Manipulated precipitation regulated carbon and phosphorus limitations of microbial metabolisms in a temperate grassland on the Loess Plateau,China

Manipulated precipitation patterns can profoundly influence the metabolism of soil microorganisms.However,the responses of soil organic carbon(SOC)and nutrient turnover to microbial metabolic limitation under changing precipitation conditions remain unclear in semi-arid ecosystems.This study measured the potential activities of enzymes associated with carbon(C:β-1,4-glucosidase(BG)andβ-D-cellobiosidase(CBH)),nitrogen(N:β-1,4-N-acetylglucosaminidase(NAG)and L-leucine aminopeptidase(LAP))and phosphorus(P:alkaline phosphatase(AP))acquisition,to quantify soil microbial metabolic limitations using enzymatic stoichiometry,and then identify the implications for soil microbial metabolic limitations and carbon use efficiency(CUE)under decreased precipitation by 50%(DP)and increased precipitation by 50%(IP)in a temperate grassland.The results showed that soil C and P were the major elements limiting soil microbial metabolism in temperate grasslands.There was a strong positive dependence between microbial C and P limitations under manipulated precipitation.Microbial metabolism limitation was promoted by DP treatment but reversed by IP treatment.Moreover,CUE was inhibited by DP treatment but promoted by IP treatment.Soil microbial metabolism limitation was mainly regulated by soil moisture and soil C,N,and P stoichiometry,followed by available nutrients(i.e.,NO^(-)_(3),NH^(+)_(4),and dissolved organic C)and microbial biomass(i.e.,MBC and MBN).Overall,these findings highlight the potential role of changing precipitation in regulating ecosystem C turnover by limiting microbial metabolism and CUE in temperate grassland ecosystems.

Real-Time Monitoring of Dynamic Chemical Processes in Microbial Metabolism with Optical Sensors

Monitoring microbial metabolism is vital for revealing the mechanism of disease related to microbial metabolism and providing guidance for biomanufacturing processes optimization.However,it remains a grand challenge to offer real-time insights into microbial metabolism owing to the complex and dynamic process.In this paper,the recent advances and prospects of optical biosensors including the organic,genetic coding and inorganic optical biosensors are briefly described for real-time monitoring of dynamic microbial metabolism.This paper points out that challenges remain in microbial heterogeneity.We believe that this work will inspire the application of developing new methods for single cell real-time analysis.

Nitrogen availability regulates deep soil priming effect by changing microbial metabolic efficiency in a subtropical forest

In terrestrial ecosystems,deep soils(below 30 cm)are major organic carbon(C)pools.The labile carbon input could alter soil organic carbon(SOC)mineralization,resulting in priming effect(PE),which could be modified by nitrogen(N)availability,however,the underlying mechanism is unclear for deep soils,which complicates the prediction of deep soil C cycling in response to N deposition.A series of N applications with ^(13)C labeled glucose was set to investigate the effect of labile C and N on deep SOC mineralization.Microbial biomass,functional community,metabolic efficiency and enzyme activities were examined for their effects on SOC mineralization and PE.During incubation,glucose addition promoted SOC mineralization,resulting in positive PE.The magnitude of PE decreased significantly with increasing N.The N-regulated PE was not dependent on extracellular enzyme activities but was positively correlated with carbon use efficiency and negatively with metabolic quotient.Higher N levels resulted in higher microbial biomass and SOC-derived microbial biomass than lower N levels.These results suggest that the decline in the PE under high N availability was mainly controlled by higher microbial metabolic efficiency which allocated more C for growth.Structural equation modelling also revealed that microbial metabolic efficiency rather than enzyme activities was the main factor regulating the PE.The negative effect of additional N suggests that future N deposition could promote soil C sequestration.

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.

