Continuous flow method in soil microbiology

Folia Microbiologica - A continuous flow method is described as applied to the investigation of microbiological processes taking place in soil samples. The principle of the method and its technical...     

Continuous flow method in soil microbiology

The decomposition of glycine in soil was studied by the continuous flow method. Glycine solution was added continuously to soil samples of different weights, i.e. soil columns of different heights. It was found that the extent of glycine mineralization was related to the weight of the soil. Glycine was nitrified most effectively in the soil sample weighing 30 g., in which 65.8% of the added (91.6% of the retained) glycine nitrogen was oxidized to nitrites and nitrates. No steady state was observed in the rate of nitrite and nitrate formation. The rate of nitrification rose at first, in relation to the weight of the soil, but fell after reaching the maximum. The factor limiting the rate of nitrification was the adsorption of ammonium nitrogen in the soil. By using soil samples of different weights and heights it was found possible to localize the process of ammonia release and the oxidation of ammonia and nitrites in the soil column and to influence the ratio of ammonification and nitrification or of the oxidation of ammonium ions and nitrites.     

Continuous flow method in soil microbiology

С применением непрерывно-проточного метода изучался метаболизм глюкозы в почве. Было установлено, что в применявшихся образцах почвы при данных условиях опыта от двух третей до трех четвертей прибавляемой глюкозы минерализуются и превращаются в CO₂. Ни степень минерализации глюкозы, прибавляемой к почве с начала опыта, ни скорость минерализации глюкозы в постоянном состоянии не зависят ни от концентрации глюкозы, ни от навески почвы, ни от присутствия минеральных форм азота и фосфора. Однако присутствие минеральных соединений азота и фосфора влияет на скорость минерализации гиюкозы в первой стадии процесса. Непрерывная подача глюкозы выразительно влияет на состав микробного сообщества почвы. При непрерывном протоке раствора одной только глюкозы число бактерий меняется лишь незначительно, но, с другой стороны, существенно повышается количество азотобактера. После предварительного насыщения почвы ионами фосфата аммония, или же при условии одновременной подачи минеральных питательных веществ и раствора глюкозы, наблюдается значительное повышение числа бактерий, тогда как азотобактер не размножается.     

Visualization, modelling and prediction in soil microbiology

The introduction of new approaches for characterizing microbial communities and imaging soil environments has benefited soil microbiology by providing new ways of detecting and locating microorganisms. Consequently, soil microbiology is poised to progress from simply cataloguing microbial complexity to becoming a systems science. A systems approach will enable the structures of microbial communities to be characterized and will inform how microbial communities affect soil function. Systems approaches require accurate analyses of the spatio-temporal properties of the different microenvironments present in soil. In this Review we advocate the need for the convergence of the experimental and theoretical approaches that are used to characterize and model the development of microbial communities in soils.     

Standardisation of methods in soil microbiology: progress and challenges

A plethora of methods have been developed over the few last decades to enable a better understanding of the ecology of soil microbial communities and their roles in soil functioning. However, there is generally considerable variation (both subtle and more extensive) in the actual realisation of these methods, and limited efforts have been devoted to their standardisation, despite this being crucial to underpin data comparison and integration. Ensuring comparable data across studies through standardisation is arguably best-practice, as well as necessary to effectively meet the objectives of various schemas, which require assessment of the consequences of the global change and intensification of human activities on the functioning of the soil ecosystem and its biological diversity. This article presents an overview of the existing and forthcoming ISO standards in soil microbiology and highlights possible future research efforts to be undertaken for developing new standards. We also discuss some practical and theoretical bottlenecks and hurdles that have limited standardisation in soil microbiology up to now.     

Continuous flow method for extraction and bioluminescence assay of ATP in baker's yeast

Summary The intracellular ATP of baker's yeast (Saccharomyces cerevisiae) was measured using the bioluminescent firefly luciferase assay. Benzalkonium chloride and trichloro-acetic acid served in the experiments as extracting agents and optimal conditions for the extraction and assay of the intracellular ATP are reported. Using the results obtained from manually performed experiments two continuous flow systems were designed for the measurement of ATP in yeast cells during cell growth. Good correlation between the amount of cellular ATP and cell growth was found during the exponential growth phase.     

Current and future applications of flow cytometry in aquatic microbiology

Flow cytometry has become a valuable tool in aquatic and environmental microbiology that combines direct and rapid assays to determine numbers, cell size distribution and additional biochemical and physiological characteristics of individual cells, revealing the heterogeneity present in a population or community. Flow cytometry exhibits three unique technical properties of high potential to study the microbiology of aquatic systems: (i) its tremendous velocity to obtain and process data; (ii) the sorting capacity of some cytometers, which allows the transfer of specific populations or even single cells to a determined location, thus allowing further physical, chemical, biological or molecular analysis; and (iii) high-speed multiparametric data acquisition and multivariate data analysis. Flow cytometry is now commonly used in aquatic microbiology, although the application of cell sorting to microbial ecology and quantification of heterotrophic nanoflagellates and viruses is still under development. The recent development of laser scanning cytometry also provides a new way to further analyse sorted cells or cells recovered on filter membranes or slides. The main infrastructure limitations of flow cytometry are: cost, need for skilled and well-trained operators, and adequate refrigeration systems for high-powered lasers and cell sorters. The selection and obtaining of the optimal fluorochromes, control microorganisms and validations for a specific application may sometimes be difficult to accomplish.