QMEC:a tool for high-throughput quantitative assessment of microbial functional potential in C,N,P,and S biogeochemical cycling

Microorganisms are major drivers of elemental cycling in the biosphere. Determining the abundance of microbial functional traits involved in the transformation of nutrients, including carbon(C), nitrogen(N), phosphorus(P) and sulfur(S), is critical for assessing microbial functionality in elemental cycling. We developed a high-throughput quantitative-PCR-based chip, Quantitative microbial element cycling(QMEC), for assessing and quantifying the genetic potential of microbiota to mineralize soil organic matter and to release C, N, P and S. QMEC contains 72 primer pairs targeting 64 microbial functional genes for C, N, P, S and methane metabolism. These primer pairs were characterized by high coverage(average of 18–20 phyla covered per gene)and sufficient specificity(>70% match rate) with a relatively low detection limit(7–102 copies per run). QMEC was successfully applied to soil and sediment samples, identifying significantly different structures, abundances and diversities of the functional genes(P<0.05). QMEC was also able to determine absolute gene abundance. QMEC enabled the simultaneous qualitative and quantitative determination of 72 genes from 72 samples in one run, which is promising for comprehensively investigating microbially mediated ecological processes and biogeochemical cycles in various environmental contexts including those of the current global change.

Role of seed size, phenology, oogenesis and host distribution in the specificity and genetic structure of seed weevils (Curculio spp.) in mixed forests

Synchrony between seed growth and oogenesis is suggested to largely shape trophic breadth of seed-feeding insects and ultimately to contribute to their co-existence by means of resource partitioning or in the time when infestation occurs.Here we investigated:(i)the role of seed phenology and sexual maturation of females in the host specificity of seed-feeding weevils(Curculio spp.)predating in hazel and oak mixed forests;and(ii)the consequences that trophic breadth and host distribution have in the genetic structure of the weevil populations.DNA analyses were used to establish unequivocally host specificity and to determine the population genetic structure.We identified 4 species with different specificity,namely Curculio nucum females matured earlier and infested a unique host(hazelnuts,Corylus avellana)while 3 species(Curculio venosus,Curculio glandium and Curculio elephas)predated upon the acorns of the 2 oaks(Quercus ilex and Quercus pubescens).The high specificity of C.nucum coupled with a more discontinuous distribution of hazel trees resulted in a significant genetic structure among sites.In addition,the presence of an excess of local rare haplotypes indicated that C.nucum populations went through genetic expansion after recent bottlenecks.Conversely,these effects were not observed in the more generalist Curculio glandium predating upon oaks.Ultimately,co-existence of weevil species in this multi-host-parasite system is influenced by both resource and time partitioning.To what extent the restriction in gene flow among C.nucum populations may have negative consequences for their persistence in a time of increasing disturbances(e.g.drought in Mediterranean areas)deserves further research.

原子生态学:原子与生态的耦合

The functional roles of molecules in organisms and ecosystems are driven by the atoms that form them,including their threedimensional form,bond polarity,size,and conformation.Recent advances in environmental and ecological sciences,such as ecological stoichiometry,ionomics,biochemistry,biogeochemical-niche studies,and omic ecological approaches,have provided substantial data and results that support the associations of the elements/atoms in organisms and ecosystems with their fundamental functioning and structure in nature.

Contribution of periphytic biofilm of paddy soils to carbon dioxide fixation and methane emissions

Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane(CH_(4))flux.The accurate quantification of CH_(4)emissions from rice paddies remains problematic,in part due to uncertainties and omissions in the contribution of microbial aggregates on the soil surface to carbon fluxes.Herein,we comprehensively evaluated the contribution of one form of microbial aggregates,periphytic biofilm(PB),to carbon dioxide(CO_(2))and CH_(4)emissions from paddies distributed across three climatic zones,and quantified the pathways that drive net CH_(4)production as well as CO_(2)fixation.We found that PB accounted for 7.1%-38.5%of CH_(4)emissions and 7.2%-12.7%of CO_(2)fixation in the rice paddies.During their growth phase,PB fixed CO_(2)and increased the redox potential,which promoted aerobic CH_(4)oxidation.During the decay phase,PB degradation reduced redox potential and increased soil organic carbon availability,which promoted methanogenic microbial community growth and metabolism and increased CH_(4)emissions.Overall,PB acted as a biotic converter of atmospheric CO_(2)to CH_(4),and aggravated carbon emissions by up to 2,318 kg CO_(2)equiv ha^(-1)season^(-1).Our results provide proof-of-concept evidence for the discrimination of the contributions of surface microbial aggregates(i.e.,PB)from soil microbes,and a profound foundation for the estimation and simulation of carbon fluxes in a potential novel approach to the mitigation of CH_(4)emissions by manipulating PB growth.