Dietary citrus pectin drives more ileal microbial protein metabolism and stronger fecal carbohydrate fermentation over fructooligosaccharide in growing pigs

Fructo-oligosaccharide(FOS)and pectin are known soluble dietary fibers and can influence gut microbiota and consequently modulate gut health.To understand the differential impact patterns of pectin vs.FOS in modulating gut microbiota in the small and large intestine,an ileal-cannulated pig model was adopted to compare the temporal and spatial effects of FOS and citrus pectin(CP)on the gut microbiota.Sixteen terminal ileal-cannulated pigs were randomly divided into 2 groups and fed with a standard diet supplemented with either 3% FOS or 3% CP for 28 d.The CP group and FOS group showed different microbial composition,especially in the feces,with time and location as major factors affecting microbiota in the CP group,and with only location contribution in the FOS group.In the feces,relative to the FOS group,the CP group showed higher abundance of Christensenellaceae R-7 group and Ruminococcaceae UCG-010 and lower abundance of Mitsuokella and Olsenella(adjusted P<0.05),a higher level of shortchain fatty acids and a lower level of lactate at both d 14 and 25(P<0.05),and more copy numbers of genes encoding key enzymes related to propionate(mmd A)and butyrate(BCo AT)production and lactate utilization(Lcd A)(P<0.05),indicating a greater degree of microbial carbohydrate fermentation.In the ileum,as compared with FOS,CP increased the bacteria with high capability of fermenting amino acids,including Escherichia-Shigella and Klebsiella(adjusted P<0.05),and the expression of enzymes responsible for amino acid fermentation(i.e.lysine decarboxylase),as well as the amino acid fermentation products(cadaverine and tyramine)(P<0.05),indicating a greater degree of amino acid fermentation.Overall,our results highlight a differential dynamic impact of dietary CP vs.FOS on microbial composition and metabolism in the gut.The dietary CP has a stronger ability to promote microbial amino acid fermentation in the ileum and carbohydrate fermentation in the feces than FOS.These findings provide a new insight into the role of different fibers in gut nutrition and guidelines for the choice of fibers in manipulating gut health.

Rhamnolipids Induced by Glycerol Enhance Dibenzothiophene Biodegradation in Burkholderia sp. C3

In highly urbanized areas,pollution from anthropogenic activities has compromised the integrity of the land,decreasing soil availability for agricultural practices.Dibenzothiophene(DBT)is a heterocyclic aromatic hydrocarbon frequently found in urbanized areas,and is often used as a model chemical to study the microbial transformation of pollutants.The potential for human exposure and its health risk makes DBT a chemical of concern;thus,it needs to be environmentally managed.We utilized glycerol to stimulate Burkholderia sp.C3 in order to degrade DBT in respect to①DBT biodegradation kinetics,②bacterial growth,③rhamnolipid(RL)biosynthesis,and④RL secretion.Under an optimum glycerol-to-DBT molar ratio,the DBT biodegradation rate constants increased up to 18-fold and enhanced DBT biodegradation by 25%–30%at day 1 relative to cultivation with DBT alone.This enhancement was correlated with an increase in bacterial growth and RL biosynthesis.Proteomics studies revealed the enzymes involved in the upper and main steps of RL biosynthesis.The RL congeners Rha-C10-C10,Rha-Rha-C10-C10,Rha-Rha-C10-C12,and Rha-Rha-C12-C12 were identified in the medium supplemented with glycerol and DBT,whereas only Rha-C12-C12 was identified in cultures without glycerol or with RL inhibitors.The studies indicated that glycerol enhances DBT biodegradation via increased RL synthesis and bacterial growth.The results warrant further studies of environmental biostimulation with glycerol to advance bioremediation technologies and increase soil availability for agricultural purposes.

Advances in the Correlation between Intestinal Microbiota and Breast Cancer Development

The intestinal microbiota has a symbiotic relationship with humans. It participates in some important physiological activities in the human body and has an important impact on human health. It has become a hot topic of research by scientists in recent years. Among them, the research on the correlation between intestinal microbiota and cancer has increased rapidly. At present, the incidence rate of breast cancer is increasing, which seriously endangers the health of women. More and more studies have found that the occurrence of breast cancer is related to intestinal microbiota, and its possible mechanism includes intestinal microbiota dysbiosis, estrogen metabolism changes, immune regulation, and the participation of intestinal microbiota metabolites, etc. With the further development of high-throughput sequencing technology, the research on the correlation between intestinal microbiota and breast cancer has become more in-depth, from a structural level confined to microorganisms to a more comprehensive system structure and function level. These research results provide a new research direction for the treatment of breast cancer. In order to further study the interaction between intestinal microbes and breast cancer, this article will comprehensively describe the intestinal microbiota and breast cancer from four aspects: intestinal microbial dysbiosis, altered estrogen metabolism, immune regulation, and intestinal microbial metabolites. It also reviews the application research of intestinal microbiota in breast cancer treatment, including the influence of intestinal microbiota on the effects of breast cancer radiotherapy and chemotherapy, probiotic therapy, and dietotherapy.

