Metagenomic analysis revealing the metabolic role of microbial communities in the free amino acid biosynthesis of Monascus rice vinegar during fermentation

Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic network on FAA biosynthesis remains unclear.Through metagenomic analysis,this work aimed to elucidate the roles of microbes in FAA biosynthesis during Monascus rice vinegar fermentation.Taxonomic profiles from functional analyses showed 14 dominant genera with high contributions to the metabolism pathways.The metabolic network for FAA biosynthesis was then constructed,and the microbial distribution in different metabolic pathways was illuminated.The results revealed that 5 functional genera were closely involved in FAA biosynthesis.This study illuminated the metabolic roles of microorganisms in FAA biosynthesis and provided crucial insights into the functional attributes of microbiota in vinegar fermentation.

Coupled multiphysical model for investigation of influence factors in the application of microbially induced calcite precipitation

The study presents a comprehensive coupled thermo-bio-chemo-hydraulic(T-BCH)modeling framework for stabilizing soils using microbially induced calcite precipitation(MICP).The numerical model considers relevant multiphysics involved in MICP,such as bacterial ureolytic activities,biochemical reactions,multiphase and multicomponent transport,and alteration of the porosity and permeability.The model incorporates multiphysical coupling effects through well-established constitutive relations that connect parameters and variables from different physical fields.It was implemented in the open-source finite element code OpenGeoSys(OGS),and a semi-staggered solution strategy was designed to solve the couplings,allowing for flexible model settings.Therefore,the developed model can be easily adapted to simulate MICP applications in different scenarios.The numerical model was employed to analyze the effect of various factors,including temperature,injection strategies,and application scales.Besides,a TBCH modeling study was conducted on the laboratory-scale domain to analyze the effects of temperature on urease activity and precipitated calcium carbonate.To understand the scale dependency of MICP treatment,a large-scale heterogeneous domain was subjected to variable biochemical injection strategies.The simulations conducted at the field-scale guided the selection of an injection strategy to achieve the desired type and amount of precipitation.Additionally,the study emphasized the potential of numerical models as reliable tools for optimizing future developments in field-scale MICP treatment.The present study demonstrates the potential of this numerical framework for designing and optimizing the MICP applications in laboratory-,prototype-,and field-scale scenarios.

Afforestation increases microbial diversity in low-carbon soils

Afforestation has an important role in biodiversity conservation and ecosystem function improvement.A meta-analysis was carried out in China,which has the largest plantation area globally,to quantify the effects of plantings on soil microbial diversity.The results showed that the overall effect of afforestation on soil microbial diversity was positive across the country.Random forest algorithm suggested that soil carbon was the most important factor regulating microbial diversity and the positive response was only found with new plantings on low-carbon bare lands but not on high-carbon farmlands and grasslands.In addition,afforestation with broadleaved species increased microbial diversity,whereas planting with conifers had no effect on microbial diversity.This study clarified the effects of plantings on soil microbial diversity,which has an important implication for establishing appropriate policies and practices to improve the multiple functionalities(e.g.,biodiversity conservation and climate change mitigation)during plantation establishment.

Microbial Degradation of Organic Contaminants in Streambed/Floodplain Sediments in Passaic River—New Jersey Area

This paper is intended to explore soil organic matter and carbon isotope fractionation at three locations of the Passaic River to determine if microbial degradation of organic contaminants in soil is correlated to the surrounding physical environment. Microbial degradation of organic contaminants is important for the detoxification of toxic substances thereby minimizing stagnation in the environment and accumulating in the food chain. Since organic contaminants are not easily dissolved in water, they will penetrate sediment and end up enriching the adjacent soil. The hypothesis that we are testing is microbial activity and carbon isotope fractionation will be greater in preserved soils than urban soils. The reason why this is expected to be the case is the expectation of higher microbial activity in preserved environments due to less exposure to pollutants, better soil structure, higher organic matter content, and more favorable conditions for microbial growth. This is contrasted with urban soils, which are impacted by pollutants and disturbances, potentially inhibiting microbial activity. We wish to collect soil samples adjacent to the Passaic River at a pristine location, Great Swamp Wildlife Refuge, a suburban location, Goffle Brook Park, Hawthorne NJ, and an urban location, Paterson NJ. These soil samples will be weighed for soil organic matter (SOM) and weighed for isotope ratio mass spectrometry (IRMS) to test organic carbon isotopes. High SOM and δ13C depletion activity indicate microbial growth based on the characteristics of the soil horizon rather than the location of the soil sample which results in degradation of organic compounds.

