Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up.

BACKGROUND: Due to the outbreak and rapid spread of coronavirus disease 2019 (COVID-19), more than 160 million patients have become convalescents worldwide to date. Significant alterations have occurred in the gut and oral microbiome and metabonomics of patients with COVID-19. However, it is unknown whether their characteristics return to normal after the 1-year recovery. METHODS: We recruited 35 confirmed patients to provide specimens at discharge and one year later, as well as 160 healthy controls. A total of 497 samples were prospectively collected, including 219 tongue-coating, 129 stool and 149 plasma samples. Tongue-coating and stool samples were subjected to 16S rRNA sequencing, and plasma samples were subjected to untargeted metabolomics testing. RESULTS: The oral and gut microbiome and metabolomics characteristics of the 1-year convalescents were restored to a large extent but did not completely return to normal. In the recovery process, the microbial diversity gradually increased. Butyric acid-producing microbes and Bifidobacterium gradually increased, whereas lipopolysaccharide-producing microbes gradually decreased. In addition, sphingosine-1-phosphate, which is closely related to the inflammatory factor storm of COVID-19, increased significantly during the recovery process. Moreover, the predictive models established based on the microbiome and metabolites of patients at the time of discharge reached high efficacy in predicting their neutralizing antibody levels one year later. CONCLUSIONS: This study is the first to characterize the oral and gut microbiome and metabonomics in 1-year convalescents of COVID-19. The key microbiome and metabolites in the process of recovery were identified, and provided new treatment ideas for accelerating recovery. And the predictive models based on the microbiome and metabolomics afford new insights for predicting the recovery situation which benefited affected individuals and healthcare.

Drought-induced alterations in photosynthetic, ultrastructural and biochemical traits of contrasting sugarcane genotypes.

Drought is an important factor which limits growth of sugarcane. To elucidate the physiological and biochemical mechanisms of tolerance, a pot experiment was conducted at Sugarcane Research Institute, Kaiyuan, China. Two genotypes (Yuetang 93-159-sensitive and Yunzhe 05-51-tolerant), were subjected to three treatments; 70±5% (control), 50±5% (moderate drought) and 30±5% (severe drought) of soil field capacity. The results demonstrated that drought induced considerable decline in morpho-physiological, biochemical and anatomical parameters of both genotypes, with more pronounced detrimental effects on Yuetang 93-159 than on Yunzhe 05-51. Yunzhe 05-51 exhibited more tolerance by showing higher dry biomass, photosynthesis and antioxidant enzyme activities. Compared with Yuetang 93-159, Yunzhe 05-51 exhibited higher soluble sugar, soluble protein and proline contents under stress. Yunzhe 05-51 illustrated comparatively well-composed chloroplast structure under drought stress. It is concluded that the tolerance of Yunzhe 05-51 was attributed to improved antioxidant activities, osmolyte accumulation and enhanced photosynthesis. These findings may provide valuable information for future studies on molecular mechanism of tolerance.

Manure amendment increased the abundance of methanogens and methanotrophs but suppressed the type I methanotrophs in rice paddies.

Methane (CH4) emission is the consequence of CH4 production and consumption performed by methanogens and methanotrophs, respectively. Fertilization is an important factor that regulates the behavior of methanogens and methanotrophs; however, the effect of manure and rice straw addition combined with inorganic fertilizers on these communities is not well understood. This study aimed to explore how manure and rice straw amendments together with inorganic fertilizers influenced the methanogenic and methanotrophic communities in a 31-year fertilized rice paddy. Manure amendment significantly increased the abundance of mcrA and pmoA genes by 61.2% and 63.3% compared with the unfertilized control, whereas inorganic NPK fertilization alone or rice straw addition did not affect their abundances. Manure and rice straw amendments greatly decreased the Shannon index and ACE index of the methanogenic communities, whereas inorganic NPK fertilization alone increased the ACE index of the methanotrophic communities compared with the unfertilized control. Methanosarcinaceae and Methylococcaceae dominated at the family level, representing 23.1-35.0% and 48.7-67.2% of the total reads, for the methanogenic and methanotrophic communities, respectively. Application of manure together with inorganic fertilizers suppressed the Methanocellales methanogens and the type I methanotrophs (Methylococcus and Methylobacter). Fertilization greatly altered the community structure of methanogens and methanotrophs, and manure addition had more apparent effects than rice straw. Moreover, total nitrogen, soil organic carbon, available phosphorus, and available potassium correlated significantly to the abundance, composition, and community structure of methanogens and methanotrophs. In conclusion, our study revealed that long-term manure amendment in combination with inorganic fertilizers significantly increased the abundance of methanogens and methanotrophs, but suppressed the type I methanotrophs in rice paddies.

