Metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process:From collapse to recovery

Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.

Response and assembly of abundant and rare taxa in Zaopei under different combination patterns of Daqu and pit mud:from microbial ecology to Baijiu brewing microecosystem

The quality and aroma of strong-flavor Baijiu are mainly dependent on Daqu,pit mud(PM),and the interaction of both.However,little is known about how their combination patterns affect the microbiome and metabolome of Zaopei,especially the metabolic function of rare taxa.Here,an experiment on industrial size was designed to assess the effects of 6 combinations(3 kinds of Daqu×2 kinds of PM)on the composition and assembly of different taxa,as well as the flavor profile.The results showed that Zaopei's microbiota was composed of a few abundant taxa and enormous rare taxa,and rare bacterial and abundant fungal subcommunities were significantly affected by combination patterns.The assembly processes of abundant/rare taxa and bacterial/fungal communities were distinct,and environmental changes mediated the balance between stochastic and deterministic processes in rare bacteria assembly.Furthermore,specific combination patterns improved the flavor quality of Zaopei by enhancing the interspecies interaction,which was closely related to rare taxa,especially rare bacteria.These findings highlighted that rare bacteria might be the keystone in involving community interaction and maintaining metabolic function,which provided a scientific foundation for better understanding and regulating the brewing microbiota from the viewpoint of microbial ecology.

Microbial community structure and functional metabolic diversity are associated with organic carbon availability in an agricultural soil

Exploration of soil environmental characteristics governing soil microbial community structure and activity may improve our understanding of biogeochemical processes and soil quality. The impact of soil environmental characteristics especially organic carbon availability after 15-yr different organic and inorganic fertilizer inputs on soil bacterial community structure and functional metabolic diversity of soil microbial communities were evaluated in a 15-yr fertilizer experiment in Changping County, Beijing, China. The experiment was a wheat-maize rotation system which was established in 1991 including four different fertilizer treatments. These treatments included： a non-amended control（CK）, a commonly used application rate of inorganic fertilizer treatment（NPK）; a commonly used application rate of inorganic fertilizer with swine manure incorporated treatment（NPKM）, and a commonly used application rate of inorganic fertilizer with maize straw incorporated treatment（NPKS）. Denaturing gradient gel electrophoresis（DGGE） of the 16 S r RNA gene was used to determine the bacterial community structure and single carbon source utilization profiles were determined to characterize the microbial community functional metabolic diversity of different fertilizer treatments using Biolog Eco plates. The results indicated that long-term fertilized treatments significantly increased soil bacterial community structure compared to CK. The use of inorganic fertilizer with organic amendments incorporated for long term（NPKM, NPKS） significantly promoted soil bacterial structure than the application of inorganic fertilizer only（NPK）, and NPKM treatment was the most important driver for increases in the soil microbial community richness（S） and structural diversity（H）. Overall utilization of carbon sources by soil microbial communities（average well color development, AWCD） and microbial substrate utilization diversity and evenness indices（H＇ and E） indicated that long-term inorganic fertilizer with organic amendments incorporated（NPKM, NPKS） could significantly stimulate soil microbial metabolic activity and functional diversity relative to CK, while no differences of them were found between NPKS and NPK treatments. Principal component analysis（PCA） based on carbon source utilization profiles also showed significant separation of soil microbial community under long-term fertilization regimes and NPKM treatment was significantly separated from the other three treatments primarily according to the higher microbial utilization of carbohydrates, carboxylic acids, polymers, phenolic compounds, and amino acid, while higher utilization of amines/amides differed soil microbial community in NPKS treatment from those in the other three treatments. Redundancy analysis（RDA） indicated that soil organic carbon（SOC） availability, especially soil microbial biomass carbon（Cmic） and Cmic/SOC ratio are the key factors of soil environmental characteristics contributing to the increase of both soil microbial community structure and functional metabolic diversity in the long-term fertilization trial. Our results showed that long-term inorganic fertilizer and swine manure application could significantly improve soil bacterial community structure and soil microbial metabolic activity through the increases in SOC availability, which could provide insights into the sustainable management of China＇s soil resource.

Effect of Amino Acid Cardioplegia on Myocardial Metabolism and Function of Ischemic Canine Heart

To evaluate the effect of amino acid cardioplegia on myocardial metabolism and function of ischemic canine heart, canine cardiopulmonary bypass (CPB) model was established and the dog heart was subjected to a 120 min ischemic arrest. Animals were divided into 3 groups, group 1:warm blood cardioplegia induction and terminal perfusion plus 4 C ST. Thomas hospital solution (STS)during ischemia;group 2: warm blood cardioplegia enriched with amino acid (L-asparte and L-glutamate 13 mmol/L each) and STS without amino acid (A.G.) and group 3:both warm blood cardioplegic solution and STS enriched with A. G..The result demonstrated that the cardiac function of animals in group 2 and 3 had a significantly better recovery after ischemic-re-perfusion. By the end of ischemia the content of myocardial ATP in group 3 was distinctly higher than that in group 1(P<0. 05), with the release of cardiac enzyme being the least. Myocardial ultra-structure almost remained intact before and after ischemia. Our experiment suggests that the cardioplegia arrest with warm blood and cold crystalloid solution enriched with amino acids could diminish the ischemia-re-perfusion injuries of the heart and enhance the effect of myocardial protection.

