To evaluate bacterial cellular polyamine distributions as a chemotaxonomic marker for classification and as a growth factor for extremophilic environments, acid-extracted polyamines from new available members including various extremophiles belonging to the emended phylum Proteobacteria including the classes, Alphaproteobacteria (164 strains), Betaproteobacteria (35), Hydrogenophilalia (3), Gammaproteobacteria (113), Acidithiobacillia (11) and Zetaproteobacteria (2), and the newly validated phyla Epsilonbacteraeota (22), Bdellovibrionota (2) and Myxococcota (1) separated from the former phylum Proteobacteria, were analyzed by HPLC and HPGC-MS. Distribution of homospermidine, spermidine and aminopropylcadaverine were found within Alphaproteobacteria. 2-Hydroxyputrescine and 2-hydroxyspermidine were found within Betaproteobacteria and Hydrogenophilalia. Occurrence of 1,3-diaminopropane and norspermidine was specific to certain members of Gammaproteobacteria. Only spermidine was detected as a major polyamine in Acidithiobacillia and Zetaproteobacteria. Spermidine was a major polyamine in Epsilonbacteraeota. Spermidine-dominant or homospermidine-dominant species were found within Bdellovibrionota and Myxococcota. Thermophilic species have a high level of spermine in the four phyla. No clear polyamine profile patterns were observed in acidophiles, alkaliphiles, psychrophiles and halophiles of the four phyla.
Recently, in vitro synthetic biology has been actively engaged in the reconstitution of artificial systems implemented with life-like characteristics to understand the principle and origins of life. One of the most important characteristics of life is self-reproducibility, which is originated from the self-regeneration ability of the gene replication and expression system (i.e., central dogma). In this review, we summarize recent progress in in vitro reconstitution of biological functions that constitute central dogma, DNA replication, transcription, and translation.
The heart creates positive and negative pressure in a regular rhythm to pump blood. The cardiac chambers seen in vertebrates are an advanced pump design. Many species, such as the hagfish, still have accessory pumps, but they are considered vestigial. Additionally, the processes by which the circulatory system develops in vertebrates, including heart development, are largely unknown. In this study, we examined the heart of hagfish (Eptatretus burgeri) using histological analysis. In E. burgeri, three types of hearts were observed: branchial, cardinal, and portal. Photomicrographs showed that there are many empty spaces in all three types. These hearts pump blood in and out of the sponge to absorb and discharge water. The cardinal heart near the brain in E. burgeri may be primitive because its cell structure is similar to that of skeletal muscle.
Cellular polyamine distribution catalogues in the domain Bacteria have provided valuable information for their chemotaxonomic classifications and for polyamine profiles essential for extremophilic growth environments. Acid-extracted polyamines from 339 additional bacterial strains belonging to the eight phyla Actinobacteria (25 strains), Aquificae (21 strains), Bacteroidetes (107 strains), Cyanobacteria (3 strains), Firmicutes (132 strains), Desulfobacterota (38 strains), Tenericutes (3 strains) and Thermotogae (10 strains), including various extremophiles, were newly analyzed by HPLC and HPGC. Cellular concentrations of diaminopropane, putrescine, cadaverine, diaminohexane, norspermidine, spermidine, homospermidine, norspermine, spermine, thermospermine, aminopropylhomospermidine, canavalmine, homospermine, caldopentamine, homocaldopentamine, thermopentamine, caldohexamine, homocaldohexamine, thermohexamine, homothermohexamine, N4 -aminopropylnorspermidine, N4 -aminopropylspermidine, N4 -aminopropylspermine, N4 -bis(aminopropyl)norspermidine, N4 -bis(aminopropyl)spermidine, agamtine, and 2-phenylethylamine were analyzed. Occurrence of covalently linked polyamines in 16 new members of the class Negativicutes of the phylum Firmicutes was added in this paper. By also referring to our previous polyamine data of representative species in the taxa: genus, family, order and class, we presented here our final polyamine distribution catalogues of the eight major bacterial phyla.