Assessment of Physico-Chemical and Microbial Quality of Sugarcane Juice Sold by Street Vendors in Three Regions of Bangladesh

Sugar cane juice is a popular refreshing drink in most part of Bangladesh. It has great taste and health benefits;also it is available most of the public places at reasonable prices which consumed by road side customers including general public, shopping personals, tourists, students. In our country, street vendors crushing sugarcane between roller crusher and sold without any heat treatment or preservative, also served with or without added ice and lemon juice. The study aimed to identify and compare the physico-chemical and microbial quality of sugarcane juice. The chemical qualities of juices including moisture, PH, ash, total soluble solid, total sugar, reducing sugar and titrable acidity were found slightly different in Mymensingh, Gazipur and Narayangonj areas. The highest and lowest value of moisture, ash, PH, total soluble solids, total sugar, reducing sugar and titrable acidity were found in 84.33% - 79.26% (Gazipur-Mymensingh), 0.57% - 0.04% (Mymensingh-Gazipur), 5.9 - 2.9 (Gazipur-Narayangonj), 17.48% - 4.98% (Mymensingh-Narayangonj), 21.9% - 6.56% (Mymensingh-Gazipur), 3.7 - 2.1 (Gazipur-Mymensingh) and 0.523% - 0.007% (Narayangonj-Gazipur) respectively. For microbiological analysis, the total viable count of sugar cane juice in Mymensingh, Gazipur and Narayangonj were ranged from 0.6 × 105 - 43.6 × 105 cfu/ml, 4.6 × 105 - 21.6 × 105 cfu/ml and 3.6 × 105 - 36.6 × 105 cfu/ml respectively, where the permitted value is 1.0 × 104 cfu/ml, whereas the total coliform count was ranged from 0.4 × 105 - 6.4 × 105 cfu/ml, 0.6 × 105 - 8.4 × 105 cfu/ml and 0.00 - 8.4 × 105 cfu/ml, where the permitted value is 100 cfu/ml and total fungal count was ranged from 5.5 × 105 - 56.5 × 105 cfu/ml, 21.5 × 105 - 54.5 × 105 cfu/ml and 32.5 × 105 - 68.5 × 105 cfu/ml, where the permitted value is 1000 cfu/ml. According to the Gulf standard, the microbiological parameters of all the collected sugar cane juice were out of the permitted standards, so that a serious health outbreak can be caused anytime.

Microbial Growth and Decay: A Commented Review of the Model

The paper reviews previous publications and reports some comments about a semi empirical model of the growth and decay process of a planktonic microbial culture. After summarizing and reshaping some fundamental mathematical expressions, the paper highlights the reasons for the choice of a suitable time origin that makes the parameters of the model self-consistent. Besides the potential applications to predictive microbiology studies and to effects of bactericidal drugs, the model allows a suitable proxy of the fitness of the microbial culture, which can be of interest for the studies on the evolution across some thousand generations of a Long Term Evolution Experiment.