A comparative study of pancreatic endocrine function and related metabolism after long-term survival between the patients with combined kidneypancreas transplantation vs those with combined en bloc ' liver-pancreas transplantation

Objective To compare the effects of combined en bloc liver - pancreas transplantation ( LPT) with portal vein drainage and simultaneous combined kidney - pancreas transplantation ( KPT) with systemic venous drainage on the pancreatic endocrine function and related me-

Structure elucidation and in vitro rat intestinal fermentation properties of a novel sulfated glucogalactan from Porphyra haitanensis

This study was to investigate the structure and rat fecal microbial fermentation properties of a polysaccharide fraction(PHP2)isolated from the red marine alga Porphyra haitanensis.PHP2 was characterized as a sulfated glucogalactan,with a hypothetical backbone structure of→4)Gα(1→6)G4 Sβ(1→4)Glc(1→and a side chain of Man(1→6)Glc.PHP2 had an irregular spherical chain conformation.The 16 S r RNA sequence analysis revealed that PHP2 modulated the rat fecal micro-flora composition,with a similar effect to inulin,changing the dominant genus(Lactobacillus and Escherichia-Shigella)and promoting the growth of organisms that degrade sulfur-containing polysaccharides,such as Desulfovibrio,Ruminococcaceae_UCG-005,and Ruminococcus_2.PHP2 can promote production of acetic,propionic and butyric acid by rat fecal micro-flora.Prediction of metabolic function suggested that PHP2 could modulate cholesterol metabolism.The sulfated glucogalactan fermentation behavior may be associated with its monosaccharide composition,chain branching and chain conformation.PHP2 appeared to have considerable potential as functional food,and was associated with sulfur-containing polysaccharides in general.

Liver-related effects of chronic hepatitis C antiviral treatment

More than five years ago,the treatment of hepatitis C virus infection was revolutionized with the introduction of all-oral direct-acting antiviral(DAA)drugs.They proved highly efficient in curing patients with chronic hepatitis C(CHC),including patients with cirrhosis.The new DAA treatments were alleged to induce significant improvements in clinical outcome and prognosis,but the exact cause of the expected benefit was unclear.Further,little was known about how the underlying liver disease would be affected during and after viral clearance.In this review,we describe and discuss the liver-related effects of the new treatments in regards to both pathophysiological aspects,such as macrophage activation,and the time-dependent effects of therapy,with specific emphasis on inflammation,structural liver changes,and liver function,as these factors are all related to morbidity and mortality in CHC patients.It seems clear that antiviral therapy,especially the achievement of a sustained virologic response has several beneficial effects on liver-related parameters in CHC patients with advanced liver fibrosis or cirrhosis.There seems to be a timedependent effect of DAA therapy with viral clearance and the resolution of liver inflammation followed by more discrete changes in structural liver lesions.These improvements lead to favorable effects on liver function,followed by an improvement in cognitive dysfunction and portal hypertension.Overall,the data provide knowledge on the several beneficial effects of DAA therapy on liverrelated parameters in CHC patients suggesting short-and long-term improvements in the underlying disease with the promise of an improved longterm prognosis.

Effects of Different Protein Levels on the Growth Performance and Metabolic Rate of Nutrition in Broilers

The objective of this study is to determine the effect of different protein levels on the growth performance and metabolic rate of nutrition in broilers. Total 360 healthy and weight closed local broilers of 3 weeks were chosen and then divided into three groups randomly by one factor. Each group contains three handlings, each handling consists of 40 broilers. The period of experiment was 7 weeks. The metabolic experiment was performed at the 7th week. Three different protein levels were used in broilers＇ diet. The levels of protein were 19%, 17.5% and 16%. The results showed that the different levels of protein in crude dietary had significant difference between 19% group and the other two groups. The average daily weight gain and daily efficiency were significantly higher than that of the other two groups （P〈0.05）. Compared to protein levels of 19% and 16%, there was no significant difference in the metabolism of calcium （P〉0.05）, and the metabolic rate of the impact of phosphorus was significantly different （P〈0.05）. The result showed that when protein level was 19%, the growth of the local broiler was the best.

