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The 13th Symposium on Polar Science/Ordinary sessions [OB] Polar biology, Wed. 16 Nov.

We previously showed that novel filterable bacteria remain in “sterile” (&lt, 0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids, and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms.

The 11th Symposium on Polar Science/Ordinary sessions: [OB] Polar Biology, Poster presentations, Mon. 16 Nov. - Fri. 18 Dec.

Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts.

The Ninth Symposium on Polar Science/Ordinary sessions: [OB] Polar biology, Wed. 5 Dec. / Entrance Hall (1st floor), National Institute of Polar Research

The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria . Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%. In-depth phylogenetic analyses based on alignments of 74 protein sequences of a phylogenetically broad range of taxa suggested assignment of the strain to a new order of the class Oligoflexia . These analyses also suggested that the order Bdellovibrionales should be transferred from the class Deltaproteobacteria to the class Oligoflexia , that this order should be split into two orders, and that the family Pseudobacteriovoracaceae should be transferred from the order Bdellovibrionales to the order Oligoflexales . We propose to establish for strain MWH-Nonnen-W8redT (=DSM 23856T=CCUG 58639T) the novel species and genus Silvanigrella aquatica gen. nov., sp. nov. to be placed in the new family Silvanigrellaceae fam. nov. of the new order Silvanigrellales ord. nov.

Aurantimicrobium minutum type strain KNC T is a planktonic ultramicrobacterium isolated from river water in western Japan. Strain KNC T has an extremely small, streamlined genome of 1,622,386 bp comprising 1,575 protein-coding sequences. The genome annotation suggests that strain KNC T has an actinorhodopsin-based photometabolism.

Decomposition of humic substances (HSs) is a slow and cryptic but non-negligible component of carbon cycling in sediments. Aerobic decomposition of HSs by microorganisms in the surface environment has been well documented; however, the mechanism of anaerobic microbial decomposition of HSs is not completely understood. Moreover, no microorganisms capable of anaerobic decomposition of HSs have been isolated. Here, we report the anaerobic decomposition of humic acids (HAs) by the anaerobic bacterium Clostridium sp. HSAI-1 isolated from the deep terrestrial subsurface. The use of 14C-labelled polycatechol as an HA analogue demonstrated that the bacterium decomposed this substance up to 7.4% over 14 days. The decomposition of commercial and natural HAs by the bacterium yielded lower molecular mass fractions, as determined using high-performance size-exclusion chromatography. Fourier transform infrared spectroscopy revealed the removal of carboxyl groups and polysaccharide-related substances, as well as the generation of aliphatic components, amide and aromatic groups. Therefore, our results suggest that Clostridium sp. HSAI-1 anaerobically decomposes and transforms HSs. This study improves our understanding of the anaerobic decomposition of HSs in the hidden carbon cycling in the Earth’s subsurface.

第6回極域科学シンポジウム分野横断セッション：[IB2] 地球環境変動の解析と地球生命システム学の構築11月19日（木） 統計数理研究所 セミナー室1（D305）

第6回極域科学シンポジウム[OB] 極域生物圏11月17日（火） 統計数理研究所 セミナー室1（D305）

著者人数: 21人, Number of authors: 21, 資料番号: PA1010098000

Life on a global biosphere basis is substantiated in the form of organics and organisms, and defined as the intermediate forms (briefly expressed as CH 2 O) hovering between the reduced (CH 4 , methane) and (CO 2 , carbon dioxide) ends, different from the classical definition of life as a complex organization maintaining ordered structure and information. Both definitions consider sustenance of life meant as protection of life against chaos through an input of external energy. The CH 2 O-life connection is maintained as long as the supply of H and O lasts, which is in turn are provided by the splitting of the water molecule H 2 O. Water is split by electricity, as well-known from school-level experiments, and by solar radiation and geothermal heat on a global scale. In other words, the Sun’s radiation and the Earth’s heat as well as radioactivity split water to supply H and O for continued existence of life on the Earth. These photochemical, radiochemical and geothermal processes have influences on the evolution and current composition of the Earth’s atmosphere, compared with those of Venus and Mars, and influences on the planetary climatology. This view of life may be applicable to the “search-for-life in space” and to sustainability assessment of astrobiological habitats.