Afforestation with an age-sequence of Mongolian pine plantation promotes soil microbial residue accumulation in the Horqin Sandy Land, China

Land use change affects the balance of organic carbon(C)reserves and the global C cycle.Microbial residues are essential constituents of stable soil organic C(SOC).However,it remains unclear how microbial residue changes over time following afforestation.In this study,16-,23-,52-,and 62-year-old Mongolian pine stands and 16-year-old cropland were studied in the Horqin Sandy Land,China.We analyzed changes in SOC,amino sugar content,and microbial parameters to assess how microbial communities influence soil C transformation and preservation.The results showed that SOC storage increased with stand age in the early stage of afforestation but remained unchanged at about 1.27-1.29 kg/m2 after 52 a.Moreover,there were consistent increases in amino sugars and microbial residues with increasing stand age.As stand age increased from 16 to 62 a,soil pH decreased from 6.84 to 5.71,and the concentration of total amino sugars increased from 178.53 to 509.99 mg/kg.A significant negative correlation between soil pH and the concentration of specific and total amino sugars was observed,indicating that the effects of soil acidification promote amino sugar stabilization during afforestation.In contrast to the Mongolian pine plantation of the same age,the cropland accumulated more SOC and microbial residues because of fertilizer application.Across Mongolian pine plantation with different ages,there was no significant change in calculated contribution of bacterial or fungal residues to SOC,suggesting that fungi were consistently the dominant contributors to SOC with increasing time.Our results indicate that afforestation in the Horqin Sandy Land promotes efficient microbial growth and residue accumulation in SOC stocks and has a consistent positive impact on SOC persistence.

Dietary eubiotics of microbial muramidase and glycan improve intestinal villi,ileum microbiota composition and production trait of broiler

Background Optimal gut health is important to maximize growth performance and feed efficiency in broiler chickens.A total of 1,365 one-day-old male Ross 308 broiler chickens were randomly divided into 5 treatments groups with 21 replicates,13 birds per replicate.The present research investigated effects of microbial muramidase or a precision glycan alone or in combination on growth performance,apparent total tract digestibility,total blood carotenoid content,intestinal villus length,meat quality and gut microbiota in broiler chickens.Treatments included:NC:negative control(basal diet group);PC:positive control(basal diet+0.02%probiotics);MR:basal diet+0.035%microbial muramidase;PG:basal diet+0.1%precision glycan;and MRPG:basal diet+0.025%MR+0.1%PG,respectively.Results MRPG group increased the body weight gain and feed intake(P<0.05)compared with NC group.Moreover,it significantly increased total serum carotenoid(P<0.05)and MRPG altered the microbial diversity in ileum contents.The MRPG treatment group increased the abundance of the phylum Firmicutes,and family Lachnospiraceae,Ruminococcaceae,Oscillospiraceae,Lactobacillaceae,Peptostreptococcaceae and decreased the abundance of the phylum Campilobacterota,Bacteroidota and family Bacteroidaceae.Compared with the NC group,the chickens fed MRPG showed significantly increased in duodenum villus length at end the trial.Conclusion In this study,overall results showed that the synergetic effects of MR and PG showed enhancing growth performance,total serum carotenoid level and altering gut microbiota composition of broilers.The current research indicates that co-supplementation of MR and PG in broiler diets enhances intestinal health,consequently leading to an increased broiler production.

Research status, hot spots, difficulties and future development direction of microbial geoengineering

Microbial geoengineering technology,as a new eco-friendly rock and soil improvement and reinforcement technology,has a wide application prospect.However,this technology still has many deficiencies and is difficult to achieve efficient curing,which has become the bottleneck of large-scale field application.This paper reviews the research status,hot spots,difficulties and future development direction microbial induced calcium carbonate precipitation(MICP)technology.The principle of solidification and the physical and mechanical properties of improved rock and soil are systematically summarized.The solidification efficiency is mainly affected by the reactant itself and the external environment.At present,the MICP technology has been preliminarily applied in the fields of soil solidification,crack repair,anti-seepage treatment,pollution repair and microbial cement.However,the technology is currently mainly limited to the laboratory level due to the difficulty of homogeneous mineralization,uneconomical reactants,short microbial activity period and large environmental interference,incidental toxicity of metabolites and poor field application.Future directions include improving the uniformity of mineralization by improving grouting methods,improving urease persistence by improving urease activity,and improving the adaptability of bacteria to the environment by optimizing bacterial species.Finally,the authors point out the economic advantages of combining soybean peptone,soybean meal and cottonseed as carbon source with phosphogypsum as calcium source to induce CaCO3.

