Using genomic data and bioinformatics methods has become an important approach to rapidly identify the genes and predict the phenotypes of bacterial antibiotic resistance. Dozens of antibiotic resistance databases have been established, providing information and auxiliary tools for the identification and prediction of bacterial antibiotic resistance. As the bacterial genome data and antibiotic resistance phenotype data are increasing, the correlation between them can be establishedvia big data and machine learning. Therefore, establishing efficient models predicting antibiotic resistance phenotypes has become a research hot topic. Focusing on the gene identification and phenotype prediction of bacterial antibiotic resistance, this review discusses the related databases, the theories and methods, the machine learning algorithms, and the prediction models. In addition, we made an outlook on the future prospects in this field, aiming to provide new ideas for the related studies.

The prediction of bacteriophage host ranges is of great significance for the basic research and clinical application of bacteriophages. The conventional biological experimental methods are limited by the poor culturability of bacteriophages and strict cultivation conditions. The availability of massive genome or metagenome sequencing data provides the sequence signature of bacteriophages and bacteria. Therefore, intelligent computing serves as a feasible way to predict bacteriophage host ranges. This paper systematically reviews the studies about intelligent computing-based prediction of bacteriophage host ranges. Starting from the process of bacteriophage infecting bacteria, we describe the feature source and biological rationality of prediction models, analyze the typical intelligent models and their prediction principles, and list all the reference datasets, real-world datasets, and evaluation indicators. The review aims to improve the understanding on the mechanism of bacteriophages in invading bacterial hosts and promote the usage of bacteriophages as antibiotic substitutes in biological therapy.

[Objective] To determine the functions of two key enzymes of the mevalonate pathway, phosphomevalonate kinase (CmErg8) and mevalonate diphosphate decarboxylase (CmErg19), inCordyceps militaris and their effects on the content of ergosterol and cordycepin.[Methods] Bioinformatics analysis was conducted to identifyCmErg8 andCmErg19 inC.militaris, and yeast complementation was employed to determine whether their functions were conserved. Furthermore, we employedAgrobacterium tumefaciens-mediated transformation to overexpressCmErg8 andCmErg19 in the auxotrophic mutantCmΔpyrG ofC.militaris, so as to observe the effects ofCmErg8 andCmErg19 on the content of ergosterol and cordycepin.[Results] CmErg8 andCmErg19 could not complement the temperature sensitivity of theerg8 anderg19 mutants of yeast. The strains overexpressingCmErg8 andCmErg19 showed increased content of ergosterol and cordycepin. Particularly, the cordycepin content increased by about 5 times in the strain overexpressingCmErg19 compared with that in the control.[Conclusion] This study revealed the functions ofCmErg8 andCmErg19 inC.militaris and reported that the genes in the ergosterol synthesis pathway ofC.militaris affected the content of cordycepin for the first time.

[Objective] The long-term intense continuous cropping and abuse of mineral fertilizers result in the degradation of upland red soil and the accumulation of soil-borne plant pathogens. Fungi are the microorganisms closely related to soil health in agroecosystems. We investigated the changes of soil fungal community to explore the effects of hairy vetch (Vicia villosa Roth L.) application on the agroecosystem with upland red soil.[Methods] We employed quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (Illumina MiSeq) to investigate the responses of fungal communities to mineral fertilizer (hereinafter referred to as NPK) alone and mineral fertilizer combined with hairy vetch (hereinafter referred to as NPKG) in upland red soil.[Results] Compared with NPK, NPKG increased the soil fertility, peanut yield, and fungal abundance and decreased soil pH and soil fungal diversity. Different treatments significantly altered the soil fungal community composition. Compared with NPK, NPKG increased the relative abundance of saprophytic fungi by 37.42% and decreased the relative abundance ofCercospora arachidicola andLasidiplodia theobromae by 89.11% and 88.10%, respectively.[Conclusion] The application of hairy vetch significantly increased soil fertility, reduced the risk of peanut exposure to soil-borne diseases, and increased peanut yield in the upland red soil. Therefore, the application of hairy vetch was conducive to the sustainable development of upland red soil in southern China.

Terpenoids, a group of natural products possessing diverse chemical structures and biological activities, have been widely used in the production of food additives, medicines, and cosmetics. Terpenoids are mainly produced by plants. With the rapid development of synthetic biology, heterologous production of terpenoids by engineered microbial strains is more economical and environmentally friendly compared with the conventional methods of extraction from plants and chemical synthesis. The catalytic activities of terpene synthases and the structural specificity of their products are pivotal for the heterologous biosynthesis of terpenoids. Directed evolution and rational design can be adopted to optimize the catalytic properties and product profile of target terpene synthases. However, this requires a feasible high-throughput method to screen mutant libraries. In recent years, various high-throughput screening methods have been developed to boost the sensitivity and efficiency in screening terpene synthases. We review recently established high-throughput screening methods for terpene synthases and briefly outline the principles and advantages and disadvantages of each method. Eventually, we envision the future directions of the application of high-throughput screening in the engineering of terpene synthases.