Loss of soil microbial diversity exacerbates spread of antibiotic resistance

Loss of biodiversity is a major threat to the ecosystem processes upon which society depends.Natural ecosystems differ in their resistance to invasion by alien species,and this resistance can depend on the diversity in the system.Little is known,however,about the barriers that microbial diversity provides against microbial invasion.The increasing prevalence of antibioticresistant bacteria is a serious threat to public health in the 21st century.We explored the consequences of the reduction in soil microbial diversity for the dissemination of antibiotic resistance.The relationship between this diversity and the invasion of antibiotic resistance was investigated using a dilution-to-extinction approach coupled with high-capacity quantitative PCR.Microbial diversity was negatively correlated with the abundance of antibiotic-resistance genes,and this correlation was maintained after accounting for other potential drivers such as incubation time and microbial abundance.Our results demonstrate that high microbial diversity can act as a biological barrier resist the spread of antibiotic resistance.These results fill a critical gap in our understanding of the role of soil microbial diversity in the health of ecosystems.

Effects of Different Types of Sludge on Soil Microbial Properties:A Field Experiment on Degraded Mediterranean Soils

The recycling of suitable organic wastes can enhance soil fertility via effects on soil physical, chemical and biological properties. To compare the effects of digested (DS), thermally dried (TDS) and composted dewatered (CDS) sewage sludge on soil microbiological properties, an experiment was conducted at field sites for more than one year (401 d) when applied to two Mediterranean degraded soils (loam and loamy sand soils). All three types of sewage sludge had a significant effect on measured parameters. In a short time, the plots of both loamy sand and loam soils amended with TDS showed the highest microbial basal respiration (loam soil: P < 0.01; loamy sand soil: P < 0.001) and carbon mineralization coefficient (loam soil: P < 0.01; loamy sand soil: P < 0.001). Furthermore, on loamy sand soil, the plots amended with TDS showed the highest microbial metabolic quotient (qCO 2 ) (P < 0.05). This study revealed that the addition of sludge caused transient non-equilibrium effects on almost all soil microbial properties. However, there were no differences one year later because the remaining organic carbon was stable and quite similar in all treatments. These results may have practical implications for the rehabilitation of degraded soils.

Potential medicinal plants involved in inhibiting 3CL^(pro) activity:A practical alternate approach to combating COVID-19

At present,a variety of vaccines have been approved,and existing antiviral drugs are being tested to find an effective treatment for coronavirus disease 2019(COVID-19).However,no standardized treatment has yet been approved by the World Health Organization.The virally encoded chymotrypsin-like protease(3CL^(pro))from severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),which facilitates the replication of SARS-CoV in the host cells,is one potential pharmacological target for the development of antiSARS drugs.Online search engines,such as Web of Science,Google Scholar,Scopus and PubMed,were used to retrieve data on the traditional uses of medicinal plants and their inhibitory effects against the SARS-CoV 3CL^(pro).Various pure compounds,including polyphenols,terpenoids,chalcones,alkaloids,biflavonoids,flavanones,anthraquinones and glycosides,have shown potent inhibition of SARS-CoV-2 3CL^(pro) activity with 50% inhibitory concentration(IC_(50))values ranging from 2-44μg/mL.Interestingly,most of these active compounds,including xanthoangelol E(isolated from Angelica keiskei),dieckol 1(isolated from Ecklonia cava),amentoflavone(isolated from Torreya nucifera),celastrol,pristimerin,tingenone and iguesterin(isolated from Tripterygium regelii),tannic acid(isolated from Camellia sinensis),and theaflavin-3,3’-digallate,3-isotheaflav1in-3 gallate and dihydrotanshinone I(isolated from Salvia miltiorrhiza),had IC_(50)values of less than 15μg/mL.Kinetic mechanistic studies of several active compounds revealed that their mode of inhibition was dose-dependent and competitive,with K_(i)values ranging from 2.4-43.8μmol/L.Given the significance of plant-based compounds and the many promising results obtained,there is still need to explore the phytochemical and mechanistic potentials of plants and their products.These medicinal plants could serve as an effective inexpensive nutraceutical for the general public to help manage COVID-19.