Spatiotemporal variations of sand hydraulic conductivity by microbial application methods

The spatiotemporal distributions of microbes in soil by different methods could affect the efficacy of the microbes to reduce the soil hydraulic conductivity.In this study,the specimens of bio-mediated sands were prepared using three different methods,i.e.injecting,mixing,and pouring a given microbial so-lution onto compacted sand specimens.The hydraulic conductivity was measured by constant-head tests,while any soil microstructural changes due to addition of the microbes were observed by scan-ning electron microscope(SEM)and mercury intrusion porosimetry(MIP)tests.The amount of dextran concentration produced by microbes in each type of specimen was quantified by a refractometer.Results show that dextran production increased exponentially after 5-7 d of microbial settling with the supply of culture medium.The injection and mixing methods resulted in a similar amount and uniform dis-tribution of dextran in the specimens.The pouring method,however,produced a nonuniform distri-bution,with a higher concentration near the specimen surface.As the supply of culture medium discontinued,the dextran content near the surface produced by the pouring method decreased dramatically due to high competition for nutrients with foreign colonies.Average dextran concentration was negatively and correlated with hydraulic conductivity of bio-mediated soils exponentially,due to the clogging of large soil pores by dextran.The hydraulic conductivity of the injection and mixing cases did not change significantly when the supply of culture medium was absent.

Metagenomic Insight Reveals the Microbial Structure and Function of the Full-Scale Coking Wastewater Treatment System:Gene-Based Nitrogen Removal

Microbial communities play crucial roles in pollutant removal and system stability in biological systems for coking wastewater(CWW)treatment,but a comprehensive understanding of their structure and functions is still lacking.A five month survey of four sequential bioreactors,anoxic 1/oxic 1/anoxic 2/oxic 2(A1/O1/A2/O2),was carried out in a full-scale CWW treatment system in China to elucidate operational performance and microbial ecology.The results showed that A1/O1/A2/O2 had excellent and stable performance for nitrogen removal.Both total nitrogen(TN;(17.38±6.89)mgL1)and ammonium-nitrogen(NH4 t-N;(2.10±1.34)mg·L^(-1))in the final biological effluent satisfied the Chinese national standards for CWW.Integrated analysis of 16S ribosome RNA(rRNA)sequencing and metagenomic sequencing showed that the bacterial communities and metagenomic function profiles of A1 and O1 shared similar functional structures,while those of A2 significantly varied from those of other bioreactors(p<0.05).The results indicated that microbial activity was strongly connected with activated sludge function.Nitrosospira,Nitrosomonas,and SM1A02 were responsible for nitrification during the primary anoxic-oxic(AO)stage and Azoarcus and Thauera acted as important denitrifiers in A2.Nitrogen cycling-related enzymes and genes work in the A1/O1/A2/O2 system.Moreover,the hao genes catalyzing hydroxylamine dehydrogenase(EC 1.7.2.6)and the napA and napB genes catalyzing nitrate reductase(EC 1.9.6.1)played important roles in the nitrification and denitrification processes in the primary and secondary AO stages,respectively.The mixed liquor suspended solids(MLSS)/total solids(TS),TN removal rate(RR),total organic carbon(TOC)(RR),and NH_(4)^(+)t-N(RR)were the most important environmental factors for regulating the structure of core bacterial genera and nitrogen-cycling genes.Proteobacteria were the potential main participants in nitrogen metabolism in the A1/O1/A2/O2 system for CWW treatment.This study provides an original and comprehensive understanding of the microbial community and functions at the gene level,which is crucial for the efficient and stable operation of the full-scale biological process for CWW treatment.

