Algae and bacteria are both the oldest forms of life on our planet, and billions of years of natural evolution have driven the algae and their microbiomes to evolve into interactive phycobionts. Through complex, flexible, intelligent, and multi-interface interactions between algae and bacteria, the functions of both sides of the phycobionts are exquisitely regulated. The creation, innovation, and development of the phycobiont theory shows vital scientific value for revealing the mystery of the origin and evolution of the life on Earth, and this theory is also being transformed into diverse practical applications in significant fields for sustainable development. After centuries of incubation, knowledge accumulation and development, currently, it is the right time to promote Phycosphere Microbiology to develop into an emerging interdiscipline. In this review, we comprehensively discussed the core concepts of Phycosphere Microbiology, sorted out its vital relationships with environment protection, human health maintenance, resource utilization, and green-oriented transition of energy, then reviewed its development history, and summarized the main research achievements during three development periods. Finally, we also proposed and discussed the future development trends and potential research directions for this emerging interdiscipline.

Activation induced cytidine deaminase (AID) and apolipoprotein B mRNA editing enzyme catalytic peptide (APOBEC) constitute a conserved family of cytidine deaminase enzymes. The family members have different functions in the body, and they play an important role in the immune defense of the host. AID plays a role mainly in the adaptive immune systems of vertebrates, mediating class switch recombination, antibody affinity maturation, and antibody diversity generation. APOBEC1 capable of catalyzing cytosine deamination, mediating RNA editing for cellular regulation, and resisting retroviral infection is involved in tumorigenesis and cancer development. APOBEC2, most abundant in cardiac and skeletal muscle, is associated with muscle fiber type switch, loss of weight, muscle development, and myopathy. Moreover, it may have potential indirect effects in controlling gene expression. APOBEC3s play key roles in both innate and adaptive immune responses. They are involved in the inhibition of retrotransposon functioning and viral infection, DNA degradation, RNA editing, and cell cycle regulation. The APOBEC4 gene is conserved in various animal species, with the active center sequence different from those of other APOBEC proteins. It is widely recognized that APOBEC4 is a uridine-editing enzyme, which has antiviral activity. The research is limited regarding the animal-derived APOBEC family members. This review describes the structural characteristics and biological functions of APOBEC family members, providing reference for research on the roles of animal-derived APOBEC family members in the immune responses and disease control. In addition, this review provides new ideas for the development of antivirals by enhancing the activities of APOBEC family members.

Bacillus subtilis is a generally recognized as safe (GRAS) probiotic and an excellent industrial chassis strain. It possesses advantages such as strong heterologous protein secretion capability, robust growth with low-quality carbon sources, and negligible codon bias. Since 2016, clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing has been successfully applied to B. subtilis, enabling precise genetic modifications, including point mutations, gene knockout, foreign gene insertion, gene expression regulation, and base editing. These advancements have significantly promoted the development of B. subtilis as an efficient microbial cell factory and have shown broad application potential in agriculture, pharmaceuticals, food production, and synthetic biology. This paper systematically review the development of the CRISPR system in B. subtilis and summarize its application in the efficient production of various products. The aim is to provide insights into the targeted optimization of metabolic pathways in B. subtilisvia the CRISPR system to achieve efficient and stable industrial production of target products, as well as to offer references for the further development and application of novel gene editing systems.

Organic contamination of crops poses a threat to the safety of food products and human health, and it is urgently needed to be solved. Endophytic bacteria are indispensable in microecosystems. In recent years, researchers have screened and isolated endophytic bacteria with the function of degrading pollutants from the environment. These bacteria have been used to regulate the metabolic processes of organic pollutants in crops, which achieve the efficient reducing of toxic organic pollutants in crops. This paper reviews the research progress in the reduction of toxic organic pollutant accumulation in crops by functional endophytic bacteria, focusing on the degradation genes, products, and pathways of toxic organic pollutants in crops after the colonization of functional endophytic bacteria. Furthermore, it discusses the factors affecting the degradation efficiency of functional endophytic bacteria and emphasizes the importance of these bacteria in reducing organic pollutants in crops. This review provides ideas and a basis for the further utilization of endophytic bacteria to control the risk of organic contamination in crops.

Tuberculosis is an ancient zoonotic disease that poses a serious threat to the health of humans and animals worldwide. Mycobacteriumtuberculosis (Mtb) is the primary causative agent of tuberculosis. As a bridge between innate and adaptive immunity, dendritic cells (DCs) play a pivotal role in controlling Mtb infection by utilizing their potent antigen-presenting capacity to activate the adaptive immune response of the host and thus resist further infection. In recent years, more and more studies have shown that Mtb can evade host immune defenses by regulating DC differentiation and maturation, interfering with phagocytosis and autophagy, and inhibiting the expression of antigen presentation-related molecules, thus causing persistent infection. This review summarizes the current research on the molecular mechanisms of Mtb in regulating DC antigen presentation, aiming to provide insights for further study of Mtb-DC interaction mechanism and development of prevention and control strategies for tuberculosis.