[Objective] Pseudomonas aeruginosa is a major Gram-negative pathogen that can exacerbate lung infections in the patients with cystic fibrosis, which can ultimately lead to death. The emerging multi-drug resistant and pan-drug resistant strains pose challenges to the prevention and control ofP.aeruginosa infection.[Methods] A phage capable of lysing multi-drug resistantP.aeruginosa was isolated from farm sewage. The morphological characteristics, biological characteristics, host range, genomic features, andin vitro inhibitory ability of the isolate were studied. The biofilm inhibition test was conducted with both the phage and antibiotics.[Results] The phage PH826 was identified to be a member of the genus Nankokuvirus and it can keep stability within a wide temperature range from 4 ℃ to 60 ℃ and pH range (pH 3.0–11.0). The host range test showed that PH826 could lyse 13P.aeruginosa strains from human and animals. The antibacterial testin vitro showed that PH826 was strongly lytic againstP.aeruginosa at multiplicity of infection (MOI) of 10, 1, and 0.1. The genome of PH826 was 87 956 bp in length, with the G+C content of 54.70%, encoding 165 open reading frames (ORFs) including an endolysin gene. The combination of PH826 at 1×MIC (minimum inhibitory concentration, MIC), 2×MIC, or 4×MIC and ciprofloxacin reduced biofilm formation by more than 80% at the time points of 24 h and 48 h. The combination of PH826 at 2×MIC or 4×MIC and meropenem reduced biofilm formation by more than 80% at the time points of 24 h and 48 h.[Conclusion] PH826 may be a potential disinfectant and therapeutic agent that can be used alone or in combination with antibiotics for the prevention and treatment of pathogenicP.aeruginosa.

Salinization is a global soil problem. Plant growth-promoting rhizobacteria (PGPR) have unique advantages in remediating saline-alkali soils and promoting plant growth. Screening the rhizosphere microorganisms ofTamarix chinensis, a typical halophyte, and revealing the growth-promoting effect and mechanism of these microorganisms are of great significance for developing microbial fertilizers. [Objective] To screen out the microorganisms from the rhizosphere soil of saline-alkaline tolerantT.chinensis and measure their basic characteristics, salt and alkali tolerance, and plant growth-promoting effects.[Methods] A saline-alkali tolerant strain Bachu 26 was screened out from the rhizosphere soil of wildT.chinensis in Bachu, Xinjiang and identified based on the morphological, physiological, and biochemical characteristics and 16S rRNA gene sequence. We cultured the strain Bachu 26 in the media with different salt concentrations (0%–20%) and pH values (7.0–13.0) to evaluate its salt and alkali tolerance. We then used multiple functional media to examine the growth-promoting function of Bachu 26 and measured the production of indole-3-acetic acid (IAA). The petri dishes with two compartments were used to verify the ability of Bachu 26 to produce acidic volatile substances.Arabidopsis thaliana seedlings were co-cultured with strain Bachu 26 in common culture dishes, based on which the growth-promoting effect of Bachu 26 onA.thaliana seedlings was analyzed. Furthermore,A.thaliana seedlings and Bachu 26 were cultured dividually in the petri dishes with two compartments, based on which the growth-promoting effect of volatile acidic substances produced by Bachu 26 on the seedlings was analyzed. The growth-promoting effect of Bachu 26 on maize seedlings was analyzed by pot experiments.[Results] Strain Bachu 26 was identified as a species ofHalomonas and namedHalomonas sp. Bachu 26, with the maximum tolerance to 20% salt and pH 11.0.Halomonas sp. Bachu 26 could solubilize organic phosphorus, fix nitrogen, and produce ACC deaminase, IAA, and volatile acidic substances, with the IAA yield reaching 45.885 6 mg/L.Halomonas sp. Bachu 26 significantly increased the fresh weight, lateral roots, taproot length, and leaves ofA.thaliana seedlings under saline-alkali stress. In pot experiments,Halomonas sp. Bachu 26 significantly increased the fresh weight of aboveground part, fresh weight of underground part, and plant height of maize under saline-alkali stress.[Conclusion] The newly isolated PGPR strain Bachu 26 has a significant plant growth-promoting effect. The findings provide material and theoretical support for the remediation of saline-alkali soil and development of saline-alkali tolerant plant growth-promoting microbial fertilizers. Furthermore, the results will promote the applied and basic research onHalomonas.