Impacts of prenatal nutrition on animal production and performance： a focus on growth and metabolic and endocrine function in sheep

The concept of foetal programming（FP） originated from human epidemiological studies, where foetal life nutrition was linked to health and disease status later in life. Since the proposal of this phenomenon, it has been evaluated in various animal models to gain further insights into the mechanisms underlying the foetal origins of health and disease in humans. In FP research, the sheep has been quite extensively used as a model for humans. In this paper we will review findings mainly from our Copenhagen sheep model, on the implications of late gestation malnutrition for growth, development, and metabolic and endocrine functions later in life, and discuss how these implications may depend on the diet fed to the animal in early postnatal life. Our results have indicated that negative implications of foetal malnutrition, both as a result of overnutrition and, particularly, late gestation undernutrition, can impair a wide range of endocrine functions regulating growth and presumably also reproductive traits. These implications are not readily observable early in postnatal life, but are increasingly manifested as the animal approaches adulthood. No intervention or cure is known that can reverse this programming in postnatal life. Our findings suggest that close to normal growth and slaughter results can be obtained at least until puberty in animals which have undergone adverse programming in foetal life, but manifestation of programming effects becomes increasingly evident in adult animals.Due to the risk of transfer of the adverse programming effects to future generations, it is therefore recommended that animals that are suspected to have undergone adverse FP are not used for reproduction. Unfortunately, no reliable biomarkers have as yet been identified that allow accurate identification of adversely programmed offspring at birth,except for very low or high birth weights, and, in pigs, characteristic changes in head shape（dolphin head）. Future efforts should be therefore dedicated to identify reliable biomarkers and evaluate their effectiveness for alleviation/reversal of the adverse programming in postnatal life. Our sheep studies have shown that the adverse impacts of an extreme, high-fat diet in early postnatal life, but not prenatal undernutrition, can be largely reversed by dietary correction later in life. Thus, birth（at term） appears to be a critical set point for permanent programming in animals born precocial,such as sheep. Appropriate attention to the nutrition of the late pregnant dam should therefore be a priority in animal production systems.

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy,Metabolic Function,and Natural Products

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic diversity.Here,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep microbiomes.The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 phyla.In addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition.Heterotrophic and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold seeps.Furthermore,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria.Overall,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

Abnormal energy metabolism and tau phosphorylation in the brains of middle-aged mice in response to atmospheric PM2.5 exposure

In light of the accelerated aging of the global population and the deterioration of the atmosphere pollution, we sought to clarify the potential mechanisms by which fine particulate matter（PM_（2.5）） can cause cognitive impairment and neurodegeneration through the alteration of mitochondrial structure and function. The results indicate that PM_（2.5） inhalation reduces ATP production by disrupting the aerobic tricarboxylic acid cycle and oxidative phosphorylation, thereby causing the hypophosphorylation of tau in the cortices of middle-aged mice. Furthermore, excessive reactive oxygen species generation was involved in the impairment. Interestingly, these alterations were partially reversed after exposure to PM_（2.5） ended. These findings clarify the mechanism involved in mitochondrial abnormality-related neuropathological dysfunction in response to atmospheric PM_（2.5） inhalation and provide an optimistic sight for alleviating the adverse health outcomes in polluted areas.

Bacillus amyloliquefaciens 40 regulates piglet performance,antioxidant capacity,immune status and gut microbiota

Probiotics can improve animal growth performance and intestinal health.Bacillus species,Lactobacillus species,Bifidobacterium species,yeast etc.are the common types of probiotics.However,understanding the effects of probiotics on the immune status and gut microbiota of weaning piglets and how the probiotics exert their impact are still limited.This study aimed to investigate the effects of Bacillus amyloliquefaciens 40(BA40)on the performance,immune status and gut microbiota of piglets.A total of 12 litters of newborn piglets were randomly divided into 3 groups.Piglets in control group were orally dosed with phosphate buffered saline;BA40 group and probiotics group were orally gavaged with resuspension BA40 and a probiotics product,respectively.The results showed that BA40 treatment significantly decreased(P<0.05)the diarrhea incidence(from d 5 to 40),diamine oxidase,D-lactate,interleukin(IL)-1βand interferon-γconcentrations compared with control group and probiotics group.Meanwhile BA40 dramatically increased the total antioxidant capacity,IL-10 and secretory immunoglobulin-A concentrations in contrast to control group.For the microbial composition,BA40 modulated the microbiota by improving the abundance of Bacteroides,Phascolarctobacterium(producing short-chain fatty acids)and Desulfovibrio and reducing the proliferation of pathogens(Streptococcus,Tyzzerella,Vellionella and paraeggerthella).Meanwhile,a metabolic function prediction explained that carbohydrate metabolism and amino acid metabolism enriched in BA40 group in contrast to control group and probiotics group.For correlation analysis,the results demonstrated that BA40-enriched Phascolarctobacterium and Desulfovibrio provide insights into strategies for elevating the health status and performance of weaned piglets.Altogether,BA40 exerted stronger ability in decreasing diarrhea incidence and improved antioxidant activity,gut barrier function and immune status of piglets than the other treatments.Our study provided the experimental and theoretical basis for the application of BA40 in pig production.

