Peter Lasch
Dec 1, 2020; 19:2125-2138
Technological Innovation and Resources

Over the past decade, modern methods of MS (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. Although MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem MS (LC-MS²) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be laborious and time-consuming, especially if the experimental LC-MS² data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC–MS measurements. Peptide masses are then extracted from MS¹ data and systematically tested against an in silico library of all possible peptide mass data compiled in-house. The library has been computed from the UniProt Knowledgebase covering Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from correlation coefficients between experimental and strain-specific in silico peptide mass profiles and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient – less than 2 mins per sample - and has been successfully tested by a test set of 39 LC-MS¹ peak lists obtained from 19 different microbial pathogens. The proposed method is rapid, simple and automatable and we foresee wide application potential for future microbiological applications.

Almost a quarter of the world’s non-polar land surface experiences light pollution, and there is concern that this adversely affects illuminated ecosystems. Currently there is a global move from yellow sodium lighting to white LED lighting, which emits different wavelengths of light. A recent study found that LED artificial light at night (ALAN) reduced the biomass of periphyton by 62% in a freshwater drainage ditch in Westhavelland Nature Park, Brandenburg, Germany.

Recent research has found that silver nanoparticles in sewage sludge, which is used on agricultural land as a fertiliser, can be toxic to soil microorganisms. The researchers calculated that a maximum of 30mg of silver nanoparticles per kilogram of sludge can be applied to land before harm occurs, based on typical application rates in Germany of five tons per hectare of farmland every three years.

Nanotechnology is a key enabling technology predicted to have many societal benefits, but there are also concerns about its risks to the environment. This study reviewed the effects of nanoparticles on soil microorganisms, showing that toxicity depends on the type of particle. The researchers make recommendations for improving environmental risk assessment, including performing experiments in soil and over longer time periods.

Methods of separating renewable materials, such as lipids, from microorganisms, such as oleaginous yeasts, may include conditioning cell walls of the microorganisms to form, open or enlarge pores, and removing at least a portion of the renewable material through the pores. These methods may result in delipidated microorganisms with cell walls that are substantially intact and with mesopores. These delipidated microorganisms may be used to produce biofuels.

A method and processes to solubilize and transform phosphorus contents of rock phosphate (RP) into bio-organo-phosphate (BOP) fertilizer have been developed and integrated. The methods include collecting and sorting of organic wastes; blending with RP; subjecting the blend to biocomposting; collection, isolation, selection and growth optimization of consortia of efficient phosphorus solubilizing microorganisms (PSM) and novel plant growth regulating microorganisms (PGRM); where in PSM produce organic acids and other organic compounds using compost substrate at mesophillic stage, whereas the organic acids released during composting also act in synergism of PSM, thus forming a carbon rich acidic culture resulting in the solubilization of rock phosphate.

The present disclosure is directed toward a composition and method of treating and preventing infection of pathogenic microorganisms and endopyhtic microorganisms in a plant through the use of phosphite compositions.

A composition of matter comprising: a combination of a phytate and a plurality of microorganisms comprising a Trichoderma virens fungus, a Bacillus amyloliquefaciens bacterium, and one or a plurality of mycorrhizae fungi that is placed in the vicinity of a plant root in a manner that allows the microorganisms in the composition of matter to colonize said plant root; and a method for increasing plant yield comprising: placing a combination of a phytate and a plurality of microorganisms comprising a Trichoderma virens fungus, a Bacillus amyloliquefaciens bacterium, and one or a plurality of mycorrhizae fungi in the vicinity of a plant root in a manner that allows the microorganisms in the composition of matter to colonize said plant root.

The invention includes novel devices and methods for inhibiting or preventing colonization of fluid flow networks by bacteria that have upstream surface motility. In certain aspects, the devices and methods of the invention prevent or minimize undesirable bacterial colonization of medical devices and/or treat or prevent bacterial infections.

(University of California - Irvine) Cyanobacteria living in rocks in Chile's Atacama Desert extract water from the minerals they colonize and, in doing so, change the phase of the material from gypsum to anhydrite. Researchers at the University of California, Irvine and Johns Hopkins University gained verification of this process through experiments, and the work points to possible strategies for humans to stay hydrated in harsh environments.

Quentin Perraud
Apr 1, 2020; 19:589-607
Research

Bacteria secrete siderophores to access iron, a key nutrient poorly bioavailable and the source of strong competition between microorganisms in most biotopes. Many bacteria also use siderophores produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa, an opportunistic pathogen, produces two siderophores, pyoverdine and pyochelin, and is also able to use a panel of exosiderophores. We first investigated expression of the various iron-uptake pathways of P. aeruginosa in three different growth media using proteomic and RT-qPCR approaches and observed three different phenotypic patterns, indicating complex phenotypic plasticity in the expression of the various iron-uptake pathways. We then investigated the phenotypic plasticity of iron-uptake pathway expression in the presence of various exosiderophores (present individually or as a mixture) under planktonic growth conditions, as well as in an epithelial cell infection assay. In all growth conditions tested, catechol-type exosiderophores were clearly more efficient in inducing the expression of their corresponding transporters than the others, showing that bacteria opt for the use of catechol siderophores to access iron when they are present in the environment. In parallel, expression of the proteins of the pyochelin pathway was significantly repressed under most conditions tested, as well as that of proteins of the pyoverdine pathway, but to a lesser extent. There was no effect on the expression of the heme and ferrous uptake pathways. Overall, these data provide precise insights on how P. aeruginosa adjusts the expression of its various iron-uptake pathways (phenotypic plasticity and switching) to match varying levels of iron and competition.

Since the discovery of Asgard archaea in 2015, evidence has mounted that these peculiar single-celled organisms could be the source of all complex life – including us

npj Microgravity, Published online: 08 April 2020; doi:10.1038/s41526-020-0101-4

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