{"title":"Basidiomycetes to the rescue: Mycoremediation of metal-organics co-contaminated soils.","authors":"Lea Traxler, Katrin Krause, Erika Kothe","doi":"10.1016/bs.aambs.2024.06.001","DOIUrl":"10.1016/bs.aambs.2024.06.001","url":null,"abstract":"<p><p>The increasing need for metals leads to contaminated post-mining landscapes. At the same time, the contamination with organic, recalcitrant contamination increases. This poses a problem of reuse of large areas, often co-contaminated with both, metals, and organic pollutants. For the remediation of areas contaminated with multiple contaminants and combining many stress factors, technical solutions including groundwater treatment, where necessary, have been devised. However, this is applied to highly contaminated, small sites. The reuse of larger, co-contaminated landscapes remains a major challenge. Mycoremediation with fungi offers a good option for such areas. Fungi cope particularly well with heterogeneous conditions due to their adaptability and their large hyphal network. This chapter summarizes the advantages of basidiomycetes with a focus on wood rot fungi in terms of their ability to tolerate metals, radionuclides, and organic contaminants such as polycyclic aromatic hydrocarbons. It also shows how these fungi can reduce toxicity of contaminants to other organisms including plants to allow for restored land-use. The processes based on diverse molecular mechanisms are introduced and their use for mycoremediation is discussed.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"129 ","pages":"83-113"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development and applications of genome-scale metabolic network models.","authors":"Jinyi Qian, Chao Ye","doi":"10.1016/bs.aambs.2024.02.002","DOIUrl":"10.1016/bs.aambs.2024.02.002","url":null,"abstract":"<p><p>The genome-scale metabolic network model is an effective tool for characterizing the gene-protein-response relationship in the entire metabolic pathway of an organism. By combining various algorithms, the genome-scale metabolic network model can effectively simulate the influence of a specific environment on the physiological state of cells, optimize the culture conditions of strains, and predict the targets of genetic modification to achieve targeted modification of strains. In this review, we summarize the whole process of model building, sort out the various tools that may be involved in the model building process, and explain the role of various algorithms in model analysis. In addition, we also summarized the application of GSMM in network characteristics, cell phenotypes, metabolic engineering, etc. Finally, we discuss the current challenges facing GSMM.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"126 ","pages":"1-26"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140848508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chiara Tarracchini, Christian Milani, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Douwe van Sinderen, Marco Ventura
{"title":"The infant gut microbiota as the cornerstone for future gastrointestinal health.","authors":"Chiara Tarracchini, Christian Milani, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Douwe van Sinderen, Marco Ventura","doi":"10.1016/bs.aambs.2024.02.001","DOIUrl":"10.1016/bs.aambs.2024.02.001","url":null,"abstract":"<p><p>The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"126 ","pages":"93-119"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140855226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Remediation of toxic metal and metalloid pollution with plant symbiotic fungi.","authors":"Qing Zhen, Xinru Wang, Xianxian Cheng, Weiguo Fang","doi":"10.1016/bs.aambs.2024.04.001","DOIUrl":"https://doi.org/10.1016/bs.aambs.2024.04.001","url":null,"abstract":"<p><p>Anthropogenic activities have dramatically accelerated the release of toxic metal(loid)s into soil and water, which can be subsequently accumulated in plants and animals, threatening biodiversity, human health, and food security. Compared to physical and chemical remediation, bioremediation of metal(loid)-polluted soil using plants and/or plant symbiotic fungi is usually low-cost and environmentally friendly. Mycorrhizal fungi and endophytic fungi are two major plant fungal symbionts. Mycorrhizal fungi can immobilize metal(loid)s via constitutive mechanisms, including intracellular sequestration with vacuoles and vesicles and extracellular immobilization by cell wall components and extracellular polymeric substances such as glomalin. Mycorrhizal fungi can improve the efficacy of phytoremediation by promoting plant symplast and apoplast pathways. Endophytic fungi also use constitutive cellular components to immobilize metal(loid)s and to reduce the accumulation of metal(loid)s in plants by modifying plant physiological status. However, a specific mechanism for the removal of methylmercury pollution was recently discovered in the endophytic fungi Metarhizium, which could be acquired from bacteria via horizontal gene transfer. In contrast to mycorrhizal fungi that are obligate biotrophs, some endophytic fungi, such as Metarhizium and Trichoderma, can be massively and cost-effectively produced, so they seem to be well-placed for remediation of metal(loid)-polluted soil on a large scale.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"129 ","pages":"171-187"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G Flores-Cosío, J A García-Béjar, D Sandoval-Nuñez, L Amaya-Delgado
