Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges.

This review is a part of the SI 'Genome-Scale Modeling of Microorganisms in the Real World'. The goal of GEM is the accurate prediction of the phenotype from its respective genotype under specified environmental conditions. This review focuses on the dynamic phenotype; prediction of the real-life behaviors of microorganisms, such as cell proliferation, dormancy, and mortality; balanced and unbalanced growth; steady-state and transient processes; primary and secondary metabolism; stress responses; etc.

True and Illusory Benefits of Modeling: Comment on "Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic Acid Producing . Microorganisms 2020, , 539".

Lee et al. [1] recently published a paper that is part of the special issue "Genome-Scale Modeling of Microorganisms in the Real World"[..

A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation.

Soil proteomics, the large-scale characterization of the entire protein complement in soils, provides a promising approach for deciphering the role of microbial functioning in terrestrial ecosystems. However, the extraction of soil proteins in sufficient quantities and of adequate purity remains a challenging task mainly due to the co-extraction of interfering humic substances. Up to now, the treatment of soil extracts with liquid phenol has been the "gold standard" for reducing humics, while the NoviPure cleanup kit was recently launched as a non-toxic approach.

Near-zero growth kinetics of Pseudomonas putida deduced from proteomic analysis.

Intensive microbial growth typically observed in laboratory rarely occurs in nature. Because of severe nutrient deficiency, natural populations exhibit near-zero growth (NZG). There is a long-standing controversy about sustained NZG, specifically whether there is a minimum growth rate below which cells die or whether cells enter a non-growing maintenance state.

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium.

Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1(T), ACB7(T) and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1(T) and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7(T) grew weakly on sucrose only.

Comparative proteomic analysis reveals mechanistic insights into Pseudomonas putida F1 growth on benzoate and citrate.

Pseudomonas species are capable to proliferate under diverse environmental conditions and thus have a significant bioremediation potential. To enhance our understanding of their metabolic versatility, this study explores the changes in the proteome and physiology of Pseudomonas putida F1 resulting from its growth on benzoate, a moderate toxic compound that can be catabolized, and citrate, a carbon source that is assimilated through central metabolic pathways. A series of repetitive batch cultivations were performed to ensure a complete adaptation of the bacteria to each of these contrasting carbon sources.

Bacterial genome replication at subzero temperatures in permafrost.

Microbial metabolic activity occurs at subzero temperatures in permafrost, an environment representing ∼25% of the global soil organic matter. Although much of the observed subzero microbial activity may be due to basal metabolism or macromolecular repair, there is also ample evidence for cellular growth. Unfortunately, most metabolic measurements or culture-based laboratory experiments cannot elucidate the specific microorganisms responsible for metabolic activities in native permafrost, nor, can bulk approaches determine whether different members of the microbial community modulate their responses as a function of changing subzero temperatures.

The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis.

Regulatory T cells (Tregs) that express the transcription factor Foxp3 are critical for regulating intestinal inflammation. Candidate microbe approaches have identified bacterial species and strain-specific molecules that can affect intestinal immune responses, including species that modulate Treg responses. Because neither all humans nor mice harbor the same bacterial strains, we posited that more prevalent factors exist that regulate the number and function of colonic Tregs.

Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity.

A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645(T) was isolated from human subgingival dental plaque. Bacterial cells were 4-40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles.

Draft genome sequence for Microbacterium laevaniformans strain OR221, a bacterium tolerant to metals, nitrate, and low pH.

Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals, such as uranium, nickel, cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome sequence.

Skew-laplace and cell-size distribution in microbial axenic cultures: statistical assessment and biological interpretation.

We report a skew-Laplace statistical analysis of both flow cytometry scatters and cell size from microbial strains primarily grown in batch cultures, others in chemostat cultures and bacterial aquatic populations. Cytometry scatters best fit the skew-Laplace distribution while cell size as assessed by an electronic particle analyzer exhibited a moderate fitting. Unlike the cultures, the aquatic bacterial communities clearly do not fit to a skew-Laplace distribution.

Polaromonas hydrogenivorans sp. nov., a psychrotolerant hydrogen-oxidizing bacterium from Alaskan soil.

Psychrotolerant (0-25 degrees C), chemolithotrophic Gram-negative cocci were isolated from Alaskan forest soil. The novel isolate was found to grow autotrophically on H(2) : CO(2) mixtures and to switch to heterotrophic growth on media containing organic substrates. The novel strain utilized a wide range of organic acids, some simple sugars and alcohols.

Growth kinetics of microorganisms isolated from Alaskan soil and permafrost in solid media frozen down to -35 degrees C.

We developed a procedure to culture microorganisms below freezing point on solid media (cellulose powder or plastic film) with ethanol as the sole carbon source without using artificial antifreezes. Enrichment from soil and permafrost obtained on such frozen solid media contained mainly fungi, and further purification resulted in isolation of basidiomycetous yeasts of the genera Mrakia and Leucosporidium as well as ascomycetous fungi of the genus Geomyces. Contrary to solid frozen media, the enrichment of liquid nutrient solutions at 0 degrees C or supercooled solutions stabilized by glycerol at -1 to -5 degrees C led to the isolation of bacteria representing the genera Polaromonas, Pseudomonas and Arthrobacter.