Methane emissions responding to Azolla inoculation combined with midseason aeration and N fertilization in a double-rice cropping system.

Methane (CH4) is an important greenhouse gas (GHG), and paddy fields are major sources of CH4 emissions. This pot experiment was conducted to investigate the integrated effects of Azolla inoculation combined with water management and N fertilization on CH4 emissions in a double-rice cropping system of Southern China. Results indicated that midseason aeration reduced total CH4 emissions by 46.9%, 38.6%, and 42.4%, followed by N fertilization with 32.5%, 17.0%, and 29.5% and Azolla inoculation with 32.5%, 17.0%, and 29.5%, on average, during the early, late, and annual rice growing seasons, respectively. The CH4 flux peaks and total CH4 emissions observed in the late rice growing season were significantly higher than those in the early rice growing season. Additionally, CH4 fluxes correlated negatively to soil redox potential (Eh) and dissolved oxygen (DO) concentration. Azolla inoculation and N fertilization greatly increased the rice grain yields, whereas midseason aeration had distinct effects on grain yields in both rice seasons. The highest annual rice grain yields of approximately 110 g pot-1 were obtained in the Azolla inoculation and N fertilization treatments. In terms of yield-scaled CH4 emission, Azolla inoculation combined with midseason aeration and N fertilization generated the lowest yield-scaled CH4 emissions both in the early and in the late rice growing seasons, as well as during the annual rice cycle. In contrast, the highest yield-scaled CH4 emission was obtained in the treatment employed continuous flooding, without Azolla and no N application. Our results demonstrated that Azolla inoculation, midseason aeration, and N fertilization practices mitigated total CH4 emissions by 18.5-42.4% during the annual rice cycle. We recommend that the combination of Azolla inoculation, midseason aeration, and appropriate N fertilization can achieve lower CH4 emissions and yield-scaled CH4 emissions in the double-rice growing system.

[Effects of long-term different fertilization regimes on the abundance and community structure of ammonia oxidizers in paddy soils]. / 长期不同施肥制度对水稻土氨氧化微生物数量和群落结构的影响.