Influence of Panax ginseng Continuous Cropping on Metabolic Function of Soil Microbial Communities

Objective To investigate the influence of Panax ginseng continuous cropping on the carbon substrate metabolic activity of microbes in soils sampled from Dafang,Huangni,and Wulidi in Jilin Province,China.Methods Soil metabolisms of soil communities were characterized by community level physiological profiles using BIOLOGTM EcoPlate.Results Soils sampled from the three sites were analyzed and their metabolic activities were compared.Principal component analysis explored the significant variance in metabolic function of microbial communities in soils,though the Shannon index and the evenness index of them were similar.Futhermore,two principal components(PC1 and PC2),which contributed 67.83% and 10.78% of total variance,were extracted respectively.And also,substrates significantly correlated with PC1 and PC2 at the three sampling sites were identified.Conclusion Characteristic of soil is the primary factor influencing microbial communities,and P.ginseng continuous cropping has significant influence on microbial community.Though soil samples show similar microbial metabolic profiles,microbial communities in rhizosphere soil are changed obviously during the cultivation of P.ginseng,which would finally result in the unbalance of microbial community.Phytopathogens would gradually be the predominants in rhizosphere soil and make P.ginseng sick.

The “neighbor avoidance effect” of microplastics on bacterial and fungal diversity and communities in different soil horizons

Microplastics are a new type of environmental pollutant,and pose a serious threat to soil ecosystems.It is important to study microplastics effects on soil microorganisms to better understand their effects on terrestrial ecosystems.Therefore,we collected soil and microplastic samples from corn,pepper,peanut and cucumber fields in Shunyi District,Beijing,China,and used Illumina MiSeq high-throughput sequencing technology to analyze bacterial and fungal community composition and diversity.We focused on microplastic surface and its surrounding“rhizosphere-like”soil in the 0e10 cm(humus)and 10e20 cm(eluvial)deep horizons.Microbial richness and diversity on microplastic surface were significantly lower than those in surrounding“rhizosphere-like”soil,and microbial richness and diversity were reduced to a greater extent in the humus horizon than in the eluvial horizon.Microplastics likely enriched the microbes involved in their biodegradation.The relative abundance levels of Cyanobacteria and Basidiomycota on microplastic surfaces were significantly higher than those in surrounding“rhizosphere-like”soil,while the relative abundance levels of Acidobacteria,Chloreflexi,and Mortierellomycota were higher in“rhizosphere-like”soil.Furthermore,the relative abundance levels of pathways related to human diseases,animal pathogen,and fungal parasites were significantly higher on microplastic surfaces than in“rhizosphere-like”soil.These results show that the microbial diversity,richness,community structure and function between microplastic surfaces and surrounding“rhizosphere-like”soil are significantly different,leading to a“rhizosphere-like neighbor avoidance effect”between microplastic surfaces and the surrounding soil.

Microbial community characterization,activity analysis and purifying efficiency in a biofilter process

The growth and metabolism of microbial communities on biologically activated carbon （BAC） play a crucial role in the purification of drinking water. To gain insight into the growth and metabolic characteristics of microbial communities and the efficiency of drinking water treatment in a BAC filter, we analyzed the heterotrophic plate count （HPC）, phospholipid, dehydrogenase, metabolic function and water quality parameters during start-up and steady-state periods. In the start-up process of the filter with natural biofilm colonization, the variation in heterotrophic plate count levels was S-curved. The total phospholipid level was very low during the first 5 days and reached a maximum value after 40 days in the filter. The activity of dehydrogenase gradually increased during the first 30 days and then reached a plateau. The functional diversity of the microbial community in the filter increased, and then reached a relatively stable level by day 40. After an initial decrease, which was followed by an increase, the removal rate of NH4＋-N and COD_Mn became stable and was 80% and 28%, respectively, by day 40. The consumption rate of dissolved oxygen reached a steady level after 29 days, and remained at 18%. At the steady operation state, the levels of HPC, phospholipid, dehydrogenase activity and carbon source utilization had no significant differences after 6 months compared to levels measured on day 40. The filter was shown to be effective in removing NH4＋-N, NO2--N, CODMn, UV254, biodegradable dissolved organic carbon and trace organic pollutants from the influent. Our results suggest that understanding changes in the growth and metabolism of microorganisms in BAC filter could help to improve the efficiency of biological treatment of drinking water.