Cellular polyamines acid-extracted from newly available 31 strains of the class Halobacteria, one strain of the class Methanobacteria, one strain of the class Methanocococi, five strains of the class Methanomicrobia, one strain of the class Thermoplasmata and three strains of the class Thermococci of the phylum Euryarchaeota, and two strains of the class Thermoprotei of the phylum Crenarchaeota, and one strain of the class Nitrososphaeria and one strain of the class Conexivisphaeria of the phylum Thaumarchaeota, were additionally analyzed by HPLC and HPGC-MS. The anaerobic sulfur-respirating extremely- halophilic archaea Halanaeroarchaeum and Natrarchaeobaculum were poor in agmatine, spermidine, and spermine. Extremely-thermophilic methanogenic Methanofervidicoccus abyssi contained spermidine, spermine, and a quaternary branched penta-amine, N4 -bis(aminopropyl)spermidine. In thaumarchaeotes, mesophilic ammonia-oxidizing Nitrosopumilus zosterae contained putrescine and homospermidine, whereas thermoacidophilic, sulfur- and iron-reducing Conexivisphaera calida contained putrescine, spermidine and spermine. Two alkanolpolyamines, N-(2-hydroxyethyl)-1,3-diaminopropane (N-(3-aminopropyl)aminoethanol) and N-(3-hydroxypropyl)-1,3-diaminopropane (N-(3-aminopropyl)aminopropanol) were detected in thermoacidophilic Sulfuracidifex metallicus belonging to the class Thermoprotei. New polyamine data were combined into our final archaeal polyamine distribution catalogue for a chemotaxonomy in the domain Archaea.
Rhodopsins are photoreceptive membrane proteins using retinal chromophore. Two large families of rhodopsins, animal and microbial rhodopsins, were known so far, and they are used by diverse animals and microorganisms, respectively. In contrast, Asgard archaea are living prokaryotes which is being considered to be closest to the last common ancestor between prokaryotes and eukaryotes, and they were not thought to use light for their survival. However, we have recently discovered many rhodopsins in their metagenome-assembled genomes. In particular, one of them, schizorhodopsin, is revealed to be a new rhodopsin family which functions as a light-driven inward proton pump. In this review, we will introduce the history of rhodopsins and our studies on the rhodopsins of Asgard archaea.
Cellular aliphatic polyamines and alkanolpolyamines, acid-extracted from new members belonging to the phylum Deinococcus-Thermus, were analyzed by HPLC and HPGC. In the order Deinococcales whose members are known as mesophilic, neutrophilic and radio-resistant, spermidine was the major polyamine and putrescine and agmatine were sporadically distributed in the 29 new additionally analyzed Deinococcus species. When a strain of Deinococcus misasensis was grown at 25, 30 and 40°C and under the dark or light, no major change of its polyamine profile was observed. In the thermophilic order Thermales, caldopentamine, homocaldopentamine and thermopentamine, in addition to usual diamines, triamines and tetra-amines, were detected in Thermus caldifontis grown at 70°C. Alkaliphilic T. sediminis grown at 70°C contained pyropentamine, homopyropentamine and caldohexamine in addition to the three penta-amines. T. tenuipuniceus grown at 60°C contained a quaternary branched penta-amine but not the three penta-amines. Penta-amines were not detected in T. caldimili grown at 60°C, or five newly analyzed species of Calidithermus and Meiothermus, grown at 45-60°C. Three alkanolpolyamines, N-(3-aminopropyl)aminopropanol, N-(4-aminobutyl)aminoethanol and N-(4-aminobutyl)aminopropanol were sporadically detected as a minor component in the three genera of Thermales.
Cultivation of uncultured microorganisms is a critical step in uncovering their phenotypic features, such as cell structure and metabolic function.However, due to difficulties in cultivation, there may be more than 80 candidate phyla in prokaryotes, significantly outnumbering phyla with cultivated representatives.