Characteristics of the microbial communities regulate soil multi-functionality under different cover crop amendments in Ultisol

The use of cover crops is a promising strategy for influencing the soil microbial consortium,which is essential for the delivery of multiple soil functions(i.e.,soil multifunctionality).Nonetheless,relatively little is known about the role of the soil microbial consortium in mediating soil multifunctionality under different cover crop amendments in dryland Ultisols.Here,we assessed the multifunctionality of soils subjected to four cover crop amendments(control,non-amended treatment;RD,radish monoculture;HV,hairy vetch monoculture;and RDHV,radish-hairy vetch mixture),and we investigated the contributions of soil microbial richness,network complexity,and ecological clusters to soil multifunctionality.Our results demonstrated that cover crops whose chemical composition differed from that of the main plant crop promoted higher multifunctionality,and the radish-hairy vetch mixture rendered the highest enhancement.We obtained evidence that changes in soil microbial richness and network complexity triggered by the cover crops were associated with higher soil multifunctionality.Specifically,specialized microbes in a key ecological cluster(ecological cluster 2)of the soil microbial network were particularly important for maintaining soil multifunctionality.Our results highlight the importance of cover crop-induced variations in functionally important taxa for promoting the soil multifunctionality of dryland Ultisols.

The microbial community,nutrient supply and crop yields differ along a potassium fertilizer gradient under wheat-maize double-cropping systems

Soil microorganisms play critical roles in ecosystem function.However,the relative impact of the potassium(K)fertilizer gradient on the microbial community in wheat-maize double-cropping systems remains unclear.In this long-term field experiment(2008-2019),we researched bacterial and fungal diversity,composition,and community assemblage in the soil along a K fertilizer gradient in the wheat season(K0,no K fertilizer;K1,45 kg ha^(-1) K_(2)O;K_(2),90 kg ha^(-1)K_(2)O;K3,135 kg ha^(-1)K_(2)O)and in the maize season(K0,no K fertilizer;K_(1),150 kg ha^(-1) K_(2)O;K_(2),300 kg ha^(-1)K_(2)O;K_(3),450 kg ha^(-1)K_(2)O)using bacterial 16S rRNA and fungal internally transcribed spacer(ITS)data.We observed that environmental variables,such as mean annual soil temperature(MAT)and precipitation,available K,ammonium,nitrate,and organic matter,impacted the soil bacterial and fungal communities,and their impacts varied with fertilizer treatments and crop species.Furthermore,the relative abundance of bacteria involved in soil nutrient transformation(phylum Actinobacteria and class Alphaproteobacteria)in the wheat season was significantly increased compared to the maize season,and the optimal K fertilizer dosage(K2 treatment)boosted the relative bacterial abundance of soil nutrient transformation(genus Lactobacillus)and soil denitrification(phylum Proteobacteria)bacteria in the wheat season.The abundance of the soil bacterial community promoting root growth and nutrient absorption(genus Herbaspirillum)in the maize season was improved compared to the wheat season,and the K2 treatment enhanced the bacterial abundance of soil nutrient transformation(genus MND1)and soil nitrogen cycling(genus Nitrospira)genera in the maize season.The results indicated that the bacterial and fungal communities in the double-cropping system exhibited variable sensitivities and assembly mechanisms along a K fertilizer gradient,and microhabitats explained the largest amount of the variation in crop yields,and improved wheat?maize yields by 11.2-22.6 and 9.2-23.8%with K addition,respectively.These modes are shaped contemporaneously by the different meteorological factors and soil nutrient changes in the K fertilizer gradients.