A Gram-positive, endospore-forming, rod-shaped and moderately halophilic bacterium was isolated from a salt-crust sample collected from Gharsa salt lake (Chott el Gharsa), Tunisia. The newly isolated bacterium, designated SA-Vb1(T), was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. Strain SA-Vb1(T) was closely related to the type strains of Virgibacillus marismortui and Virgibacillus olivae, with 16S rRNA gene sequence similarities of 99.7 and 99.4 %, respectively. However, strain SA-Vb1(T) was distinguished from these two type strains on the basis of phenotypic characteristics and DNA-DNA relatedness (29.4 and 5.1 %, respectively). The genetic relationship between strain SA-Vb1(T) and Virgibacillus pantothenticus IAM 11061(T) (the type strain of the type species) and other type strains of the genus was 96-98 % based on 16S rRNA gene sequence similarity and 18.3-22.3 % based on DNA-DNA hybridization. Biochemical analysis resulted in determination of major fatty acids iso-C(15 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0) (33.3, 29.2 and 9.8 %, respectively); phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the main polar lipids and MK-7 was the predominant menaquinone ( approximately 100 %). The distinct characteristics demonstrated by strain SA-Vb1(T) represent properties of a novel species of the genus Virgibacillus, for which the name Virgibacillus salarius sp. nov. is proposed. The type strain is SA-Vb1(T) (=JCM 12946(T) =DSM 18441(T)).

We investigated the diversity and distribution of archaeal and bacterial 16S rRNA gene sequences in deep aquifers of mid- to late Miocene hard shale located in the northernmost region of the Japanese archipelago. A major fault in the north-west-south-east (NW-SE) direction runs across the studied area. We collected three groundwater samples from boreholes on the south-west (SW) side of the fault at depths of 296, 374 and 625 m below ground level (m.b.g.l.) and one sample from the north-east (NE) side of the fault at a depth of 458 m.b.g.l. The groundwater samples were observed to be neutral and weakly saline. The total microbial counts after staining with acridine orange were in the order 105-106 cells mL-1 and 103 cells mL-1 in the aquifers to the SW and to the NE of the fault, respectively. A total of 407 archaeal and bacterial 16S rRNA gene sequences (204 and 203 sequences, respectively) were determined for clone libraries constructed from all groundwater samples. Phylogenetic analyses showed that the libraries constructed from the SW aquifers were generally coherent but considerably different from those constructed from the NE aquifer. All of the archaeal clone libraries from the SW aquifers were predominated by a single sequence closely related to the archaeon Methanoculleus chikugoensis, and the corresponding bacterial libraries were mostly predominated by the sequences related to Bacteroidetes, Firmicutes and δ-Proteobacteria. In contrast, the libraries from the NE aquifer were dominated by uncultured environmental archaeal clones with no methanogen sequences and by β-proteobacterial clones with no sequences related to Bacteroidetes and δ-Proteobacteria. Hence, the possible coexistence of methanogens and sulphate reducers in Horonobe deep borehole (HDB) on the SW side is suggested, particularly in HDB-6 (374 m.b.g.l.). Moreover, these organisms might play an important geochemical role in the groundwater obtained from the aquifers.

The Antarctic Icecap has attracted considerable attention of scientists for many years. Many microbiological and general biological studies of the ground surface, snow and glacial cover have been performed. In recent decades, it has been discovered that the Antarctic ice sheet is a unique depository of paleoclimatic and paleomicrobiological information that reflects previous ecological events on our planet. Thus, dust particles, spores, plant pollen, and different microorganisms, which were brought onto the glacier surface by wind, appear to be gradually buried in the glacier layers and preserved in the frozen state for hundreds thousands years. These investigations have become especially important in the era of space research, many scientists consider the Antarctic as the most appropriate model to solve some methodical problems in astrobiology. Further developments and improvements of drilling methods have made it possible to penetrate into the deepest levels of the Antarctic Icecap, including the lower layers of so-called accretion ice above the sub-glacial Lake Vostok. The initial glaciological and microbiological investigations were mainly focused on the glacier ice and gave very useful information on the history of the Earth's climate and the distribution of dust particles and microorganisms in the ice sheet during different periods. However, studies of the deep accretion ice and the sub-glacial Lake Vostok are expected to provide more insight into relict microbial forms and give rise to new investigations of the Antarctic ice cover. These works should include searches for microbial life in the accretion ice and Lake Vostok, and requires new biological techniques, new multidisciplinary approaches and international cooperation. Nowadays, biological investigations of the Earth's polar regions are of paramount importance in view of current ecological problems. Of no less significance is the search for possible extraterrestrial life, since permafrost and glaciers are widely spread in the Universe; this is why, researchers have paid great attention to the Antarctic as a model for astrobiology.