Anaerobic ammonia oxidizing bacteria： ecological distribution, metabolism, and microbial interactions

Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based applications. Anammox bacteria are almost ubiquitous in the suboxic zones of almost all types of natural ecosystems and contribute significant to the global total nitrogen loss. In this paper, their ecological distributions and contributions to the nitrogen loss in marine, wetland, terrestrial ecosystems, and even extreme environments were reviewed. The unique metabolic mechanism of anammox bacteria was well described, including the particular cellular structures and genome compositions, which indicate the special evolutionary status of anammox bacteria. Finally, the ecological interactions among anammox bacteria and other organisms were discussed based on substrate availability and spatial organizations. This review attempts to summarize the fundamental understanding of anammox, provide an up-to-date summary of the knowledge of the overall anammox status, and propose future prospects for anammox. Based on novel findings, the metagenome has become a powerful tool for the genomic analysis of communities containing anammox bacteria; the metabolic diversity and biogeochemistry in the global nitrogen budget require more comprehensive studies.

Changes in soil biochemical indicators at different wheat growth stages under conservation-based sustainable intensification of rice-wheat system

Soil microbes play critical roles in soil biogeochemistry, soil biological health and crop productivity. The current study evaluated the effects of tillage and residue management on changes in soil biochemical indicators at different growth stages of wheat after 5 years of rice-wheat system. Nine treatment combinations of tillage, crop establishment and crop residue management included three main plot treatments applied to rice:(1) conventional till direct dry seeded rice(CTDSR),(2) zero till direct dry seeded rice(ZTDSR), and(3) conventional puddled manual transplanted rice(CTPTR) and three subplot treatments in subsequent wheat:(1) conventional tillage with rice residue removed(CTW-R),(2) zero tillage with rice residue removed(ZTW-R) and(3) zero tillage with rice residue retained as surface mulch(ZTW+R). Irrespective of rice treatments, ZTW+R treatment had higher soil biochemical indicators compared with ZTW-R and CTW-R at all the growth stages of wheat. Generally, all the biochemical indicators were the highest at the flowering stage of wheat. Residual effect of rice treatments was also significant on biochemical quotients in wheat, which were the highest under ZTDSR followed by CTDSR and CTPTR. The present study provided three sensitive and reliable biochemical indicators(microbial biomass, basal soil respiration and microbial quotient) which respond rapidly to change in tillage and residue management practices in RWS of South Asia.

Probe into Reverse Operation of Apoptosis Gene

Objective:The programmed death process of cells according to gene coding belongs to apoptotic natural extinction(PCD).The purpose of this study is to explore the phenomenon of“returning to old age and rejuvenating children”in the extreme anoxia,no nutrients and survival in the extreme environment of fish and earthworm.Methods:the adult earthworms were put into the sealed quartz sand or fine yellow sand plastic bottle with humidity of 35-40%70 ml and poured out 100-150 d,then put back into the natural environment(simulated natural plastic basin)and raised 100-150 d,to collect the experimental information.The same object can be observed repeatedly.Results:The earthworms which were closed in the little oxygen-free and nutrition-deficient vials were reduced by autophagy,and the rings and reproductive pores disappeared completely.When they were put back into the natural environment for two or three months,they were all restored to their original morphological structure.Conclusion:Most of the same subjects underwent 1-3 years of cyclic observation.The biological structure was adapted to the changing environment.It was helped by the resonance of many biota and complex stress factors.