Impact of Storage Temperature on Microbial Diversity and Probiotic Effect of Liquid Brewers’ Yeast

Using probiotics as animal feed additives instead of antibiotics is gaining momentum to avert adverse negative effects on human health. Liquid brewers yeast (LBY) is an industrial by-product containing probiotic microorganisms and is also used as a protein supplement for dairy animals. Nevertheless, value chain actors lack of appropriate handling practices compromises the by-products quality and safety. This study aimed to determine the effect of variation in temperature on microbial diversity and probiotic effects during the storage time of LBY sampled from distributors and farmers from Githunguri sub-county of Kenya. The samples were stored at 20C, 25C and 30C, then tested on 0, 5, 10, 15 and 20 days. The studys parameters involved determining the pH levels, lactic acid bacteria (LAB), total coliform count (TCC), mould, and yeast in LBY. The rate (k) of the reaction kinetics model was used to extrapolate the expected probiotic shelf life. The LAB and yeast populations were reduced in a first-order reaction at all storage temperatures. The rate of reduction in the numbers of LAB reduced with an increase in temperature (k = 0.019 and 0.023) at 20C and 30C, respectively. Yeasts highest rate of growth reduction was 25C (k = 0.009) and least at 30C (k = 0.043). The minimum effective concentration for probiotics of 106 CFU/mL needed to observe the beneficial physiological impact on farm animals was achieved between 34.9 and 35.5 days at the tested storage temperatures. The study provides insight into the unexploited low-cost probiotic potential of LBY in dairy production. Conversely, handling practices and environmental microbial contamination along the value chain can compromise product quality and safety. There is a need to advocate its use in dairy for improved productivity and sensitize farmers to appropriate hygienic measures along the LBY value chain.

Profound loss of microbial necromass carbon in permafrost thaw-subsidence in the central Tibetan Plateau

Climate warming is causing rapid permafrost degradation,including thaw-induced subsidence,potentially resulting in heightened carbon release.Nevertheless,our understanding of the levels and variations of carbon components in permafrost,particularly during the degradation process,remains limited.The uncertainties arising from this process lead to inaccurate assessments of the climate effects during permafrost degradation.With vast expanses of permafrost in the Tibetan Plateau,there is limited research available on SOC components,particularly in the central Tibetan Plateau.Given remarkable variations in hydrothermal conditions across different areas of the Tibetan Plateau,the existing limited studies make it challenging to assess the overall SOC components in the permafrost across the Tibetan Plateau and simulate their future changes.In this study,we examined the properties of soil organic carbon(SOC)and microbial necromass carbon(MicrobialNC)in a representative permafrost thaw-subsidence area at the southern edge of continuous permafrost in the central Tibetan Plateau.The results indicate that prior to the thaw-subsidence,the permafrost had a SOC content of 72.68±18.53 mg g^(-1),with MicrobialNC accounting for 49.6%.The thaw-subsidence of permafrost led to a 56.4%reduction in SOC,with MicrobialNC accounting for 70.0%of the lost SOC.MicrobialNC constitutes the primary component of permafrost SOC,and it is the main component that is lost during thaw-subsidence formation.Changes in MicrobialNC are primarily correlated with factors pH,plant input,and microbial properties.The present study holds crucial implications for both the ecological and biogeochemical processes associated with carbon release from permafrost,and it furnishes essential data necessary for modeling the global response of permafrost to climate warming.Based on this study and previous research,permafrost thawing in the Tibetan Plateau causes substantial loss of SOC.However,there's remarkable heterogeneity in SOC component changes across different regions,warranting further in-depth investigation.

Structure and functional heterogeneity of soil microbial communities in different farmland types on the Loess Plateau

