DSEMR: A database for special environment microorganisms resource and associating them with synthetic biological parts

Special environmental microorganisms are considered to be of great industrial application value because of their special genotypes,physiological functions and metabolites.The research and development of special environmental microorganisms will certainly bring about some innovations in biotechnology processes and change the face of bioengineering.The Special Environmental Microbial Database(DSEMR)is a comprehensive database that provides information on special environmental microbial resources and correlates them with synthetic biological parts.DSEMR aggregates information on specific environmental microbial genomes,physiological properties,culture media,biological parts,and metabolic pathways,and provides online tool analysis data,including 5268 strains from 620 genera,31 media,and 42,126 biological parts.In short,DSEMR will become an important resource for the study of microorganisms in special environments and actively promote the development of synthetic biology.

In situ identification of environmental microorganisms with Raman spectroscopy

Microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment.However,it is challenging to delineate environmental microbes'actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated.Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells.It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ.The first part of this review introduces the principles,advantages,progress,and analytical methods of Raman spectroscopy applied in environmental microbiology.The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing(SIP),fluorescence in situ hybridization(FISH),Raman-activated cell sorting and genomic sequencing,and machine learning in microbiological studies.Finally,this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms,especially for uncultured microorganisms.

Study Progress on Animal Feces Treatment by Microorganism

With the fast development of livestock breeding,serious environmental pollution issues caused by the large accumulation of animal feces have arisen increasingly. It is of great importance to re-use these organic matter resources in order to ease the environmental and resource problems. And we reviews the significance of microorganism for livestock development and particularly the close relationship between microorganism and biodegradation of animal breeding residues. These bacteria play important roles in odor control,degradation and conversion of organic matters,and even the reduction of animal waste discharging amount by adjusting the feed nutrition proportion or improving the digestibility of nutrients. Consequently,it shows good application prospect of microbe practice in the improvement of contaminated environment resulting from livestock farming residues and the utilization of livestock manure resource.

Application of Biological Nanopore Sequencing Technology in the Detection of Microorganisms

Environmental pollution and the spread of pathogenic microorganisms pose a significant threat to the health of humans and the planet.Thus,understanding and detecting microorganisms is crucial for maintaining a healthy living environment.Nanopore sequencing is a single-molecule detection method developed in the 1990s that has revolutionized various research fields.It offers several advantages over traditional sequencing methods,including low cost,label-free,time-saving detection speed,long sequencing reading,real-time monitoring,convenient carrying,and other significant advantages.In this review,we summarize the technical principles and characteristics of nanopore sequencing and discuss its applications in amplicon sequencing,metagenome sequencing,and whole-genome sequencing of environmental microorganisms,as well as its in situ application under some special circumstances.We also analyze the advantages and challenges of nanopore sequencing in microbiology research.Overall,nanopore sequencing has the potential to greatly enhance the detection and understanding of microorganisms in environmental research,but further developments are needed to overcome the current challenges.

Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines

Microbial resource influences the life activities of medicinal plants from several perspectives.Endophytes,rhizosphere microorganisms,and other environmental microorganisms play essential roles in medicinal plant growth and development,plant yield,and clinical efficacy.The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways.They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites.Microorganisms can interact with their host plants to produce long-term,targeted selection results and improve their ability to adapt to the environment.Due to the interdependence and interaction between microorganisms and medicinal plants,Chinese herbal medicines(CHMs)quality is closely related to the associated microorganisms.This review summarizes the relationship between medicinal plants and their associated microorganisms,including their species,distribution,life activities,and metabolites.Microorganisms can aid in quality control,improve the efficacy of medicinal plants,and provide markers for identifying the origin and storage time of CHMs.Therefore,a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.