The term "microorganism" refers to tiny organisms such as archaea, bacteria, protists, fungi, and viruses, and the term "microbiome" refers to a collection of microorganisms. Although they share the body space of the host, their roles as determinants in host health and diseases are ignored. As a collection of information, the microbiome includes the genomic data, structural elements, metabolites, and environmental conditions of microorganisms. Studies have demonstrated that the microbiome plays an essential role in maintaining host homeostasis and regulating host phenotypes. With the advent of new technologies, including next-generation sequencing (NGS) and sequencing-based microbiome profiling, researchers have probed into the relationship between the microbiome and host phenotypes. By an overview of microbiome, this paper elaborated on the microbiome-host genetics interactions based on genome-wide association analysis and made an outlook on the future of this field.

Gray mold caused byBotrytis cinerea is one of the major diseases affecting tomato production. The currently used fungicides are gradually restricted due to residues, pathogen resistance, and food safety. Therefore, screening out antagonistic microorganisms has gradually become an effective approach for the biocontrol of gray mold. [Objective] We screened out endophytic strains capable of endowing plants with disease resistance and promoting plant growth from tomato plants and evaluated their biocontrol potential, aiming to provide a theoretical basis for developing a new approach for the biocontrol of tomato gray mold.[Methods] The endophytic bacteria and fungi were isolated from different parts of tomato plants by the tissue culture method, and the candidate strains were preliminarily identified by 16S rRNA and ITS sequence analysis. The endophytes with antagonistic activity againstB.cinerea were screened by confrontation culture and fruit inoculationin vitro. Furthermore, we examined the abilities of the strain to secrete indole-3 acetic acid (IAA), protease, and siderophores and the promoting effects on the growth ofArabidopsis thaliana and tomato seedlings.[Results] A total of 72 endophytic bacterial strains and 31 endophytic fungal strains were isolated from different parts of tomato plants. An endophytic bacterium FQ-G3 with strong inhibitory activities against several pathogens was screened out and was identified asBacillus velezensis. FQ-G3 showed the inhibition rate of 80.93% againstB.cinereain vitro and inhibited the mycelial expansion on tomato fruitsin vivo. The strain could secrete IAA, protease, and siderophores, and promote the growth ofA.thaliana and tomato seedlings.[Conclusion] The endophytic strain FQ-G3 isolated from tomato plants endows plants with disease resistance and promotes plant growth, and thus can serve as a candidate for the prevention and control of gray mold. The findings enrich the tomato endophyte resources and provide support for the control of gray mold and the growth promotion of tomato.

[Objective] Cyanophages, the viruses specifically infecting cyanobacteria, are ubiquitous in water environments. They play a role in regulating the population dynamics and density of cyanobacteria and promote the biogeochemical cycling of the aquatic ecosystem. This study aims to isolate and identify a cyanophage.[Methods] A novel cyanophage Yong-L2-223 was isolated from fresh water samples with marineSynechococcus sp. PCC 7002 as the indicator host. The host range, genome sequence, open reading frames (ORFs), and phylogenetic relationship of Yong-L2-223 were studied.[Results] The host range tests against 31 strains of cyanobacteria showed that Yong-L2-223 could infect the indicator host PCC 7002 (Synechococcales) and two freshwater strainsMicrocystis viridis FACHB-1342 (Chroococcales) andAphanizomenon flos-aquae FACHB-1209 (Nostocales) from the Dianchi Lake. The infection of the cyanobacterial strains from both the seawater and freshwater samples indicated that Yong-L2-223 was a euryhaline cyanophage. Yong-L2-223 was myovirus-like, consisting of an icosahedral head (about 60 nm in diameter) and a contractile tail (about 136 nm in length). The genome (double-stranded DNA) of Yong-L2-223 had a length of 65 725 bp, with the G+C content of 58.6% and 100 ORFs. It was predicted to carry theCas4 gene, gene transfer factor (GTA) gene, auxiliary metabolic genes (AMGs), and a gene cluster for the synthesis of pre-Q₀. These genes may contribute to the adaptation and infection of the cyanophage in cyanobacteria of three orders. The pairwise sequence comparison (PASC) illustrated that the highest similarity sharing by cyanophage Yong-L2-223 and all the viruses in the current genome databases was only 3.78%, far below the genus boundary cut-off of 70% defined by the International Committee on Taxonomy of Viruses. In the phylogenetic tree based on the whole proteomes, Yong-L2-223 formed an independent branch, with long evolutionary distances from other phages.[Conclusion] Yong-L2-223 is a new genus of theCaudoviricetes class. For the first time, we used a marine cyanobacterial strain as the indicator host to isolate and obtain a novel cyanophage from freshwater, which broadened the understanding of cyanophages, enriched cyanophage genome database, and laid a foundation for the development of cyanophage resources.

Proper pH is crucial for the survival and functions of microorganisms, whether in the environment or within cells. Under acidic or alkaline stress, microorganisms have evolved diverse strategies, such as proton transport, production of acidic or alkaline substances, and cell membrane protection, to maintain intracellular pH homeostasis. Moreover, microorganisms have evolved the ability to actively change the extracellular pH. This article reviews the mechanisms by which microorganisms maintain intracellular pH homeostasis under acid or alkaline stress and alter extracellular pH. It aims to enhance our understanding of the interaction between microorganisms and the environment and provide a reference for further research on the synergistic mechanisms between microorganisms and the environment.

Fatty acids are not only the components of cell membrane but also the raw materials for the synthesis of bioactive molecules. Unsaturated fatty acids (UFAs) with low phase-transition temperatures are essential molecules for bacteria to regulate cell membrane fluidity. Therefore, the synthetic pathways of UFAs are key targets for the screening of antibacterial agents. Bacteria can adopt the anaerobic pathway to synthesize UFAs. For example,Escherichia coli, a model organism, synthesizes UFAsvia the classic FabA-FabB pathway. However, the anaerobic pathways for the synthesis of UFAs vary in different bacteria, and the catalytic enzymes are also different. Bacteria can synthesize UFAsvia aerobic pathways, in which fatty acid desaturase directly converts saturated fatty acids (SFAs) into UFAs. Different desaturases introduce double bond to form UFAs with different structures, which play roles in stress responses, pathogenicity and other aspects. Other enzymes involved in the synthesis of fatty acids can also participate in the synthesis of UFAs or regulation of different UFAs. Some bacteria can use monooxygenase to convert capryl-ACP (acyl carrier protein) in the fatty acid synthesis pathway intocis-3-decenyl ACP to synthesize UFAs. We comprehensively reviewed the research progress in the synthesis of UFAs in bacteria, aiming to provide theoretical support for deciphering the mechanism of bacterial synthesis of UFAs and developing the targeted antibacterial drugs.