Novel facultative anaerobic acidotolerant Telmatospirillum siberiense gen. nov. sp. nov. isolated from mesotrophic fen.

Three facultative anaerobic acidotolerant Gram-negative motile spirilla strains designated 26-4b1, 26-2 and K-1 were isolated from mesotrophic Siberian fen as a component of methanogenic consortia. The isolates were found to grow chemoorganotrophically on several organic acids and glucose under anoxic and low oxygen pressure in the dark, tolerant up to 5kPa of oxygen. At low oxygen supply, faint autotrophic growth on the H(2):CO(2) mixture was also observed.

Continuous plug-flow bioreactor: experimental testing with Pseudomonas putida culture grown on benzoate.

The goals of this work were to test the feasibility of a continuous plug-flow (PF) bioreactor and to compare the growth in the PF bioreactor to that in a batch bioreactor. A culture of Pseudomonas putida was pumped through a tube made of Teflon with varying residence times. The culture was aerated by pumping of air simultaneously with liquid medium to provide air bubbles along the tubular culture.

Uncertainties and recommendations.

An assessment of the impacts of changes in climate and UV-B radiation on Arctic terrestrial ecosystems, made within the Arctic Climate Impacts Assessment (ACIA), highlighted the profound implications of projected warming in particular for future ecosystem services, biodiversity and feedbacks to climate. However, although our current understanding of ecological processes and changes driven by climate and UV-B is strong in some geographical areas and in some disciplines, it is weak in others. Even though recently the strength of our predictions has increased dramatically with increased research effort in the Arctic and the introduction of new technologies, our current understanding is still constrained by various uncertainties.

Synthesis of effects in four Arctic subregions.

An assessment of impacts on Arctic terrestrial ecosystems has emphasized geographical variability in responses of species and ecosystems to environmental change. This variability is usually associated with north-south gradients in climate, biodiversity, vegetation zones, and ecosystem structure and function. It is clear, however, that significant east-west variability in environment, ecosystem structure and function, environmental history, and recent climate variability is also important.

Effects of changes in climate on landscape and regional processes, and feedbacks to the climate system.

Biological and physical processes in the Arctic system operate at various temporal and spatial scales to impact large-scale feedbacks and interactions with the earth system. There are four main potential feedback mechanisms between the impacts of climate change on the Arctic and the global climate system: albedo, greenhouse gas emissions or uptake by ecosystems, greenhouse gas emissions from methane hydrates, and increased freshwater fluxes that could affect the thermohaline circulation. All these feedbacks are controlled to some extent by changes in ecosystem distribution and character and particularly by large-scale movement of vegetation zones.

Effects on the function of Arctic ecosystems in the short- and long-term perspectives.

Historically, the function of Arctic ecosystems in terms of cycles of nutrients and carbon has led to low levels of primary production and exchanges of energy, water and greenhouse gases have led to low local and regional cooling. Sequestration of carbon from atmospheric CO2, in extensive, cold organic soils and the high albedo from low, snow-covered vegetation have had impacts on regional climate. However, many aspects of the functioning of Arctic ecosystems are sensitive to changes in climate and its impacts on biodiversity.

Effects on the structure of Arctic ecosystems in the short- and long-term perspectives.

Species individualistic responses to warming and increased UV-B radiation are moderated by the responses of neighbors within communities, and trophic interactions within ecosystems. All of these responses lead to changes in ecosystem structure. Experimental manipulation of environmental factors expected to change at high latitudes showed that summer warming of tundra vegetation has generally led to smaller changes than fertilizer addition.

Responses to projected changes in climate and UV-B at the species level.

Environmental manipulation experiments showed that species respond individualistically to each environmental-change variable. The greatest responses of plants were generally to nutrient, particularly nitrogen, addition. Summer warming experiments showed that woody plant responses were dominant and that mosses and lichens became less abundant.

Biodiversity, distributions and adaptations of Arctic species in the context of environmental change.

The individual of a species is the basic unit which responds to climate and UV-B changes, and it responds over a wide range of time scales. The diversity of animal, plant and microbial species appears to be low in the Arctic, and decreases from the boreal forests to the polar deserts of the extreme North but primitive species are particularly abundant. This latitudinal decline is associated with an increase in super-dominant species that occupy a wide range of habitats.

Past changes in Arctic terrestrial ecosystems, climate and UV radiation.

At the last glacial maximum, vast ice sheets covered many continental areas. The beds of some shallow seas were exposed thereby connecting previously separated landmasses. Although some areas were ice-free and supported a flora and fauna, mean annual temperatures were 10-13 degrees C colder than during the Holocene.