Background,aim,and scope Soil microbes are important drivers of nutrient transformation and energy f low.Reclaiming forest land for agricultural use may have profound effects on soil properties and microbial communities.However,the response of soil microbial communities to soil reclamation in the dryland agroecosystem is less understood.Therefore,it is necessary to investigate the changes of soil microbial communities driven by land use conversion to promote nutrient cycling in reclaimed farmland.Materials and methods Based on the metagenomic technique,we evaluated the microbial composition and function of the newly created farmland(NF)after reclamation with two types of traditional farmland(slope farmland(SF),checkdam farmland(CF))on the Loess Plateau,and explored the response of nutrient cycling function to dominant genera and soil properties.Results The results showed that Proteobacteria,Actinobacteria,and Acidobacteria were prevalent in the three types of farmlands.Compared with SF and CF,NF increased the relative abundance of Actinobacteria and Nocardioides,as well as genes related to amino acid metabolism and carbohydrate metabolism.The relative abundance of functional genes related to carbon and nitrogen cycling in the NF was higher than that in the traditional farmland(SF and CF).The relative abundance of nutrient cycling functional genes was positively correlated with dominant genera in the three types of farmlands.Except for pH,soil physicochemical factors were negatively correlated with genes related to amino acid metabolism and carbon cycle.Discussion Previous studies have shown that the nutrient conditions of the soil may intensify the competition between the eutrophic and oligotrophic microbial populations.After long-term cultivation and fertilization,the soil properties of traditional farmland were significantly different from those of NF,leading to the differentiation of dominant microbial groups.Microbes usually have functional redundancy to cope with changing environments.Soil microbes in traditional farmland may contain more genes related to replication and repair,cell growth and death,and environmental adaptation in response to disturbances caused by agricultural practices.On the contrary,the NF was less disturbed by agricultural activities,and the soil properties were more similar to forest land,so the carbon and nitrogen cycle function genes were more abundant.The nutrient cycling function was affected by the abundance of microbial dominant groups and soil properties,which may be related to the availability of soil nutrients and agricultural disturbance in different farmlands.Aspects of soil microbial-driven nutrient cycling in agriculture could be regulated in sustainable method.Conclusions The change from forest land to farmland kept more carbon and nitrogen cycling function in the newly created farmland,while long-term agricultural activities have drastically changed the functional structure of traditional farmland,resulting in the nutrient cycling function more concentrated to meet the needs of crop growth.Recommendations and perspectives Hence,it is necessary to apply sustainable agricultural method to regulate microbial-driven nutrient cycling.The insights are meaningful for sustainable agricultural development and land management in arid areas.

Solid-state NMR of the retinal protonated Schiff base in microbial rhodopsins

Rhodopsin is a seven-helical transmembrane protein with a retinal chromophore covalently bound to a conserved lysine in helix G via a retinal protonated Schiff base(RPSB).Microbial rhodopsins absorb light through chromophore and play a fundamental role in optogenetics.Numerous microbial rhodopsins have been discovered,contributing to diverse functions and colors.Solid-state NMR spectroscopy has been instrumental in elucidating the conformation of chromophores and the three-dimensional structure of microbial rhodopsins.This review focuses on the 15N chemical shift values of RPSB and summarizes recent progress in the field.We displayed the correlation between the 15N isotropic chemical shift values of RPSB and the maximum absorption wavelength of rhodopsin using solid-state NMR spectroscopy.

The competition between Bidens pilosa and Setaria viridis alters soil microbial composition and soil ecological function