Cryptococcus neoformans is a common opportunistic pathogen, exhibiting pronounced neurotropism that often results in cryptococcal meningitis. Its invasive ability is closely associated with multiple factors, including capsular polysaccharides, melanin, hydrolases, and adaptability to the host environment. Conventional diagnostic methods such as fungal culture and India ink staining, though still in use, have notable limitations, whereas emerging techniques like molecular diagnostics, imaging technologies, and biochips have significantly enhanced the diagnostic accuracy and sensitivity. In clinical treatment, amphotericin B and fluconazole are widely used as first-line antifungals, while the resistance to azoles is a growing problem and results in an elevated rate of clinical treatment failure. This is mainly attributed to target alterations, upregulation of efflux pump expression and genomic ploidy changes. Recent studies on virulence factors and resistance mechanisms have driven the development of novel antifungal therapies, including drug repurposing, novel drug development, and innovative drug delivery strategies. This article reviews the latest research in the virulence factors, diagnostic techniques, antifungal resistance mechanisms, and therapeutic development of C. neoformans, providing insights into the clinical management of cryptococcosis.

Collagen is the most abundant protein in mammals, accounting for about one-third of human protein. As an important component of the connective tissue and extracellular matrix, collagen is essential for maintaining physiological functions and repairing injuries and has important applications in the fields of medicine, food, and beauty. The main methods for producing collagen are natural extraction, chemical synthesis, and biosynthesis. Natural extraction from animal connective tissue has ethical issues, unstable quality, and infectious disease risks. Chemical synthesis is costly and it is not easy to synthesize complex collagen structures. Biosynthesis enables the production of recombinant collagen for different purposes by genetic engineering in a more controllable, safer, and more precise manner. However, due to the complex structure of collagen, its biosynthesis depends on specific molecular chaperones and modifying enzymes, and thus the production of recombinant collagen is challenging. In addition, different types of collagen need to form particular tissue structures, such as fibril, reticular, or transmembrane structures, which further increases the difficulty of production. This article clarifies the multifunctionality of recombinant human collagen, reviews the latest progress and challenges in its biosynthesis, and looks forward to future development directions. This review aims to help researchers, engineers, and industry practitioners understand the research trends of recombinant collagen and promote its further development and commercialization in different application fields.

The bacterial stringent response refers to the adaptive reaction that bacteria exhibit when faced with adverse environmental conditions, altering their metabolism and reducing the growth rate to enhance survival and adaptability. The rapid accumulation of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively referred to as (p)ppGpp in this article, mediates the stringent response, playing a crucial role in microbial adaptation to environmental changes. The levels of (p)ppGpp within bacteria are regulated by RelA/SpoT homologue (RSH) proteins, which include small alarmone synthetases (SASs), small alarmone hydrolases (SAHs), and bifunctional proteins such as Rel. Furthermore, recent studies have identified a new bacterial alarmone, adenosine tetraphosphate (ppApp) and adenosine pentaphosphate (pppApp), collectively referred to as (p)ppApp, which is involved in the regulation of various biological processes in bacteria. The enzymes involved in (p)ppGpp metabolism vary among different bacterial species. This study systematically classifies and reviews the structural and biochemical characteristics of the known RSH proteins and summarizes their biochemical functions, aiming to promote further exploration and development in this field.

