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Trends in Microbiology Apr 2020Microbiology has unraveled rich evidence of ongoing reticulate evolutionary processes and complex interactions both within and between cells. These phenomena feature... (Review)
Review
Microbiology has unraveled rich evidence of ongoing reticulate evolutionary processes and complex interactions both within and between cells. These phenomena feature real biological networks, which can logically be analyzed using network-based tools. It is thus not surprising that network sciences, a field independent from evolutionary biology and microbiology, have recently pervasively infused their methods into both fields. Importantly, network tools bring forward observations enhancing the understanding of three core evolutionary concepts: variation, fitness, and heredity. Consequently, our work shows how network sciences can enhance evolutionary theory by explaining the evolution by natural selection of a broad diversity of units of selection, while updating the popular figure of Darwin's tree of life with a comprehensive sketch of the networks of evolution.
Topics: Bacteria; Biofilms; Biological Evolution; Gene Transfer Techniques; Microbiology; Microbiota; Protein Interaction Maps; Selection, Genetic; Transcriptome
PubMed: 31866140
DOI: 10.1016/j.tim.2019.11.006 -
Viruses Apr 2021This Special Issue celebrates viruses of microbes: those viruses that infect archaea, bacteria and microbial eukaryotes [...].
This Special Issue celebrates viruses of microbes: those viruses that infect archaea, bacteria and microbial eukaryotes [...].
Topics: Archaea; Bacteria; Eukaryota; Host-Pathogen Interactions; Microbiology; Virus Physiological Phenomena; Viruses
PubMed: 33946411
DOI: 10.3390/v13050802 -
Current Opinion in Plant Biology Jun 2022Plant-fungal interactions in the soil crucially impact crop productivity and can range from highly beneficial to detrimental. Accumulating evidence suggests that some... (Review)
Review
Plant-fungal interactions in the soil crucially impact crop productivity and can range from highly beneficial to detrimental. Accumulating evidence suggests that some root-colonizing fungi shift between endophytic and pathogenic behaviour depending on the host species and that combinations of effector proteins collectively shape the fungal lifestyle on a given plant. In this review we discuss recent advances in our understanding of how fungal infection strategies on roots can lead to contrasting outcomes for the host. We highlight functional similarities and differences in compatibility determinants that control the colonization of specific-cell layers within plant roots, ultimately shaping the continuum between endophytic and pathogenic lifestyle.
Topics: Endophytes; Fungi; Plant Roots; Rhizosphere; Soil Microbiology
PubMed: 35526366
DOI: 10.1016/j.pbi.2022.102226 -
Environmental Microbiology Aug 2022Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit... (Review)
Review
Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects. Their relationships with insects range from pathogenic to mutualistic and some rhizobacteria can use insects as vectors for dispersal to new host plants. Thus, the interactions of these bacteria with their environment are even more complex than previously thought and can extend far beyond the rhizosphere. The discovery of this secret life of rhizobacteria represents an exciting new field of research that should link the fields of plant-microbe and insect-microbe interactions. In this review, we provide examples of plant-beneficial rhizosphere bacteria that use insects as alternative hosts, and of potentially rhizosphere-competent insect symbionts. We discuss the bacterial traits that may enable a host-switch between plants and insects and further set the multi-host lifestyle of rhizobacteria into an evolutionary and ecological context. Finally, we identify important open research questions and discuss perspectives on the use of these rhizobacteria in agriculture.
Topics: Animals; Bacteria; Insecta; Plant Roots; Plants; Rhizosphere; Soil Microbiology; Symbiosis
PubMed: 35315557
DOI: 10.1111/1462-2920.15968 -
Microbiological Research Aug 2022The growing interest in low-input agriculture in recent years has focused the use of microbial biofertilizers to improve plant growth and yield through a better... (Review)
Review
The growing interest in low-input agriculture in recent years has focused the use of microbial biofertilizers to improve plant growth and yield through a better mobilization of indigenous source of key nutrients such as nitrogen, phosphorus, potassium etc. In this context, soil microorganisms especially Actinobacteria might play an important role. With their multifunctional activities, they are involved in nutrient cycling, soil quality and crop productivity as well as plant health which make them not only the eco-friendly alternative for agriculture but also for humankind. Bearing this in mind, it is primordial to further explore the special link between these microorganisms and soil -plant ecosystems. Therefore, this review discusses the importance of Actinobacteria as microbial biofertilizers and highlights the future needs and challenges for using them for sustaining crop. The patents and scientific literature analysis from 2000 to 2020 show that 16 patents claiming Actinobacteria as biocontrol or biofertilizer in agriculture and 949 indexed research articles related to Actinobacteria effect on plant growth and phosphate solubilization have been published. Furthermore, Actinobacteria ability to increase growth and yield of staple crops such as wheat maize, tomato, rice, and chickpea plant have been highlighted. Much more effort and progress are expected in the industrial development of actinobacterial bioinoculants as areas such as synthetic biology and nano-biotechnology advance.