The minimal cell is the simplest bacterium designed and engineered to have almost only essential genes. It is based on a bacterium Mycoplasma, and is designed to have only 473 genes (531 kbp), reducing from 901 genes (1,079 kbp) of the wild strain. This is expected to greatly advance our understanding of the basics of life, is a major step toward the creation of artificial life, and must be a milestone in microbiology. This mini review summarizes the procedures for creating the minimal cell and examples of its use.
Polar regions are often characterized as the coldest, driest, and/or windiest habitats for life on Earth. Even under such extreme conditions, however, microorganisms exhibit remarkable phylogenetic and functional diversity. Our group has studied the microbiomes of Antarctic lake environments. Algae and cyanobacteria often develop luxuriant multi-layered mat consortia in lake bottoms. In association with such mats, aquatic mosses sometimes form unique tower-like structures called "moss pillars" in the freshwater lakes located near Syowa Station, East Antarctica. Moss pillars harbor a high diversity of microorganisms, including both bacteria and eukaryotes, but not archaea. Unexpectedly diverse eukaryotic phylotypes affiliated with algae, ciliates, fungi, nematodes, rotifers, and tardigrades, as well as unclassified phylotypes, have been detected in these pillars. This mini review provides an overview of Antarctic terrestrial ecosystems. Additionally, it presents a brief introduction to an emerging novel cyanobacterial species related to the primitive cyanobacterium Gloeobacter, an unexpected freshwater lineage of Labyrinthulomycetes (fungus-like protists), and uncultivated ultra-small bacteria. Exploration and mining of polar microorganisms would provide great insights into the diversity of life on this planet.
Antarctica is often considered an extreme environment for living organisms due to cold, windy, dry, and seasonally-fluctuating light conditions. The Southern Ocean surrounds the Antarctic continent, where water temperatures remain low (2 to +5 ) even in summer, and sea-ice extends over the large areas in winter. Despite these 'harsh' conditions, marine ecosystems flourish in the Southern Ocean with the rich fauna of cold-adapted species. Adélie penguins distribute across the Antarctic coastal regions and are considered bio-indicators of 'ecosystem health'. Their populations have decreased around the Antarctic Peninsula region but contrastingly increased in the East Antarctic region, and the effects of climate change have been debated. To fully address how changing climate affects Adélie penguins, we need better to understand their survival strategies in the Southern Ocean. Here I review the recent findings on how Adélie penguins utilize the Antarctic environment in summer and winter, based on research using animal-attached bio-logging instruments. These findings include 1) strong effects of inter-annual changes in summer sea-ice conditions on penguin foraging and breeding performance in summer, and 2) the effects of seasonally-fluctuating physical environments on penguin migration in winter. These findings highlight how Adélie penguins adapt to annually- and seasonally- fluctuating Antarctic environments.
The fermentation process is commonly employed for brewed beverages and foods e.g. amino acids, vitamins, enzymes, and antibiotics. The fundamental technology was, however, already established between the 1960s and 1970s and very few signs of progress have been made since then. The biggest reason is, such complex biological process requires precise and sensitive control which is even difficult for skilled engineers. In this paper, several experiments to evaluate the effectiveness of the bioproduction management system with artificial intelligence (AI) are described. A set of detailed-describable sensor data from cultivation batch integrates into convolutional data, which allows the AI to optimize bioproduction with appropriately formulated process control variables. The demonstration involves experimental microbial production with 5L culture tanks. The system achieved a certain degree of improvement in yield for productivity factors through prediction and control instruction by the convolutional data and the AI. We are confident with the result and the AI would become an innovator in emerging bioeconomy markets through inheriting tacit knowledge of experts and beyond them.
Hydrogen bacteria, often called hydrogen-oxidizing bacteria or knallgas bacteria, are a bacterial group that autotrophically grows utilizing hydrogen and carbon dioxide as the electron donor and the carbon source, respectively. This article presents an overview of physiological features and central metabolism, including hydrogen oxidation and carbon fixation, of hydrogen bacteria in order to explain what metabolic mechanisms endow the distinct features with these bacteria. We also discuss the potential application of hydrogen bacteria and their advantages to achieve a low-carbon society based on the metabolic features.