Several halotolerant bacteria were isolated from dust allowed to settle passively on saline medium in Higashi-Hiroshima, Japan during Asia dust events in 2005–2006. The primary identification, based on the sequence similarity of the 16S rRNA gene, revealed that these isolates were strains of Bacillus subtilis, B. licheniformis, Staphylococcus epidermidis, Gracillibacillus sp., and Halomonas venusta. A parallel investigation carried out on desert sand collected directly from sand dunes in Dunhuang, Gobi Desert, China resulted in the revivification of seven bacterial strains that were highly identical to the B. subtilis and B. licheniformis strains obtained in Higashi-Hiroshima (99.7 and 10027777730300f 16S rDNA sequence similarity, respectively). A subsequent genetic analysis on the group of B. licheniformis isolates based on the universally house-keeping genes, gyrB and parE, revealed high sequence similarities in both genes among the strains of both locations (99.0–99.4%), which clustered them in a monophyletic line. Phenotype characterized by numerical taxonomy for 150 physiological tests confirmed the close relatedness between strains (similarity coefficient S SM = 96.0%). The remarkable agreement between phenotype and genotype of the bacterial isolates allows us to conclude that there may have been an aerosolized dispersion of a Gobi Desert B. licheniformis by dust storms to Japan. This study provides evidence of microbial transport by yellow dust events in North-East Asia.

The diversity and distribution of sulfate-reducing prokaryotes (SRP) was investigated in the Nankai Trough sediments of off-central Japan by exploring the diversity of a functional gene, dissimilatory sulfite reductase (dsrAB). Bulk DNAs were extracted from five piston-cored samples (up to 4.5 m long) with 41 vertical sections, and full-length dsrAB gene sequences (ca. 1.9 kb) were PCR amplified and cloned. A total of 382 dsrAB clones yielded eight phylogenetic groups with an indigenous group forming a unique dsrAB lineage. The deltaproteobacterial dsrAB genes were found in almost all sediment samples, especially in the surface layer. One unique dsrAB clone group was also widespread in the dsrAB profiles of the studied sediments, and the percentage of its clones was generally shown gradual increase with sediment depth.

In our previous investigation on the genes of 1,5-ribulose bisphosphate carboxylase/oxygenase (RuBisCO; EC 4.1.1.39) in deep-sea chemoautotrophic and methanotrophic endosymbioses, the gene encoding the large subunit of RuBisCO form I (cbbL) had been detected in the gill of a mussel belonging to the genus Bathymodiolus from a western Pacific back-arc hydrothermal vent. This study further examined the symbiont source of the RuBisCO cbbL gene along with the genes of 16S ribosomal RNA (16S rDNA) and particulate methane monooxygenase (EC 1.14.13.25; pmoA) and probed for the presence of the ATP sulfurylase gene (EC 2.7.7.4; sopT). The 16S rDNA sequence analysis indicated that the mussel harbors a monospecific methanotrophic Gammaproteobacterium. This was confirmed by amplification and sequencing of the methanotrophic pmoA, while thiotrophic sopT was not amplified from the same symbiotic genome DNA. Fluorescence in situ hybridization demonstrated simultaneous occurrence of the symbiont-specific 16S rDNA, cbbL and pmoA, but not sopT, in the mussel gill. This is the first molecular and visual evidence for a methanotrophic bacterial endosymbiont that bears the RuBisCO cbbL gene relevant to autotrophic CO(2) fixation.

