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This is a review of microbes which live in extreme environments. We focused on natural hot springs with high temperatures and/or acidic environments. Rod shaped bacterium, Bacillus acidocaldarius with spores from Kuroyu, Akita Prefecture were cultured at 55°C under acidic conditions. Sulfur-oxidizing bacteria were cultured from Yunohanazawa, Kanagawa Prefecture. These bacteria were associated with the quality of sulfur in the springs' flow. Irregularly formed archaea were cultured at 70°C under acidic condition from a hot spring pool in the Hakone-Oowakudani geothermal area. The strain was a new species, which was then named Metallosphaera hakonensis. Then, bacterial and archaeal community structures in Japanese hot springs were revealed by 16 rRNA clone library analyses. It has been noted that only a small fraction (<1%) of the microorganisms found in nature can be cultured using traditional cultivation methods. Therefore, a culture independent method, 16S clone library analysis is useful method to reveal the bacterial and archaeal communities. For example, Satoh et al analyzed and compared the 16S rRNA gene compositions and environmental factors of four distinct solfataric acidic hot springs in Kirishima, Japan. As a result, species compositions and biodiversity were clearly different between the ponds showing different temperatures and dissolved elemental concentrations. Moreover, hot spring microalgae such as cyanobacteria, green algae, diatoms and red algae were examined. They live in about 20°C to 80°C, and in acid (pH2-3), neutral (pH6-7), and week alkaline (pH8-9) conditions. Unicellular red algae Cyanidium caldarium, Galdieria sulphuraria, and diatom Pinnularia sp. live in acid hot springs such as Noboribetsu hot springs, Hokkaido and Kusatsu hot springs, Gunma prefecture. Cyanobacteria Mastigocladus sp., Phormidium sp., and Oscillatoria sp. live in neutral and weak alkaline hot springs such as Shima hot springs, Gunma prefecture, Tsurunoyu hot springs, Akita prefecture, and Atagawa hot springs, Shizuoka prefecture. Micro algae capable of photosynthesis form the hot spring ecosystem among bacteria, protozoa and other microorganisms. [ABSTRACT FROM AUTHOR]

Members of the kingdom Nanobdellati, previously known as DPANN archaea, are characterized by ultrasmall cell sizes and reduced genomes. They primarily thrive through ectosymbiotic interactions with specific hosts in diverse environments. Recent successful cultivations have emphasized the importance of adhesion to host cells for understanding the ecophysiology of Nanobdellati. Cell adhesion is often mediated by cell surface carbohydrates, and in archaea, this may be facilitated by the glycosylated S-layer protein that typically coats their cell surface. In this study, we conducted glycoproteomic analyses on two co-cultures of Nanobdellati with their host archaea, as well as on pure cultures of both host and non-host archaea. Nanobdellati exhibited various glycoproteins, including archaellins and hypothetical proteins, with glycans that were structurally distinct from those of their hosts. This indicated that Nanobdellati autonomously synthesize their glycans for protein modifications probably using host-derived substrates, despite the high energy cost. Glycan modifications on Nanobdellati proteins consistently occurred on asparagine residues within the N-X-S/T sequon, consistent with patterns observed across archaea, bacteria, and eukaryotes. In both host and non-host archaea, S-layer proteins were commonly modified with hexose, N-acetylhexosamine, and sulfonated deoxyhexose. However, the N-glycan structures of host archaea, characterized by distinct sugars such as deoxyhexose, nonulosonate sugar, and pentose at the nonreducing ends, were implicated in enabling Nanobdellati to differentiate between host and non-host cells. Interestingly, the specific sugar, xylose, was eliminated from the N-glycan in a host archaeon when co-cultured with Nanobdella. These findings enhance our understanding of the role of protein glycosylation in archaeal interactions. [ABSTRACT FROM AUTHOR]

