Abstract
Viability and metabolic assays are commonly used as proxies to assess the overall metabolism of microorganisms. The variety of these assays combined with little information provided by some assay kits or online protocols often leads to mistakes or poor interpretation of the results. In addition, the use of some of these assays is restricted to simple systems (mostly pure cultures), and care must be taken in their application to environmental samples. In this review, the necessary data are compiled to understand the reactions or measurements performed in many of the assays commonly used in various aspects of microbiology. Also, their relationships to each other, as metabolism links many of these assays, resulting in correlations between measured values and parameters, are discussed. Finally, the limitations of these assays are discussed.
Highlights
Metabolism can be defined as the sum of all reactions in a living organism aimed at maintenance, development, and reproduction
Optical and electrochemical sensors have been preferred in many cases (Kemker, 2014; Bondyale-Juez et al, 2017), especially as some systems have been introduced as 96-well plates (Guarino et al, 2004; Dike et al, 2005)
In microbiology and the study of microbial mats, the modification of Pachmayr in 1960 (Pachmayr, 1960) using dimethyl-paraphenylene diamine sulfate (DPDS) is one of the most commonly used (Trüper and Schlegel, 1964; Gallagher et al, 2012). Such assay is more work-intensive compared to ion-selective electrode (ISE) readings, the fact that the sample can be fixed and processed at a later time point makes it useful in practice, as large batches of samples can be processed at the same time
Summary
Metabolism can be defined as the sum of all reactions in a living organism aimed at maintenance, development, and reproduction (division for microbes). For many purposes ranging from environmental sciences to medical microbiology, microbial metabolism is usually assessed by using proxies that focus on different aspects of the process. Among these so-called metabolic assays, some are nonspecific proxies focusing on various types of metabolism [such as tetrazolium reduction, fluorescein diacetate (FDA) hydrolysis, or calorimetry], while some assays are more focused on and limited to specific types of metabolism. The consumption of carbon sources and production of by-products (CO2, fermentation products, and others) are valuable tools As these assays all focus on metabolism, there are correlations between some of them, making comparison or validation possible
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