[Objective] To provide environmental sustainable, safe, and efficacious management approaches for root rot impacting a range of crops in the unique agro-ecosystems of Gansu and Qinghai Provinces. [Methods] The plate confrontation method and the organophosphorus agar plate were used for preliminary screening of 305 strains of tested bacteria, and the strains obtained from preliminary screening were re-screened with the fermentation broth method. Subsequently, the nitrogen-fixing, phosphate-solubilizing, and potassium-solubilizing abilities of the strains were determined by the Kjeldahl method, ultraviolet spectrophotometry, and flame photometry, respectively. The siderophore-producing activity, the IAA content in the fermentation broth, as well as the acid, alkali, and salt tolerance of the strains, were determined by spectrophotometric methods. Finally, targeting the pathogens causing root rot in various crops in Gansu and Qinghai Provinces, bacterial consortia were constructed with different functional strains for disease prevention and plant growth promotion. The plant growth-promoting and antifungal effects of different consortia were evaluated, and the best consortium was selected. Furthermore, the 16S rRNA gene and gyrB of the strains in the best consortia were sequenced for identification. The root rot-preventing and plant growth-promoting effects of the best consortium were evaluated by the pot culture method. [Results] A total of 86 antagonistic strains and 134 phosphate-solubilizing strains were preliminarily screened out, and 20 antagonistic strains were selected after re-screening, among which strains K87 and LB17 demonstrated excellent broad-spectrum antifungal effects. Specifically, K87 showed inhibition rates of 87.53%, 74.90%, 75.15%, 79.69%, and 88.43% against Fusarium avenaceum, F. equiseti, F. oxysporum, F. solani, and Microdochium bolleyi, respectively. LB17 exhibited inhibition rates of 61.89%, 87.52%, and 87.23% against F. oxysporum, F. solani, and Bipolaris sorokiniana, respectively. Among the 8 strains with superior plant growth-promoting abilities, LB17 had the strongest siderophore-producing activity, with an iron carrier activity unit (su) value of 0.32, and K113 exhibited a good nitrogen-fixing capability, fixing nitrogen at a rate of 0.08 g/L. K87 secreted the highest amount of IAA, which reached 9.87 mg/L. MP6 had the greatest ability to solubilize inorganic phosphorus, with a solubilization rate of 1 470.69 μg/mL, while K85 showed the best performance in solubilizing organic phosphorus, with a solubilization rate of 1 321.23 μg/mL. MP41 excelled in potassium solubilization, with a solubilization rate of 140.33 mg/L. Ultimately, 14 bacterial consortia were constructed, in which T2 exhibited the best synthetic performance, with a nitrogen-fixing rate of 0.212 g/L, a potassium solubilization rate of 86.28 mg/L, and an IAA secretion rate of 16.91 mg/L. Moreover, its inhibition rates against the 6 pathogenic fungi all reached over 60.00%, and even 87.69% against F. equiseti. Strains LB17, K87, and MP6 in this consortium were all identified as Bacillus velezensis. T2 demonstrated significant biocontrol efficacy against root rot in naked barley, with the control effects exceeding 70.00%, and exhibited remarkable plant growth-promoting properties. [Conclusion] This study developed an efficient bacterial consortium for the management of crop root rot and the promotion of crop growth in the unique agro-ecosystems in Gansu and Qinghai Provinces.

[Objective] The rhizosphere microorganism-plant combined approach has high application potential for the remediation of heavy metal-contaminated soil. This study observed the effects of adding exogenous plant growth-promoting bacteria (PGPB) on the growth and molybdenum (Mo) accumulation of alfalfa (Medicago sativa), aiming to provide theoretical references for plant-microbial remediation of Mo-contaminated soil. [Methods] The endophytic bacteria were isolated from dominant plants of Mo tailing and they were identified based on morphological characteristics and molecular evidence. The plant growth-promoting (PGP) properties of molybdate-reducing strains were determined. By adding exogenous PGPB into the soil, we investigated the effects of adding exogenous PGPB on the biomass, physiological activity, and Mo accumulation of alfalfa. [Results] Two molybdate-reducing strains M9 and M13 were obtained and identified as Serratia plymuthica based on morphological characteristics, 16S rRNA gene sequence, and gyrB sequence. M9 and M13 had the abilities to fix nitrogen, solubilize phosphorus, solubilize potassium, and secrete indole-3-acetic acid (IAA), siderophores, and 1-amino cyclopropane-1-carboxylic acid (ACC) deaminase. Under Mo stress, the inoculation of M9, M13, and M9+M13 significantly promoted the growth of alfalfa, increasing the plant height, root length, and fresh weight of alfalfa compared with the non-inoculation control group. At the same time, the inoculation increased the chlorophyll content and peroxidase (POD) activity while decreasing the malondialdehyde (MDA) content in alfalfa. M9 and M13 significantly affected the Mo accumulation of alfalfa. The Mo content in the above-ground and under-ground parts of alfalfa inoculated with M9, M13, and M9+M13 significantly decreased compared with that in the non-inoculation control group. The decreased enrichment factor of Mo in alfalfa indicated that inoculation with molybdate-reducing strains reduced the uptake and transport of Mo in alfalfa. [Conclusion] The molybdate-reducing strains M9 and M13 can promote the growth and reduce the Mo content of alfalfa in Mo-contaminated soil. This finding can provide theoretical reference for revealing the mechanism of microbial-enhanced Mo remediation by plants as well as the joint remediation of Mo-contaminated soil by plants and microorganisms.