Ammonia oxidation, driven by the ammonia oxidizers, is the rate-limiting step of nitrification and plays a key role in soil nitrogen cycling. In this study, real-time PCR and Illumina MiSeq sequencing approaches were used to investigate the effects of long-term different fertilization regimes on the abundance and community structure of ammonia oxidizers, targeting the amoA genes, in a 30-year located experimental paddy soil in Ningxiang County, Hunan Province. Four treatments were compared, including control without fertilizer (CK), fertilizers NPK (CF), 70% NPK plus 30% manure (CFM1), and 40% NPK plus 60% manure (CFM2). The results showed that the abundance of amoA genes in AOA and AOB was in the range of 3.09×107-8.37×107 and 1.04×107-7.03×107 copies·g-1 dry soil, respectively. Fertilization significantly increased the AOA and AOB abundances. However, no significant difference was observed in AOB abundance between CFM2 and CK. Manure fertilization rate greatly affected the α diversity index of AOB rather than AOA. The Shannon index of AOA and ACE and Chao1 indexes of AOB observed in CFM1 were significantly higher than that in CK, respectively. Thaumarchaeota and Crenarchaeota were the predominant AOA phyla and Nitrosospira, environmental_samples_norank, Bacteria_unclassified and Nitrosomonadales_unclassified were the main AOB genus groups which accounted for 83.4% and 97.8% of the total AOA and AOB amoA gene reads, respectively. Venn diagram indicated that manure fertilization rate had a stronger effect on the OTU number of AOB amoA gene than that of AOA in different treatments, but it slightly altered the proportion of shared AOA and AOB amoA gene reads. Furthermore, there were pronounced differences in the community structure of AOB among different treatments than that of AOA. These results suggested that manure fertilization rate significantly affected the abundance, diversity and community structure of AOA and AOB. The Shannon index of AOA and the abundance and ACE and Chao1 indexes of AOB in CFM1 were significantly higher than that in the rest treatments, respectively. Our results provided basis for further exploring the response mechanism of ammonia oxidizers to different fertilization strategies and the roles of ammonia oxidizers in nitrogen transformation in agricultural systems.

Variations of the nirS-, nirK-, and nosZ-denitrifying bacterial communities in a northern Chinese soil as affected by different long-term irrigation regimes.

Denitrification causes nitrogen loss from agricultural soils and emission of nitrous oxide (N2O). Water addition leads to an increase in soil moisture which greatly influenced soil denitrification. However, it is unclear how irrigation management affected the denitrifying bacterial communities in agricultural systems. In the present study, we investigated the abundance, diversity, and composition of the nirS-, nirK-, and nosZ-denitrifying bacterial communities in the soil under different long-term irrigation regimes by using real-time PCR (qPCR) and Illumina MiSeq sequencing approaches. Results showed that the abundance of nosZ gene was 3.94-6.01 and 35.09-60.21 times more than that of nirS and nirK genes, and the abundance of nirS gene was 5.84-15.30 times higher than that of nirK gene, respectively, in different irrigation treatments. However, the Alpha diversity indices of the nirK-denitrifying bacterial community were higher than those of the nirS- and nosZ-denitrifying bacterial communities. Proteobacteria was the predominant phylum for all the denitrifying bacterial communities, and significant differences were observed in relative abundance of Alphaproteobacteria and Betaproteobacteria in predominant class between different irrigation treatments for the nirS- and nosZ-denitrifying bacterial communities, respectively. Irrigation significantly affected the abundance, Shannon and Invsimpson indices, and structure of the nirS- and nosZ-denitrifying bacterial communities, whereas it only minor influenced the structure of the nirK-denitrifying bacterial community. Furthermore, the shifts in abundance, diversity, and structure of the nirS- and nosZ-denitrifying bacterial communities correlated significantly with the soil property variations; however, no soil property was significantly correlated with the abundance and Alpha diversity index of the nirK-denitrifying bacterial community. Our results demonstrate that different long-term irrigation regimes greatly altered the abundance, diversity, and structure of the nirS- and nosZ- rather than the nirK-denitrifying bacterial communities.

[Effects of legume-oat intercropping on abundance and community structure of soil N2-fixing bacteria]. / 豆科作物间作燕麦对土壤固氮微生物丰度和群落结构的影响.

In this study, real-time PCR and high-throughput sequencing approaches were employed to investigate the abundance and community structure of N2-fixing bacteria in a field experiment with three planting patterns (Oat monoculture, O; Soybean-oat intercropping, OSO; Mung bean-oat intercropping, OMO). The results showed that soil chemical properties varied significantly in different soil samples (P＜0.05). The abundance of nifH gene varied from 1.75×1010 to 7.37×1010 copies·g-1 dry soil in all soil samples. The copy numbers of nifH gene in OSO and OMO were 2.18, 2.64, and 1.92, 2.57 times as much as that in O at jointing and mature stages, with a significant decline from jointing to mature stage for all treatments (P＜0.05). Rarefaction curve and cove-rage results proved the nifH gene sequencing results were reliable, and the diversity index showed that the N2-fixing bacteria diversity of OSO was much higher than that of O. Azohydromonas, Azotobacter, Bradyrhizobium, Skermanella and other groups that could not be classified are the dominant genera, with significant differences in proportion of these dominant groups observed among all soil samples (P＜0.05). Venn and PCA analysis indicated that there were greater differences of nifH gene communities between jointing and mature stages; however, the OSO and OMO had similar communities in both stages. All these results confirmed that legume-oat intercropping significantly increased the abundance and changed the community composition of N2-fixing bacteria in oat soils.