Plant above-ground biomass and litter quality drive soil microbial metabolic limitations during vegetation restoration of subtropical forests

Changes in litter quality(carbon:nitrogen,C:N)and above-ground biomass(AGB)following vegetation restoration significantly impact soil physicochemical properties,yet their effects on soil microbial metabolic limitations remain unclear.We measured litter quality,AGB,soil physicochemical properties,and extracellular enzyme activity(EEA)along a vegetation restoration gradient(7,14,49,70 years,and nearly climax evergreen broadleaved forests)in southern China.We also evaluated soil microbial metabolic limitations by a vector analysis of the EEA.Results revealed the soil microbial metabolisms were co-limited by C and phosphorus(P).The microbial C limitation initially decreased(before 14 years)and then increased,while the microbial P limitation initially increased(before 49 years)and then decreased.Partial least squares path modeling(PLS-PM)showed that the microbial C limitation was mainly attributed to microbial C use efficiency induced by litter quality,suggesting that microorganisms may transfer cellular energy between microbial growth and Cacquiring enzyme production.The microbial P limitation was primarily correlated with AGB-driven change in soil elements and their stoichiometry,highlighting the importance of nutrient stoichiometry and balance in microbial metabolism.The shifts between microbial C and P limitations and the strong connections of plant–soil-microbe processes during vegetation restoration revealed here will provide us with helpful information for optimal management to achieve forest restoration success.

Soil microbial attributes along a chronosequence of Scots pine(Pinus sylvestris var. mongolica) plantations in northern China

Soil microorganisms play a key role in soil organic matter dynamics, nutrient cycling, and soil fertility maintenance in forest ecosystems, and they are influenced by stand age and soil depth. However, few studies have simultaneously considered these two factors. In this study, we measured soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), soil basal respiration (SBR) rate, and potential extracellular enzyme activity (EEA) in soil to a depth of 60 cm under 10-, 30-, and 40-year-old Scots pine (Pinus sylvestris var. mongolica) stands (Y10, Y30, and Y40, respectively) in plantations in northern China in 2011. Soil water content (SWC), soil pH, soil organic carbon (SOC), and soil total nitrogen (STN) were also measured to explore their effects on soil microbial indices across different stand ages and soil depths. Our results showed that SMBC, SMBN, and the SBR rate were generally higher for the Y30 stand than for the Y10 and Y40 stands. Potential EEA, except forα-glucosidase, decreased significantly with increasing stand age. Soil organic carbon,STN, SWC, and soil pH explained 67%of the variation in soil microbial attributes among the three stand ages. For the same stand age, soil microbial biomass and the SBR rate decreased with soil depth. Lower microbial biomass, lower SBR rate, and lower EEA for the mature Y40 stand indicate lower substrate availability for soil microorganisms, lower soil quality, and lower microbial adaptability to the environment. Our results suggest that changes in soil quality with stand age should be considered when determining the optimum rotation length of plantations and the best management practices for afforestation programs.

Heavy metal pollution increases soil microbial carbon limitation:Evidence from ecological enzyme stoichiometry

Heavy metals can exist in soil for a long time and seriously affect soil quality.The coexistence of various heavy metal pollutants leads to biotoxicity and alters the activity of microorganisms.Soil microbial metabolism plays an important role in nutrient cycling and biochemical processes of soil ecosystem.However,the effects of heavy metal contamination on microbial metabolism in soil are still unclear.This study aims to reveal the responses of microbial metabolic limitation to heavy metals using extracellular enzyme stoichiometry,and further to evaluate the potential impacts of heavy metal pollution on soil nutrient cycle.The results showed that soil microbial metabolism reflected by the ecoenzymatic activities had a significant response to soil heavy metals pollution.The metabolism was limited by soil carbon(C)and phosphorus(P)under varied heavy metal levels,and the increase of heavy metal concentration significantly increased the microbial C limitation,while had no effect on microbial P limitation.Microorganisms may increase the energy investment in metabolism to resist heavy metal stress and thus induce C release.The results suggest that energy metabolism selected by microorganisms in response to long-term heavy metal stress could increase soil C release,which is not conducive to the soil C sequestration.Our study emphasizes that ecoenzymatic stoichiometry could be a promising methodology for evaluating the toxicity of heavy metal pollution and its ecological effects on nutrient cycling.

