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Prod 2020-50 EA BIOmE INRA; International audience; The activity of microorganisms in soil is important for a robust functioning of soil and related ecosystem services. Hence, there is a necessity to identify the composition, diversity, and function of the soil microbiome in order to determine its natural properties, functioning, and operating range as well as to assess ecotoxicological effects due to anthropogenic activities. Numerous microbiological methods currently exist in the literature and new, more advanced methods continue to be developed; however, only a limited number of these methods are standardised. Consequently, there is a need to identify the most promising non-standardised methods for assessing soil quality and to transform them into standards. In agreement with the “Ecosystem Service Approach”, new methods should focus more on soil microbial functions, including nutrient cycling and greenhouse gas emission, pest control and plant growth promotion, carbon cycling and sequestration, as well as soil structure development and filter function. The few existing standardised methods available that focus on the function of the soil microbiome mostly include measurements, like basal respiration, enzyme activities, and biodegradation of organic matter, under well-defined conditions in the lab. This paper sets out to summarise and expand on recent discussions within the International Organization for Standardization (ISO), Soil Quality – Biological Characterization sub-committee (ISO TC 190/SC 4), where a need was identified to develop scientifically sound methods which would best fulfil the practical needs of future users for assessing soil quality, going beyond the existing test systems. Of particular note is the current evolution of molecular methods in microbial ecology that use quantitative real-time PCR (qPCR) to produce a large number of new functional endpoints which are more sensitive as compared to “classical” methods. Quantitative PCR assesses the abundance of microbes that catalyse major transformation steps in nitrogen and phosphorus cycling, greenhouse gas emissions, chemical transformations including pesticide degradation, and plant growth promotion pathways based on the assessment of marker gene sequences that drive the related processes. In the assessment of soil quality methods, it was found that most methods focus on bacteria and related endpoints. Techniques to describe fungal communities as well as their functional traits are far less represented. As such, techniques to analyse fungal enzyme activities are proposed. Additionally, methods for the determination of microbial growth rates and efficiencies, including the use of glomalin as a biochemical marker for soil aggregation, are discussed. Furthermore, field methods 18 S. Thiele-Bruhn et al.: Identification of new microbial functional standards for soil quality assessment indicative of carbon turnover, including the litter bag test and a modification to the tea bag test, are presented. However, it is obvious that with increasing developments in high throughput sequencing technologies and big data analyses, including metagenomics analysis, it will be possible to implement these technologies into the standardisation process for assessing the functions of the soil microbiome. Overall, it is suggested that endpoints should represent a potential function of soil microorganisms rather than actual activity levels, as the latter can largely be dependent on short-term variable soil properties such as pedoclimatic conditions, nutrient availability, and anthropogenic soil cultivation activities.

Two methods were used to compare the biodegradation of six polychlorinated biphenyl (PCB) congeners by 12 white rot fungi. Four fungi were found to be more active than Phanerochaete chrysosporium ATCC 24725. Biodegradation of the following congeners was monitored by gas chromatography: 2,3-dichlorobiphenyl, 4,4′-dichlorobiphenyl, 2,4′,5-trichlorobiphenyl (2,4′,5-TCB), 2,2′,4,4′-tetrachlorobiphenyl, 2,2′,5,5′-tetrachlorobiphenyl, and 2,2′,4,4′,5,5′-hexachlorobiphenyl. The congener tested for mineralization was 2,4′,5-[U- 14 C]TCB. Culture supernatants were also assayed for lignin peroxidase and manganese peroxidase activities. Of the fungi tested, two strains of Bjerkandera adusta (UAMH 8258 and UAMH 7308), one strain of Pleurotus ostreatus (UAMH 7964), and Trametes versicolor UAMH 8272 gave the highest biodegradation and mineralization. P. chrysosporium ATCC 24725, a strain frequently used in studies of PCB degradation, gave the lowest mineralization and biodegradation activities of the 12 fungi reported here. Low but detectable levels of lignin peroxidase and manganese peroxidase activity were present in culture supernatants, but no correlation was observed among any combination of PCB congener biodegradation, mineralization, and lignin peroxidase or manganese peroxidase activity. With the exception of P. chrysosporium , congener loss ranged from 40 to 96%; however, these values varied due to nonspecific congener binding to fungal biomass and glassware. Mineralization was much lower, ≤11%, because it measures a complete oxidation of at least part of the congener molecule but the results were more consistent and therefore more reliable in assessment of PCB biodegradation.

This past century has been a scientific revolution in the understanding of the cell as the basic unit of life. However an immense paucity of knowledge exists on microbial growth, survival, function and structure in space. However, there are significant constraints placed on conducting biological research in space such as time, available stowage space, trained personnel, power requirements, weight and the possibility of accidental microbiological contamination. One Earth-based approach is to use a modification of a clinostat known as a HARV (high-aspect-ratio-vessel; Synthecon Inc., Houston, Texas, USA) to conduct this research. In this note we describe the use of the HARV to examine the effects of randomized microgravity (RMG) on bacterial growth and membrane polarization.