Topics: Actinobacteria; Agriculture; Bacteria; Crops, Agricultural; Ecosystem; Fertilizers; Soil; Soil Microbiology
PubMed: 35584559
DOI: 10.1016/j.micres.2022.127059 -
FEMS Microbiology Letters Dec 2020A student-centered, interactive course-based undergraduate research experience (CURE) was implemented in a microbiology course in order to provide an authentic research...
A student-centered, interactive course-based undergraduate research experience (CURE) was implemented in a microbiology course in order to provide an authentic research experience and to stimulate student interest and improve understanding of fermentation, probiotics, the human microbiome and related topics. Students were immersed in the scientific process as they used fundamental techniques to investigate the probiotic composition of a fermented milk beverage, kefir-an unknown question with no predetermined outcomes. In order to assess the benefits and effect of this learning experience on the students, pre- and post-study surveys were administered using Qualtrics. Post-study, 93% of participants agreed that fermented foods are beneficial to human health (compared to 52% pre-study), and notably, 100% of participants indicated that they plan to apply this material in both their personal and professional lives and would suggest consuming probiotics or fermented products to alleviate gastrointestinal issues. As evidenced by demographic data, this CURE is suitable for implementation at both large and small institutions with diverse student populations. Collectively, these data indicate that this collaborative, discovery-based learning experience is a powerful educational tool, encouraging students to make real-life connections between microbiology, medicine and their own health.
Topics: Adolescent; Adult; Female; Fermentation; Humans; Male; Microbiology; Microbiota; Probiotics; Research; Surveys and Questionnaires; Teaching; Universities; Young Adult
PubMed: 33232449
DOI: 10.1093/femsle/fnaa191 -
MSphere Feb 2023
Topics: Science; Virology
PubMed: 36519923
DOI: 10.1128/msphere.00607-22 -
MBio Feb 2023
Topics: Science; Virology
PubMed: 36519848
DOI: 10.1128/mbio.03339-22 -
International Journal of Molecular... Jun 2020D-enantiomers of amino acids (D-AAs) are only present in low amounts in nature, frequently at trace levels, and for this reason, their biological function was... (Review)
Review
D-enantiomers of amino acids (D-AAs) are only present in low amounts in nature, frequently at trace levels, and for this reason, their biological function was undervalued for a long time. In the past 25 years, the improvements in analytical methods, such as gas chromatography, HPLC, and capillary electrophoresis, allowed to detect D-AAs in foodstuffs and biological samples and to attribute them specific biological functions in mammals. These methods are time-consuming, expensive, and not suitable for online application; however, life science investigations and industrial applications require rapid and selective determination of D-AAs, as only biosensors can offer. In the present review, we provide a status update concerning biosensors for detecting and quantifying D-AAs and their applications for safety and quality of foods, human health, and neurological research. The review reports the main challenges in the field, such as selectivity, in order to distinguish the different D-AAs present in a solution, the simultaneous assay of both L- and D-AAs, the production of implantable devices, and surface-scanning biosensors. These innovative tools will push future research aimed at investigating the neurological role of D-AAs, a vibrant field that is growing at an accelerating pace.
Topics: Amino Acids; Animals; Biosensing Techniques; Food Microbiology; Humans
PubMed: 32605078
DOI: 10.3390/ijms21134574 -
Environmental Science & Technology Aug 2021Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative...
Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.
Topics: Environmental Microbiology; Real-Time Polymerase Chain Reaction; Reproducibility of Results
PubMed: 34286966
DOI: 10.1021/acs.est.1c01767