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Critical Reviews in Food Science and... Nov 2023With the rapid development of systems biology technology, there is a deeper understanding of the molecular biological mechanisms and physiological characteristics of... (Review)
Review
With the rapid development of systems biology technology, there is a deeper understanding of the molecular biological mechanisms and physiological characteristics of microorganisms. Yeasts are widely used in the food industry with their excellent fermentation performances. While due to the complex environments of food production, yeasts have to suffer from various stress factors. Thus, elucidating the stress mechanisms of food yeasts and proposing potential strategies to improve tolerance have been widely concerned. This review summarized the recent signs of progress in the variety, functions, and stress tolerance of food yeasts. Firstly, the main food yeasts occurred in fermented foods, and the taxonomy levels are demonstrated. Then, the main functions of yeasts including aroma enhancer, safety performance enhancer, and fermentation period reducer are discussed. Finally, the stress response mechanisms of yeasts and the strategies to improve the stress tolerance of cells are reviewed. Based on sorting out these related recent researches systematically, we hope that this review can provide help and approaches to further exert the functions of food yeasts and improve food production efficiency.
Topics: Yeasts; Fermentation; Food; Food Microbiology; Fermented Foods
PubMed: 35875880
DOI: 10.1080/10408398.2022.2098688 -
Microbial Ecology Nov 2023Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to... (Review)
Review
Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.
Topics: Soil; Agricultural Inoculants; Carbon; Agriculture; Soil Microbiology
PubMed: 37280438
DOI: 10.1007/s00248-023-02250-6 -
Applied Microbiology and Biotechnology Dec 2023Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has...
Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.
Topics: Triticum; Nitrogen; Plant Roots; Soil Microbiology; Microbiota; Soil; Bacteria; Archaea; Rhizosphere
PubMed: 37747613
DOI: 10.1007/s00253-023-12787-8 -
The New Phytologist Oct 2023Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant...
Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with N-N gas to detect in situ N fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% N (average and median of 3.36 and 2.85 at% N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.
Topics: Rhizosphere; Bacteria; In Situ Hybridization; Plants; Oryza; Plant Roots; Soil Microbiology
PubMed: 37381111
DOI: 10.1111/nph.19112 -
Brazilian Journal of Microbiology :... Dec 2023Brazilian medical mycology considerably expanded in the last decades due to the efforts of several pioneers who started and expanded mycology during the twentieth... (Review)
Review
Brazilian medical mycology considerably expanded in the last decades due to the efforts of several pioneers who started and expanded mycology during the twentieth century. In this manuscript, we highlight some of the contributions of one of these pioneers: Professor Luiz R. Travassos, who started his career in the field of microbiology in the 1960s. We will discuss his contributions to the areas of medical mycology and glycobiology, with a focus on glycosphingolipids, sialic acids, and surface enzymes.
Topics: Mycology; Brazil
PubMed: 36720842
DOI: 10.1007/s42770-023-00916-4 -
FEMS Microbiology Reviews Mar 2024Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall... (Review)
Review
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
Topics: Animals; Humans; One Health; Microbiota; Biological Evolution; Soil Microbiology; Plants
PubMed: 38425054
DOI: 10.1093/femsre/fuae008 -
Applied Microbiology and Biotechnology Sep 2023Climate change due to the continuous increase in the release of green-house gasses associated with anthropogenic activity has made a significant impact on the... (Review)
Review
Climate change due to the continuous increase in the release of green-house gasses associated with anthropogenic activity has made a significant impact on the sustainability of life on our planet. Methane (CH) is a green-house gas whose concentrations in the atmosphere are on the rise. CH measurement is important for both the environment and the safety at the industrial and household level. Methanotrophs are distinguished for their unique characteristic of using CH as the sole source of carbon and energy, due to the presence of the methane monooxygenases that oxidize CH under ambient temperature conditions. This has attracted interest in the use of methanotrophs in biotechnological applications as well as in the development of biosensing systems for CH quantification and monitoring. Biosensing systems using methanotrophs rely on the use of whole microbial cells that oxidize CH in presence of O, so that the CH concentration is determined in an indirect manner by measuring the decrease of O level in the system. Although several biological properties of methanotrophic microorganisms still need to be characterized, different studies have demonstrated the feasibility of the use of methanotrophs in CH measurement. This review summarizes the contributions in methane biosensing systems and presents a prospective of the valid use of methanotrophs in this field. KEY POINTS: • Methanotroph environmental relevance in methane oxidation • Methanotroph biotechnological application in the field of biosensing • Methane monooxygenase as a feasible biorecognition element in biosensors.