[Objective] To explore the roles of phytochrome genesPaPhy1 andPaPhy2 in the sexual reproduction and asexual development ofPodospora anserina and decipher the regulatory mechanisms.[Methods] The homologous recombination method was employed to knock out the two phytochrome genes, and the resulting mutants, ΔPaPhy1 and ΔPaPhy2, were obtained. A double mutant, ΔPaPhy1ΔPaPhy2, was constructedvia genetic cross. We compared the sexual production, asexual development, growth rate, and reactive oxygen metabolism between the mutants and wild-type strains under different light conditions to reveal the main roles of the phytochrome genes inP.anserina.[Results] Blue light and white light induced the formation ofP.anserina ascospore shells. ΔPaPhy produced fewer ascospores in the light and showed prolonged life cycle.[Conclusion] Phytochrome genes are associated with the sexual reproduction ofP.anserina. The aging delay of ΔPaPhy is related to reactive oxygen metabolism. The results of this study provide new ideas for further exploring the mechanism of light in regulating the reproduction of filamentous fungi as well as anti-aging studies.

[Objective] The increasing antibiotic resistant bacteria (ARB) caused by the horizontal transfer of antibiotic resistance genes (ARGs) have aroused increasing concern, and it is particularly important to monitor the ARB in the environment.[Methods] We collected seawater and sand samples from three different bathing beaches in Zhanjiang. The plate coating method and agar diffusion method were employed to study the bacterial counts, diversity, and susceptibility to antibiotics.[Results] The seawater samples had higher content of inorganic nitrogen than the normal value and the bacterial counts increased with the increase in the visitor flow. The bacteria counts in the sand samples were higher than those in the seawater samples. The bacteria from the bathing beaches belonged into 18 genera, 12 families of 3 phyla.Proteobacteria (49.64%) was dominant in the seawater samples, whileFirmicutes (54.74%) was dominant in the sand samples. The bacteria showed stronger resistance to beta-lactams, with the resistance rates of 23.25%, 20.53%, and 17.42% to penicillin, vancomycin, and ceftriaxone, respectively. The resistant bacteria were mainlyBacillus,Vibrio,Pseudomonas,Streptomyces, andEnterobacter. The multidrug-resistant bacterial strains from seawater were significantly more than those from sand, and increased with the increase in the visitor flow.[Conclusion] There are diverse drug-resistant bacteria from bathing beaches, and continuous surveillance is required to assess its potential impact on public health.

[Objective] We isolated bacteria from the rhizosphere soils of three blueberry varieties, explored the bacterial diversity, and screened out the strains with acid-producing, plant growth-promoting, and antifungal properties, aiming to provide high-quality strain resources and a theoretical basis for the research on blueberry-specialized microbial fertilizers.[Methods] Five different media were used to isolate the bacteria from rhizosphere soils, and 16S rRNA gene sequencing and phylogenetic analysis were performed. The strains capable of producing acid, indole-3-acetic acid (IAA), and siderophores, fixing nitrogen, solubilizing phosphorus, and inhibiting the growth ofBotrytis cinerea were screened out. The suitable strains with excellent properties were selected and then inoculated in blueberry seedlings cultivated in pots. The effects on the growth and element absorption of the seedlings and fertility of rhizosphere soil were examined.[Results] A total of 124 strains were isolated from the rhizosphere soils of three blueberry varieties. Seventy representative strains were selected for 16S rRNA gene sequencing, belonging to 21 genera of 3 phyla, among whichBacillus,Pseudomonas,Streptomyces, andRhodococcus were the dominant bacteria. Among the representative strains, 21.4%, 21.4%, 47.1%, 65.7%, and 14.3% could produce acids, produce IAA, fix nitrogen, solubilize phosphorus, and secrete siderophores, respectively. A few strains displayed the abilities of producing acids and IAA, fixing nitrogen, solubilizing phosphorus, and inhibitingB.cinerea simultaneously.Pseudomonas chlororaphis CSM-70 andPseudomonas piscium CSM-129 with acid-producing and growth-promoting characteristics were selected and inoculated in blueberry seedlings. Both strains significantly promoted the growth and development of blueberry seedlings and regulated the pH of the rhizosphere soil. In addition, strain CSM-70 significantly promoted the absorption of nitrogen and phosphorus in blueberry leaves and increased the content of available potassium and available nitrogen in the soil.[Conclusion] The blueberry rhizosphere soil has high bacterial diversity and harbors abundant plant growth-promoting strains.P.chlororaphis CSM-70 andP.piscium CSM-129 can promote the growth of blueberry seedlings, regulate rhizosphere soil pH and fertility, and promote nutrient absorption, demonstrating the potential of serving as blueberry-specific microbial fertilizers.