[Selenium (Se)uptake and transformation mechanisms and physiological function in plant: A review]. / æ¤ç‰©ç¡’å¸æ”¶è½¬åŒ–æœºåˆ¶åŠç”Ÿç†ä½œç”¨ç ”ç©¶è¿›å±•.

Selenium (Se) is an essential nutrient for many organisms, including microbe, animal and human, but the Se uptake and transformation mechanisms and physiological roles in plant still are controversial until now. Se could improve the growth and tolerance of plant at an appropriate le-vel, but could be toxic at higher levels. Research concerning Se uptake and metabolism in plant were promoted by Se biofortification and Se phytoremediation induced by the issues of Se deficiency in food and Se pollution in special areas. Recently, the results of Se uptake and transformation in plant have indicated that there are significant differences of Se accumulation and physiological roles in various plants and significant influence of soil conditions on Se uptake of plant. In addition, the process of Se metabolism in Se hyperaccumulators and its regulation were revealed gradually with the studies on improvement of Se uptake in plant. According to the results of Se biofortification in crop and Se phytoremediation so far, we summarized the advances in the studies with the reference to Se distribution in environment, the detail process of Se uptake, key regulators of transformation and its physiological roles in plant. We hope this can provide a novel insight to further research upon Se in plant.

Characterization of ampicillin-stressed proteomics and development of a direct method for detecting drug-binding proteins in Edwardsiella tarda.

Antibiotic-resistant Edwardsiella tarda poses a severe challenge to aquaculture. An understanding for antibiotic-resistant mechanisms is crucial to control the disease. The present study characterizes E. tarda ampicillin-stressed proteome and shows the importance of energy metabolism including the TCA cycle and glycolysis/gluconeogenesis in the antibiotic resistance. Further combination with antibiotic measurement develops a new method for identification of antibiotic-binding proteins out of differential abundances of proteins and results in determination of ETAE_0175 and ETAE_3367 as ampicillin-binding proteins in E. tarda. Genes of the two proteins are cloned and recombinant proteins are purified for validation of antibiotic-binding capability. Results show that higher binding capability is detected in ETAE_3367 than ETAE_0175. Out of the two proteins, ETAE_3367 is first reported here to be an antibiotic-binding protein, while ETAE_0175 homology in other bacteria has been shown to bind with other antibiotics. Bioinformatics analysis shows that ETAE_3367 may closely interact with aceF and sucA belonging to the TCA cycle and glycolysis/gluconeogenesis, respectively. These results indicate that energy metabolism contributes to ampicillin resistance in E. tarda and a new method to identify antibiotic-binding proteins is developed. These findings highlight the way to an understanding of antibiotic-resistant mechanisms in content of antibiotic-binding proteins. BIOLOGICAL SIGNIFICANCE: Our data characterizes Edwardsiella tarda ampicillin-stressed proteome and shows the importance of energy metabolism including the TCA cycle and glycolysis/gluconeogenesis in the antibiotic resistance. Furthermore, a new method based 2-DE proteomics is developed for identification of antibiotic-binding proteins, which results in determination of ETAE_0175 and ETAE_3367 as ampicillin-binding proteins in E. tarda. ETAE_3367 is closely interacted with proteins of the TCA cycle and glycolysis/gluconeogenesis, suggesting the drug-resistant mechanism.