{"title":"Stress response and adaptation mechanisms in Kluyveromyces marxianus.","authors":"G Flores-Cosío, J A García-Béjar, D Sandoval-Nuñez, L Amaya-Delgado","doi":"10.1016/bs.aambs.2024.02.003","DOIUrl":"10.1016/bs.aambs.2024.02.003","url":null,"abstract":"<p><p>Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins. However, several studies highlighted the metabolic trait variations among the K. marxianus strains, suggesting genetic diversity within the species that determines its metabolic functions; this diversity can be attributed to its high adaptation capacity against stressful environments. The outstanding metabolic characteristics of K. marxianus have motivated this yeast to be a study model to evaluate its easy adaptability to several environments. This chapter will discuss overview characteristics and applications of K. marxianus and recent insights into the stress response and adaptation mechanisms used by this non-Saccharomyces yeast.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"126 ","pages":"27-62"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140846709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Effects of gut bacteria and their metabolites on gut health of animals.","authors":"Zhuang Hao, Xuedong Ding, Jing Wang","doi":"10.1016/bs.aambs.2024.02.007","DOIUrl":"10.1016/bs.aambs.2024.02.007","url":null,"abstract":"<p><p>The intestine tract is a vital site for the body to acquire nutrients, serving as the largest immune organ. Intestinal health is crucial for maintaining a normal physiological state. Abundant microorganisms reside in the intestine, colonized in a symbiotic manner. These microorganisms can generate various metabolites that influence host physiological activities. Microbial metabolites serve as signaling molecules or metabolic substrates in the intestine, and some intestinal microorganisms act as probiotics and promote intestinal health. Researches on host, probiotics, microbial metabolites and their interactions are ongoing. This study reviews the effects of gut bacteria and their metabolites on intestinal health to provide useful references for animal husbandry.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"127 ","pages":"223-252"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The function and application of edible fungal polysaccharides.","authors":"Qian Zhang, Yingyin Xu, Liyuan Xie, Xueqin Shu, Shilin Zhang, Yong Wang, Haixia Wang, Qian Dong, Weihong Peng","doi":"10.1016/bs.aambs.2024.02.005","DOIUrl":"10.1016/bs.aambs.2024.02.005","url":null,"abstract":"<p><p>Edible fungi, commonly known as mushrooms, are precious medicinal and edible homologous gifts from nature to us. Edible fungal polysaccharides (EFPs) are a variety of bioactive macromolecular which isolated from fruiting bodies, mycelia or fermentation broths of edible or medicinal fungus. Increasing researches have confirmed that EFPs possess multiple biological activities both in vitro and in vivo settings, including antioxidant, antiviral, anti-inflammatory, immunomodulatory, anti-tumor, hypoglycemic, hypolipidemic, and regulating intestinal flora activities. As a result, they have emerged as a prominent focus in the healthcare, pharmaceutical, and cosmetic industries. Fungal EFPs have safe, non-toxic, biodegradable, and biocompatible properties with low immunogenicity, bioadhesion ability, and antibacterial activities, presenting diverse potential applications in the food industries, cosmetic, biomedical, packaging, and new materials. Moreover, varying raw materials, extraction, purification, chemical modification methods, and culture conditions can result in variances in the structure and biological activities of EFPs. The purpose of this review is to provide comprehensively and systematically organized information on the structure, modification, biological activities, and potential applications of EFPs to support their therapeutic effects and health functions. This review provides new insights and a theoretical basis for prospective investigations and advancements in EFPs in fields such as medicine, food, and new materials.