Molecular analysis is a common tool for marine ecological and biological research. For genomic analysis of zooplankton, ethanol preservation and freezing are often used to preserve samples until analysis. However, these methods have disadvantages, such as the loss of morphological information. Recently, 10% Lugol's iodine solution (10% Lugol) has been shown to be an effective preservative of plankton samples for molecular analysis, even after 18 months. However, that study only reported a PCR-based molecular study using copepods. We tested the preservation effectiveness of 10% Lugol on various zooplankton over 33 months by comparing them to samples preserved by freezing or in 5% formalin seawater. The results revealed that the total amounts of DNA extracted from crustacean and gelatinous zooplankton preserved in 10% Lugol were the same or higher than those preserved in formalin or by freezing. Gel electrophoresis of the extracted DNA indicated that the DNA of the samples preserved in 10% Lugol was not fragmented during the preservation period. PCR amplification of a partial 18S rRNA gene using DNA extracted from various zooplankton taxa (siphonophores, copepods, ostracods, doliolids, polychaetes, pteropods, euphausiids, and chaetognaths) was successful. Sequences of morphologically identified species preserved in 10% Lugol had BLAST hits to sequences of these species deposited in Genbank, with a similarity of 100%, which indicated there was no sequence alteration during the preservation period. Thus, we conclude that 10% Lugol is a suitable preservative for molecular analysis of various zooplankton taxonomic groups. [ABSTRACT FROM AUTHOR]

Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales. Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera--Metallosphaera, Acidianus, and Saccharolobus--originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales. Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions. [ABSTRACT FROM AUTHOR]

In order to obtain knowledge of taxonomy about microorganisms habiting in Indonesian hot springs, the spring water samples from geothermal areas Kawah Domas and Gunung Pancar in western Java, Indonesia, were applied to enrichment cultivation and identification of microorganisms. Only archaea were detected in the enrichment cultures derived from Kawah Domas, and only bacteria were detected in the enrichment cultures derived from Gunung Pancar. Thermoacidophilic archaeon Metallosphaera sedula and Thermoplasma acidophilum were detected as described species from Kawah Domas. In addition, novel species of the genus Sulfurisphaera which was thermoacidophilic archaeon was detected. Moreover, Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) and Miscellaneous Crenarchaeota Group (MCG) which were uncultured archaeal group were detected in enrichment cultures. On the other hand, Thermus brockianus, Thermus arciformis, Sulfurihydrogenibium subterraneum, and Geobacillus icigianus were detected as described bacterial species from Gunung Pancar hot spring. Additionally, a novel specie of the genus Thermus was detected. As described above, the detected microorganisms include two archaeal species, which are difficult to culture and highly novel, as well as multiple new species, and reaffirm the value of Indonesian hot springs as a research field of microbial taxonomy. [ABSTRACT FROM AUTHOR]

Abstract  Bacterial community succession in the start-up of a large-scale, completely-mixed composting reactor was analyzed by 16S rRNA gene (16S rDNA) clone analysis and denaturing gradient gel electrophoresis (DGGE) combined with measurements of temperature, pH, moisture contents, and decomposing rate. DGGE analysis and physicochemical parameters showed that bacterial community succession occurred in four phases; (1) at the start of operation and pH decreasing period (day 0–3), (2) pH decreased and increased period (day 4–11), (3) middle term, moisture content decreasing and maximum temperature increased period (day 12–16) and (4) latter term, temperature decreasing period (day 17–24). Lactobacillus spp. and Bacillus coagulans were detected from the initial phase and middle term, respectively. 16S rDNA clone analysis showed that the dominant bacteria shifted from the order “Lactobacillales” to Bacillales and Actinomycetales. The order “Lactobacillales” was unique which may be caused by using the plastic bottle flakes (polyethylene terephthalate, PET) as bulking agent. [ABSTRACT FROM AUTHOR]

Abstract  Long term fed-batch composting experiments were conducted for 200 days using two types of bulking agents; woodchip and PET flake, with periodic compost withdrawal through a washing process. The bacterial communities of composting materials in the two different bulking agents were also investigated by 16S rRNA gene clone analysis. The decomposition rate in both composting reactors was 86.1% and 88.2% of the total organic load, respectively. The control experiment of dead-end operation without compost withdrawal by washing process could not be maintained for more than 102 days because of its low performance. The reactor with compost withdrawal, however, improved the decomposition rate in the composting process, and could be applied in the long run. There was a significant difference in the bacterial community between the FBC reactor with woodchip and another with PET flake as the bulking agent though the decomposition rates were similar. The reactor with woodchip as the bulking agent consisted of 95% Bacillales while the PET flake reactor contained 54% of total bacteria count. In addition, Lactobacillales was dominant at 38% in the PET flake reactor and the bacterial community in general significantly differed from the woodchip reactor. Furthermore, there was a difference in the species composition in the Bacillales and the bacterial community showed a significant difference at the species level between the two reactors. Although bacterial community differed, the decomposition rates between the two reactors were similar and PET flake showed greater viability than woodchip as a bulking agent due to its high abrasion resistance and non-biodegradability. [ABSTRACT FROM AUTHOR]