Evaluation methods of heavy metal pollution in soils based on enzyme activities:A review

Soil enzyme activities have been suggested as suitable indicators for the evaluation of metal contamination because they are susceptible to microbial changes caused by heavy metal stress and are strictly related to soil nutrient cycles.However,there is a growing lack of recognition and summary of the historic advancements that use soil enzymology as the proposal of evaluation methods.Here,we review the most common methods of heavy metal pollution evaluation based on enzyme activities,which include single enzyme index,combined enzyme index,enzyme-based functional diversity index,microbiological stress index,and ecoenzymatic stoichiometry models.This review critically examines the advantages and disadvantages of these methods based on their execution complexity,performance,and ecological implications and gets a glimpse of avenues to come to improved future evaluation systems.Indices based on a single enzyme are variable and have no consistent response to soil heavy metals,and the following three composite indices are characterized by the loss of many critical microbial processes,which thus not conducive to reflect the effects of heavy metals on soil ecosystems.Considering the dexterity of ecoenzymatic stoichiometry methods in reflecting changes in soil functions under heavy metal stress,we propose that microbial metabolic limitations quantified by ecoenzymatic stoichiometry models could be promising indicators for enhancing the reality and acceptance of results and further improving the potential for actual utility in environmental decision-making.

Convergent pathways of the gut microbiota–brain axis and neurodegenerative disorders

Recent research has been uncovering the role of the gut microbiota for brain health and disease.These studies highlight the role of gut microbiota on regulating brain function and behavior through immune,metabolic,and neuronal pathways.In this review we provide an overview of the gut microbiota axis pathways to lay the groundwork for upcoming sessions on the links between the gut microbiota and neurogenerative disorders.We also discuss how the gut microbiota may act as an intermediate factor between the host and the environment to mediate disease onset and neuropathology.Based on the current literature,we further examine the potential for different microbiota-based therapeutic strategies to prevent,to modify,or to halt the progress of neurodegeneration.

Dredging effects on selected nutrient concentrations and ecoenzymatic activity in two drainage ditch sediments in the lower Mississippi River Valley

Agricultural drainage ditches are conduits between production acreage and receiving aquatic systems.Often overlooked for their mitigation capabilities,agricultural drainage ditches provide an important role for nutrient transformation via microbial metabolism.Variations in ecoenzyme activities have been used to elucidate microbial metabolism and resource demand of microbial communities to better understand the relationship between altered nutrient ratios and microbial activity in aquatic ecosystems.Two agricultural drainage ditches,one in the northeast portion of the Arkansas Delta and the other in the lower Mississippi Delta,were monitored for a year.Sediment samples were collected prior to each ditch being dredged(cleaned),and subsequent post-dredging samples occurred as soon as access was available.Seasonal samples were then collected throughout a year to examine effects of dredging on selected nutrient concentrations and ecoenzymatic activity recovery in drainage ditch sediments.Phosphorus concentrations in sediments after dredging decreased 33–66%,depending on ditch and phosphorus extraction methodology.Additionally,ecoenzymatic activity was significantly decreased in most sediment samples after dredging.Fluorescein diacetate hydrolysis activity,an estimate of total microbial activity,decreased 56–67%after dredging in one of the two ditches.Many sample sites also had significant phosphorus and ecoenzymatic activity differences between the post-dredge samples and the year-long follow-up samples.Results indicate microbial metabolism in dredged drainage ditches may take up to a year or more to recover to pre-dredged levels.Likewise,while sediment nutrient concentrations may be decreased through dredging and removal,runoff and erosion events over time tend to quickly replenish nutrient concentrations in replaced sediments.Understanding nutrient dynamics and microbial metabolism within agricultural drainage ditches is a crucial step toward addressing issues of nutrient enrichment in aquatic receiving systems,especially those contributing to the Gulf of Mexico.

Advances in engineering methylotrophic yeast for biosynthesis of valuable chemicals from methanol

Methylotrophic yeasts and bacteria, which can use methanol as carbon and energy source, have beenwildly used as microbial cell factories for biomanufacturing. Due to their robustness in industrial harshconditions, methylotrophic yeasts such as Pichia pastoris have been explored as a cell factory forproduction of proteins and high-value chemicals. Methanol utilization pathway （MUT） is highlyregulated for efficient methanol utilization, and the downstream pathways need extensively constructedand optimized toward target metabolite biosynthesis. Here, we present an overview of methanolmetabolism and regulation in methylotrophic yeasts, among which we focus on the regulation of keygenes involved in methanol metabolism. Besides, the recent progresses in construction and optimizationof downstream biosynthetic pathways for production of high value chemicals, such as polyketides, fattyacids and isoprenoids, are further summarized. Finally, we discuss the current challenges and feasiblestrategies toward constructing efficient methylotrophic cell factories may promote wide applications inthe future.