophytic bacterial groups, which mainly affiliated to Chryseobacterium, Sphingomonas, Rhizobium, Morganella, Methylobacterium and Comamonadaceae, could parasitize different tissues, and the average relative abundance of endophytic bacteria was as high as 72.57%. Some endophytic fungal populations, such as Colletotrichum, Uwebraunia, Cladosporium, and Devriesia, could also parasitize tea, and the relative abundance accounted for approximately 25.70–97.26%. The cooperative relationship between endophytic bacteria and fungi in the new leaves was stronger than that in the old leaves, which can better participate in the metabolism of tea material.

Infection is a severe complication of allo-HSCT in children, however, the accurate detection of the infection is hard. In this study, we traced the records of 101 pediatric recipients with allo-HSCT to investigate the pathogens of infection, and collected 54 bronchoalveolar lavage fluid, 32 blood, and 15 cerebrospinal fluid samples. In these samples, 87 was with post-transplant infection and 14 without infection. Using the metagenomic next-generation sequencing (mNGS) and traditional pathogen detection, we compared their sensitivity and specificity to detect pathogens of infection. Our results showed that mNGS was more sensitive (89.7%) than conventional pathogen detection (21.8%), with a difference of 67.9% (P < 0.001), However, mNGS was less specific (78.5%) than traditional methods (92.9%), with a difference of 14.4% (P = 0.596). The sensitivity of mNGS for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 91.7, 85.7, and 90.9%, respectively. In contrast, the sensitivity of conventional testing for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 22.9, 21.4, and 18.2%, respectively. There were significant differences in the sensitivity of mNGS and conventional testing in BALF, blood, and CSF samples, with P values of 0.000, 0.000, and 0.002 respectively. Among the patients with pulmonary infection, 11 pathogens were both identified by mNGS and conventional testing, and 33 by mNGS only. The percentage with the mNGS-positive result was 44/48 (91.7%), including viruses (n = 12), bacteria (n = 17), fungi (n = 9) and mixed infections (n = 6). Among the patients diagnosed with fungal pneumonia (n = 9), the most prevalent pathogenic fungi were Pneumocystis jiroveci (n = 6), which were also detected in 4 patients with mixed infectious pneumonia. In the 28 blood specimens of patients with bloodstream infections or viremia, five patients were positive by both mNGS and conventional testing, 19 were positive by mNGS, and 1 was positive by traditional testing only. The percentage with the mNGS-positive results was 24/28 (85.7%), including viruses (n = 12), bacteria (n = 4), fungi (n = 3), and mixed infections (n = 5). Of the 15 CSF specimens enrolled, 11 patients were eventually diagnosed with CNS infections. Ten pathogens were identified by mNGS in the 11 patients, including viruses (n = 8), bacteria (n = 1), and fungi (n = 1). These results suggest that mNGS is more sensitive than conventional pathogen detection for diagnosing infections post HSCT in children which may help the clinic diagnosis. Pneumocystis jiroveci was the most frequent pathogen of pulmonary infections post-transplant, while viruses were the most common pathogens of CNS infections in allo-HSCT recipients.