Bidens pilosa is recognized as one of the major invasive plants in China.Its invasion has been associated with significant losses in agriculture,forestry,husbandry,and biodiversity.Soil ecosystems play an important role in alien plant invasion.Microorganisms within the soil act as intermediaries between plants and soil ecological functions,playing a role in regulating soil enzyme activities and nutrient dynamics.Understanding the interactions between invasive plants,soil microorganisms,and soil ecological processes is vital for managing and mitigating the impacts of invasive species on the environment.In this study,we conducted a systematic analysis focusing on B.pilosa and Setaria viridis,a common native companion plant in the invaded area.To simulate the invasion process of B.pilosa,we constructed homogeneous plots consisting of B.pilosa and S.viridis grown separately as monocultures,as well as in mixtures.The rhizosphere and bulk soils were collected from the alien plant B.pilosa and the native plant S.viridis.In order to focus on the soil ecological functional mechanisms that contribute to the successful invasion of B.pilosa,we analyzed the effects of B.pilosa on the composition of soil microbial communities and soil ecological functions.The results showed that the biomass of B.pilosa increased by 27.51% and that of S.viridis was significantly reduced by 66.56%.The organic matter contents in the bulk and rhizosphere soils of B.pilosa were approximately 1.30 times those in the native plant soils.The TN and NO_(3)^(-)contents in the rhizosphere soil of B.pilosa were 1.30 to 2.71 times those in the native plant soils.The activities of acid phosphatase,alkaline phosphatase,and urease in the rhizosphere soil of B.pilosa were 1.98-2.25 times higher than in the native plant soils.Using high-throughput sequencing of the16S rRNA gene,we found that B.pilosa altered the composition of the soil microbial community.Specifically,many genera in Actinobacteria and Proteobacteria were enriched in B.pilosa soils.Further correlation analyses verified that these genera had significantly positive relationships with soil nutrients and enzyme activities.Plant biomass,soil p H,and the contents of organic matter,TN,NO_(3)^(-),TP,AP,TK,and AK were the main factors affecting soil microbial communities.This study showed that the invasion of B.pilosa led to significant alterations in the composition of the soil microbial communities.These changes were closely linked to modifications in plant traits as well as soil physical and chemical properties.Some microbial species related to C,N and P cycling were enriched in the soil invaded by B.pilosa.These findings provide additional support for the hypothesis of soil-microbe feedback in the successful invasion of alien plants.They also offer insights into the ecological mechanism by which soil microbes contribute to the successful invasion of B.pilosa.Overall,our research contributes to a better understanding of the complex interactions between invasive plants,soil microbial communities,and ecosystem dynamics.

Flow-Slip Stability Behavior of Calcareous Sand Treated by Microbially Induced Carbonate Precipitation Technology

Flow-slip damage commonly destabilizes coastal slopes.Finding a slope stabilization method for calcareous sands in the South China Sea is crucial.Microbially induced calcite precipitation is a promising,eco-friendly method for soil stabilization.This study investigates the effect of microbial treatments,initial relative density,initial cell pressure,and initial stress ratio on the flow-slip stability of calcareous sand specimens by using constant shear drained tests.These tests lay the foundation to study the mechanical instability of sand slopes.Results show that the microbial-treated specimens maintain stable stresses longer,take longer to reach the instability,and withstand larger volumetric strains.Microbial treatment effectively enhances sand stability under constant shear drainage,with improvements amplified by higher initial relative density and initial cell pressure.In addition,a smaller initial stress ratio reduces shear effects on the specimen and increases resistance to flow slides.Microanalysis reveals that the flow-slip stability of calcareous sand slopes is enhanced by contact cementation,particle coating,void filling,and mutual embedment of calcium carbonate crystals.

Effects of land-use patterns on soil microbial diversity and composition in the Loess Plateau,China

In the Loess Plateau of China,land-use pattern is a major factor in controlling underlying biological processes.Additionally,the process of land-use pattern was accompanied by abandoned lands,potentially impacting soil microbe.However,limited researches were conducted to study the impacts of land-use patterns on the diversity and community of soil microorganisms in this area.The study aimed to investigate soil microbial community diversity and composition using high-throughput deoxyribonucleic acid(DNA)sequencing under different land-use patterns(apricot tree land,apple tree land,peach tree land,corn land,and abandoned land).The results showed a substantial difference(P<0.050)in bacterial alpha-diversity and beta-diversity between abandoned land and other land-use patterns,with the exception of Shannon index.While fungal beta-diversity was not considerably impacted by land-use patterns,fungal alpha-diversity indices varied significantly.The relative abundance of Actinobacteriota(34.90%),Proteobacteria(20.65%),and Ascomycota(77.42%)varied in soils with different land-use patterns.Soil pH exerted a dominant impact on the soil bacterial communities'composition,whereas soil available phosphorus was the main factor shaping the soil fungal communities'composition.These findings suggest that variations in land-use pattern had resulted in changes to soil properties,subsequently impacting diversity and structure of microbial community in the Loess Plateau.Given the strong interdependence between soil and its microbiota,it is imperative to reclaim abandoned lands to maintain soil fertility and sustain its function,which will have significant ecological service implications,particularly with regards to soil conservation in ecologically vulnerable areas.