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"127 ","pages":"45-142"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular aspects of copper homeostasis in fungi.","authors":"Dayane Moraes, Mirelle Garcia Silva-Bailão, Alexandre Melo Bailão","doi":"10.1016/bs.aambs.2024.08.001","DOIUrl":"https://doi.org/10.1016/bs.aambs.2024.08.001","url":null,"abstract":"<p><p>Copper homeostasis in fungi is a tightly regulated process crucial for cellular functions. Fungi acquire copper from their environment, with transporters facilitating its uptake into the cell. Once inside, copper is utilized in various metabolic pathways, including respiration and antioxidant defense. However, excessive copper can be toxic by promoting cell damage mainly due to oxidative stress and metal displacements. Fungi employ intricate regulatory mechanisms to maintain optimal copper levels. These involve transcription factors that control the expression of genes involved in copper transport, storage, and detoxification. Additionally, chaperone proteins assist in copper trafficking within the cell, ensuring its delivery to specific targets. Furthermore, efflux pumps help remove excess copper from the cell. Altogether, these mechanisms enable fungi to balance copper levels, ensuring proper cellular function while preventing toxicity. Understanding copper homeostasis in fungi is not only essential for fungal biology but also holds implications for various applications, including biotechnology and antifungal drug development.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"129 ","pages":"189-229"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Treatment of agricultural wastewater using microalgae: A review.","authors":"Jiayi Li, Tong Li, Dongzhe Sun, Yueqiang Guan, Zhao Zhang","doi":"10.1016/bs.aambs.2024.05.004","DOIUrl":"10.1016/bs.aambs.2024.05.004","url":null,"abstract":"<p><p>The rapid development of agriculture has led to a large amount of wastewater, which poses a great threat to environmental safety. Microalgae, with diverse species, nutritional modes and cellular status, can adapt well in agricultural wastewater and absorb nutrients and remove pollutants effectively. Besides, after treatment of agricultural wastewater, the accumulated biomass of microalgae has broad applications, such as fertilizer and animal feed. This paper reviewed the current progresses and further perspectives of microalgae-based agricultural wastewater treatment. The characteristics of agricultural wastewater have been firstly introduced; Then the microalgal strains, cultivation modes, cellular status, contaminant metabolism, cultivation systems and biomass applications of microalgae for wastewater treatment have been summarized; At last, the bottlenecks in the development of the microalgae treatment methods, as well as recommendations for optimizing the adaptability of microalgae to wastewater in terms of wastewater pretreatment, microalgae breeding, and microalgae-bacterial symbiosis systems were discussed. This review would provide references for the future developments of microalgae-based agricultural wastewater treatment.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"128 ","pages":"41-82"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141764789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lorena Cuervo, Carmen Méndez, Carlos Olano, Mónica G Malmierca
{"title":"Volatilome: Smells like microbial spirit.","authors":"Lorena Cuervo, Carmen Méndez, Carlos Olano, Mónica G Malmierca","doi":"10.1016/bs.aambs.2024.02.008","DOIUrl":"10.1016/bs.aambs.2024.02.008","url":null,"abstract":"<p><p>In recent years, the study of volatile compounds has sparked interest due to their implications in signaling and the enormous variety of bioactive properties attributed to them. Despite the absence of analysis methods standardization, there are a multitude of tools and databases that allow the identification and quantification of volatile compounds. These compounds are chemically heterogeneous and their diverse properties are exploited by various fields such as cosmetics, the food industry, agriculture and medicine, some of which will be discussed here. In virtue of volatile compounds being ubiquitous and fast chemical messengers, these molecules mediate a large number of interspecific and intraspecific interactions, which are key at an ecological level to maintaining the balance and correct functioning of ecosystems. This review briefly summarized the role of volatile compounds in inter- and intra-specific relationships as well as industrial applications associated with the use of these compounds that is emerging as a promising field of study.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"127 ","pages":"1-43"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}