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Environmental Microbiology Oct 2019The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of... (Review)
Review
The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy ( ) define the direction and energy yield of a reaction; they do not. is one part of the actual Gibbs energy of a reaction (ΔG ), with a second part accounting for deviations from the standard composition. It is also frequently assumed that applies only to 25 °C and 1 bar; it does not. is a function of temperature and pressure. Here, we review how to determine ΔG as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔG and highlighting the large effects when multi-valent ions are part of the reaction. We also calculate ΔG for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.
Topics: Bacteria; Ecosystem; Energy Metabolism; Environmental Microbiology; Geologic Sediments; Water Microbiology
PubMed: 31403238
DOI: 10.1111/1462-2920.14778 -
The New Phytologist Oct 2022
Topics: Fungi; Mycorrhizae; Plant Roots; Soil; Soil Microbiology
PubMed: 36161302
DOI: 10.1111/nph.18388 -
Brazilian Journal of Biology = Revista... 2022The essence of food security centers on ensuring availability and accessibility of foods in adequate amounts and quality for all populations at all times for an active... (Review)
Review
The essence of food security centers on ensuring availability and accessibility of foods in adequate amounts and quality for all populations at all times for an active and healthy life. Microorganisms are tiny bioreactors, which represent sustainable resources and promising approaches to bridging the gap between food production and consumption globally via various biotechnological applications. This review focuses on plant-growth promoting bacteria (PGPB) which exert their potential impacts on increasing soil fertility, plant growth, and productivity through a variety of processes, including direct, indirect, and synergistic mechanisms. PGPB plays a substantial role in accelerating nutrients' availability such as (N, P), producing phytohormones such as gibberellins, IAA, and bioactive compounds against biotic and abiotic stressors. Recent advances in PGPB will be addressed as a sustainable approach to satisfy global food demand.
Topics: Plant Development; Bacteria; Soil; Soil Microbiology; Food Security
PubMed: 36515299
DOI: 10.1590/1519-6984.267257 -
Current Opinion in Plant Biology Aug 2021Plant immunity is modulated by several abiotic factors, and microbiome has emerged as a major biotic driver of plant resistance. Recently, a few studies showed that... (Review)
Review
Plant immunity is modulated by several abiotic factors, and microbiome has emerged as a major biotic driver of plant resistance. Recently, a few studies showed that plants also modify resistance to pests and pathogens in their neighborhood. Several types of neighborhood could be identified depending on the biological processes at play: intraspecific and interspecific competition, kin and stranger recognition, plant-soil feedbacks, and danger signaling. This review highlights that molecules exchanged aboveground and belowground between plants can modulate plant immunity, either constitutively or after damage or attack. An intriguing relationship between allelopathy and immunity has been evidenced and should merit further investigation. Interestingly, most reported cases of modulation of immunity by the neighbors are positive, opening new perspectives for the understanding of natural plant communities as well as for the design of more diverse cultivated systems.
Topics: Plant Immunity; Plants; Soil; Soil Microbiology
PubMed: 33965754
DOI: 10.1016/j.pbi.2021.102045 -
Trends in Plant Science Oct 2020It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further... (Review)
Review
It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further involves a hierarchy of constraints with varying strengths across spatial and temporal scales. However, our knowledge of rhizosphere microbiomes is largely based on single-location and time-point studies. Consequently, it remains difficult to predict patterns at large landscape scales, and we lack a clear understanding of how the rhizosphere microbiome forms and is maintained by drivers beyond the influence of the plant. By synthesizing recent literature and collating data on rhizosphere microbiomes, we point out the opportunities and challenges offered by advances in molecular biology, bioinformatics, and data availability. Specifically, we highlight the use of exact sequence variants, coupled with existing and newly generated data to decipher the rules of rhizosphere community assembly across large spatial and taxonomic scales.
Topics: Microbiota; Plant Roots; Plants; Rhizosphere; Soil Microbiology
PubMed: 32467065
DOI: 10.1016/j.tplants.2020.04.015 -
FEMS Microbiology Reviews Nov 2020Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so... (Review)
Review
Why do evolutionarily distinct microorganisms display similar physiological behaviours? Why are transitions from high-ATP yield to low(er)-ATP yield metabolisms so widespread across species? Why is fast growth generally accompanied with low stress tolerance? Do these regularities occur because most microbial species are subject to the same selective pressures and physicochemical constraints? If so, a broadly-applicable theory might be developed that predicts common microbiological behaviours. Microbial systems biologists have been working out the contours of this theory for the last two decades, guided by experimental data. At its foundations lie basic principles from evolutionary biology, enzyme biochemistry, metabolism, cell composition and steady-state growth. The theory makes predictions about fitness costs and benefits of protein expression, physicochemical constraints on cell growth and characteristics of optimal metabolisms that maximise growth rate. Comparisons of the theory with experimental data indicates that microorganisms often aim for maximisation of growth rate, also in the presence of stresses; they often express optimal metabolisms and metabolic proteins at optimal concentrations. This review explains the current status of the theory for microbiologists; its roots, predictions, experimental evidence and future directions.