Topics: Methane; Oxidation-Reduction; Gases; Biotechnology; Climate Change; Soil Microbiology
PubMed: 37486352
DOI: 10.1007/s00253-023-12629-7 -
A Systematic Review on the Continuous Cropping Obstacles and Control Strategies in Medicinal Plants.International Journal of Molecular... Aug 2023Continuous cropping (CC) is a common practice in agriculture, and usually causes serious economic losses due to soil degeneration, decreased crop yield and quality, and... (Review)
Review
Continuous cropping (CC) is a common practice in agriculture, and usually causes serious economic losses due to soil degeneration, decreased crop yield and quality, and increased disease incidence, especially in medicinal plants. Continuous cropping obstacles (CCOs) are mainly due to changes in soil microbial communities, nutrient availability, and allelopathic effects. Recently, progressive studies have illustrated the molecular mechanisms of CCOs, and valid strategies to overcome them. Transcriptomic and metabolomics analyses revealed that identified DEGs (differently expressed genes) and metabolites involved in the response to CCOs are involved in various biological processes, including photosynthesis, carbon metabolism, secondary metabolite biosynthesis, and bioactive compounds. Soil improvement is an effective strategy to overcome this problem. Soil amendments can improve the microbial community by increasing the abundance of beneficial microorganisms, soil fertility, and nutrient availability. In this review, we sum up the recent status of the research on CCOs in medicinal plants, the combination of transcriptomic and metabolomics studies, and related control strategies, including uses of soil amendments, crop rotation, and intercropping. Finally, we propose future research trends for understanding CCOs, and strategies to overcome these obstacles and promote sustainable agriculture practices in medicinal plants.
Topics: Plants, Medicinal; Soil Microbiology; Agriculture; Soil; Carbon
PubMed: 37569843
DOI: 10.3390/ijms241512470 -
Pest Management Science Aug 2023The incidence of herbicide-resistant barnyardgrass is escalating in paddy fields, yet the interactions between resistant weeds and rice are largely unknown. The...
BACKGROUND
The incidence of herbicide-resistant barnyardgrass is escalating in paddy fields, yet the interactions between resistant weeds and rice are largely unknown. The microbiota of herbicide-resistant barnyardgrass rhizosphere soil is critical for both barnyardgrass and rice fitness.
RESULTS
Rice has different biomass allocation and root traits in the presence of penoxsulam-resistant versus penoxsulam-susceptible barnyardgrass or in their conditioned soil. Compared to susceptible barnyardgrass, resistant barnyardgrass led to an allelopathic increase in rice root, shoot, and whole-plant biomasses. Resistant barnyardgrass recruited distinct core and unique microbes in rhizosphere soil compared to susceptible barnyardgrass. In particular, resistant barnyardgrass assembled more Proteobacteria and Ascomycota to enhance plant stress tolerance. Furthermore, the root exudates from resistant and susceptible barnyardgrass were responsible for the assembly and establishment of the root microbial structure. Importantly, (-)-loliolide and jasmonic acid in root exudates were correlated with the core microbes in the rhizosphere soil.
CONCLUSION
The interference of barnyardgrass with rice can be mediated by rhizosphere microbial communities. Biotype-specific variation in the ability to generate soil microbial communities appears to ameliorate the negative consequences for rice growth, providing an intriguing possibility for modulation of the rhizosphere microbiota to increase crop productivity and sustainability. © 2023 Society of Chemical Industry.
Topics: Oryza; Echinochloa; Rhizosphere; Plant Roots; Soil; Soil Microbiology; Herbicides; Microbiota
PubMed: 36883589
DOI: 10.1002/ps.7445 -
Viruses Jul 2023In this Special Issue of , we showcase some of the fascinating and diverse virology being undertaken in Canada that was presented at the 4th Symposium of the Canadian...
In this Special Issue of , we showcase some of the fascinating and diverse virology being undertaken in Canada that was presented at the 4th Symposium of the Canadian Society for Virology 2022 [...].
Topics: Canada; Viruses; Virology
PubMed: 37515198
DOI: 10.3390/v15071512