QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.

Innovative test method for the estimation of the foaming tendency of substrates for biogas plants

Excessive foaming in anaerobic digestion occurs at many biogas plants and can cause problems including plugged gas pipes. Unfortunately, the majority of biogas plant operators are unable to identify the causes of foaming in their biogas reactor. The occurrence of foaming is often related to the chemical composition of substrates fed to the reactor. The consistency of the digestate itself is also a crucial part of the foam formation process. Thus, no specific recommendations concerning substrates can be given in order to prevent foam formation in biogas plants. The safest way to avoid foaming is to test the foaming tendency of substrates on-site. A possible solution is offered by an innovative foaming test. With the help of this tool, biogas plant operators can evaluate the foaming disposition of new substrates prior to use in order to adjust the composition of substrate mixes.

Microbial methods for assessing contaminant effects in sediments

Contaminated sediments influence drastically the long-term toxicological and ecological properties of aquatic ecosystems. During the past three decades, scientific knowledge about sediment-water exchange processes and the deposition and distribution of pollutants in water and sediment phases has been supplemented by extensive research on the effects of sediment-associated pollutants on aquatic organisms. Basic research in microbiology, ecology, and toxicology has uncovered the crucial role of sediment microorganisms for the biodegradation of organic matter and for the cycling of nutrients, as well as the susceptibility of these processes to toxic pollution events. Microorganisms have been extensively applied in aquatic toxicology, and various microbial toxicity tests are today available that successfully couple microbial toxicity endpoints to the specificity of the sediment matrix. Sediment-associated toxicants can be brought in contact with test bacteria using sediment pore waters, elutriates, extracts, or whole-sediment material. Toxicity indication principles for microorganisms are versatile and comprise growth and biomass determinations, respiration or oxygen uptake, bacterial luminescence, the activity of a variety of enzymes, and a compendium of genotoxicity assays. The border between toxicological and ecological contaminant effect evaluations in sediments is flexible, and long-term ecological predictions should also include an assessment of pollutant degradation capacities and of key reactions in element cycling. Evaluating microbial community structure and function in environmental systems makes use of modern molecular techniques and bioindicators that could trigger a new quality in the assessment of contaminated sediments in terms of indication of subtoxic effects and early-warning requirements.

Phosphine by bio-corrosion of phosphide-rich iron

Phosphine is a toxic agent and part of the phosphorus cycle. A hitherto unknown formation mechanism for phosphine in the environment was investigated. When iron samples containing iron phosphide were incubated in corrosive aquatic media affected by microbial metabolites, phosphine was liberated and measured by gas chromatography. Iron liberates phosphine especially in anoxic aquatic media under the influence of sulfide and an acidic pH. A phosphine-forming mechanism is suggested: Phosphate, an impurity of iron containing minerals, is reduced abioticly to iron phosphide. When iron is exposed to the environment (e.g. as outdoor equipment, scrap, contamination in iron milled food or as iron meteorites) and corrodes, the iron phosphide present in the iron is suspended in the medium and can hydrolyze to phosphine. Phosphine can accumulate to measurable quantities in anoxic microbial media, accelerating corrosion and preserving the phosphine formed from oxidation.

Balancing phosphine in manure fermentation

The evolution of phosphine gas during the anaerobic batch fermentation of fresh swine manure was detected and correlated to the production of methane and hydrogen sulphide. A close temporal relationship between phosphine liberation and methane formation was found. However, the gaseous phosphine released from manure during fermentation only represents a tiny fraction of the overall phosphine balance. The majority of phosphine is captured in solid manure constituents. This matrix-bound phosphine is eliminated by more than 50% during anaerobic batch-fermentation. Seasonally determined phosphine concentrations in biogas and manure from two large-scale manure treatment plants also revealed net losses of phosphine in fermentation. Consequently, manure has to be considered more as a sink of phosphine rather than a phosphine-generating medium. Furthermore, a close relationship between phosphine in the feed of swine and manure of these swine was observed, implying that phosphine residues in the feed (possibly as a result of grain fumigation) represent an important source of phosphine in manure technologies that is relevant before the faecals of swine enter manure treatment plants.

Microbial phenol degradation of organic compounds in natural systems: Temperature-inhibition relationships

The combined influence of high phenol concentrations and low temperatures on aerobic and anaerobic phenol degradation kinetics was investigated in microbial enrichment cultures to evaluate temperature-inhibition relationships with respect to the ambient conditions in polluted habitats. The inhibition of microbial phenol degradation by excess substrate was found to be temperature-dependent. Substrate inhibition was intensified when temperatures were lower. This results in an elevated temperature sensitivity of phenol degradation at inhibitory substrate concentrations. The synergistic amplification of substrate inhibition at low temperatures may help to explain the limited self-purification potential of contaminated habitats such as soils, sediments and groundwater aquifers where high pollutant concentrations and low temperatures prevail.