Topics: Bacteria; Bacterial Physiological Phenomena; Microbiology; Systems Biology
PubMed: 33099619
DOI: 10.1093/femsre/fuaa034 -
Biomolecules Apr 2023is a widespread Gram-negative bacterium occurring in water reservoirs and soils [...].
is a widespread Gram-negative bacterium occurring in water reservoirs and soils [...].
Topics: Legionella; Water Microbiology; Gram-Negative Bacteria; Water
PubMed: 37238644
DOI: 10.3390/biom13050775 -
Clinical Microbiology and Infection :... Nov 2021There is wide variation in the availability and training of specialists in the diagnosis and management of infections across Europe. (Review)
Review
BACKGROUND
There is wide variation in the availability and training of specialists in the diagnosis and management of infections across Europe.
OBJECTIVES
To describe and reflect on the current objectives, structure and content of European curricula and examinations for the training and assessment of medical specialists in Clinical (Medical) Microbiology (CM/MM) and Infectious Diseases (ID).
SOURCES
Narrative review of developments over the past two decades and related policy documents and scientific literature.
CONTENT
Responsibility for curricula and examinations lies with the European Union of Medical Specialists (UEMS). The ID Section of UEMS was inaugurated in 1997 and the MM Section separated from Laboratory Medicine in 2008. The sections collaborate closely with each other and the European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Updated European Training Requirements (ETR) were approved for MM in 2017 and ID in 2018. These comprehensive curricula outline the framework for delivery of specialist training and quality control for trainers and training programmes, emphasizing the need for documented, regular formative reviews of progress of trainees. Competencies to be achieved include both specialty-related and generic knowledge, skills and professional behaviours. The indicative length of training is typically 5 years; a year of clinical training is mandated for CM/MM trainees and 6 months of microbiology laboratory training for ID trainees. Each Section is developing examinations using multiple choice questions to test the knowledge base defined in their ETR, to be delivered in 2022 following pilot examinations in 2021.
IMPLICATIONS
The revised ETRs and European examinations for medical specialists in CM/MM and ID provide benchmarks for national authorities to adapt or adopt locally. Through harmonization of postgraduate training and assessment, they support the promotion and recognition of high standards of clinical practice and hence improved care for patients throughout Europe, and improved mobility of trainees and specialists.
Topics: Curriculum; Europe; European Union; Humans; Infectious Disease Medicine; Microbiology; Specialization
PubMed: 34260952
DOI: 10.1016/j.cmi.2021.07.009 -
Genome Biology Apr 2021Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have... (Review)
Review
Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology.
Topics: Bacteria; DNA Transposable Elements; Gene Expression Regulation; Genetic Association Studies; Genetic Fitness; Genetic Variation; Genome-Wide Association Study; Genomics; Metagenome; Metagenomics; Microbiological Techniques; Microbiology; Mutagenesis, Insertional
PubMed: 33926534
DOI: 10.1186/s13059-021-02344-9 -
Scientific Reports Jan 2023Arbuscular mycorrhizal fungal diversity can be altered by intercropping plant species, as well as N fertilizer applications. This study examined the effects of oat-pea...
Arbuscular mycorrhizal fungal diversity can be altered by intercropping plant species, as well as N fertilizer applications. This study examined the effects of oat-pea intercropping and N fertilizer addition on the richness and diversity of mycorrhizal species, as well as identified the most common arbuscular mycorrhizal fungi (AMF) genera recruited for oats and peas in two growing seasons (2019 and 2020). The AMF diversity was higher in an intercropped system compared to their respective monocropping system. Under drier conditions in 2019, arbuscular mycorrhizal richness decreased with N fertilizer addition in sole peas and increased with N fertilizer addition in sole oats, but no significant change in richness was observed in oat-pea intercropping. During the wetter growing season 2020, arbuscular mycorrhizal diversity increased when oat and pea were intercropped, compared to either sole oat or sole pea. Diversispora in sole pea was a significant indicator differentiating the root associated AMF community from sole oat. Claroideoglomus richness increased in peas in 2020, thus this genus could be moisture dependent. Paraglomus richness in oat-pea intercropping was similar to sole oat in 2019, and similar to sole pea in 2020. This can suggest that Paraglomus is an indicator of plant stress under intercropping, as based on the premise that stressed plants release more exudates, and the subsequent mycorrhizal associations favor these plants with higher exudation. Future investigations can further reveal the functions and benefits of these mycorrhizal genera in annual monocrop and intercropping systems.
Topics: Mycorrhizae; Avena; Pisum sativum; Fertilizers; Glomeromycota; Edible Grain; Plant Roots; Soil Microbiology; Fungi; Soil
PubMed: 36624112
DOI: 10.1038/s41598-022-22743-7