This study provides the first empirical evidence for the conservation of the ets proto-oncogene transcription factor family throughout the Metazoa. Using the polymerase chain reaction with degenerate primers corresponding to conserved sequences within the ETS DNA-binding domain, we have detected ets genes in a range of lower metazoans, including sponges, ctenophores, anemones, flatworms and nematodes, and in severai higher invertebrate metazoans. Many of these sequences are significantly divergent from the original v-eta-1 oncogene, although most can be aligned with recently defined groups within the ets gene family. Multiple ETS domain sequences were detected in a number of the lower metazoan species, providing evidence for the existence of an ets multigene family at the earliest stages of metazoan evolution. In contrast, we were unable to detect any ETS sequences in fungal, plant or several protozoan DNAs. Our findings suggest that the duplication and divergence of ets proto-oncogenes responsible for generating the multigene family occurred concomitantly with the development of metazoan animals. In addition, these data corroborate other recent molecular evidence in providing strong support for the monophyletic origin of all multicellular animals, including sponges.

Antarctic “moss pillars” are lake-bottom biocenoses that are primarily comprised of aquatic mosses. The pillars consist of distinct redox-affected sections: oxidative exteriors and reductive interiors. Batteries of SSU rRNA genotypes of eukaryotes, eubacteria, and cyanobacteria, but no archaea, have been identified in these pillars. However, rRNA-based phylogenetic analysis provides limited information on metabolic capabilities. To investigate the microorganisms that have the potential for CO2 fixation in the pillars, we studied the genetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, EC 4.1.1.39)—an enzyme involved in CO2 fixation. PCR clone libraries targeting all forms of the RuBisCO large subunit-encoding gene were constructed and 1,092 clones were randomly sequenced. Phylogenetic analysis indicated that proteobacterial form IA operational RuBisCO units (ORUs) were detected at the same frequency as the cyanobacterial form IB ORUs. Surprisingly, the form IA ORU, which was closely related to the sequences from deep-sea environments, was detected from all moss pillar sections. The form IB ORU related to Bryophyta, considered to be derived from moss, was identical to the sequence of Leptobryum sp. isolated from Lake Hotoke-Ike where the pillars were found. Moreover, certain cyanobacterial ORUs were found exclusively in the exterior of the pillar, whereas form II ORUs related to chemolithoautotrophic sulfur oxidizers and purple sulfur bacteria were found exclusively in the interior. No forms IC, ID, or III RuBisCO genes were detected. This is the first report demonstrating that bacteria with the potential for CO2 fixation and chemoautotrophy are present in the Antarctic moss pillar ecosystem.

Organisms living in the Arctic terrains such as Greenland have to deal with low temperature conditions. The mechanisms by which bacteria resist to low temperature are largely unknown; however, a well-known survival strategy of the microorganisms inhabiting the Arctic is spore forming. Moreover, halophilic bacteria are often resistant to various stresses. We have attempted isolation of spore-forming halophilic bacteria from Arctic terrains. We isolated 10 strains of spore-forming halophilic bacteria from the samples collected from a glacial moraine in Qaanaaq, Greenland in July 2007. Identification based on 16S rRNA gene sequence similarities showed that the isolates were closely related to the Oceanobacillus , Ornithinibacillus , Virgibacillus , Gracilibacillus , and Bacillus genera. In addition, the 16S rRNA sequences of some isolates were extremely similar to those of strains from the desert sand in China (100% identity, near full length), the source of the so-called “yellow dust.” Previous research indicated that yellow dust had been transported to Greenland by the wind. Our research implies the long-range transportation of these microorganisms to locations such as the Arctic.

An integrated program, “Microbiological and ecological responses to global environmental changes in polar regions” (MERGE), was proposed in the International Polar Year (IPY) 2007–2008 and endorsed by the IPY committee as a coordinating proposal. MERGE hosts original proposals to the IPY and facilitates their funding. MERGE selected three key questions to produce scientific achievements. Prokaryotic and eukaryotic organisms in terrestrial, lacustrine, and supraglacial habitats were targeted according to diversity and biogeography; food webs and ecosystem evolution; and linkages between biological, chemical, and physical processes in the supraglacial biome. MERGE hosted 13 original and seven additional proposals, with two full proposals. It respected the priorities and achievements of the individual proposals and aimed to unify their significant results. Ideas and projects followed a bottom-up rather than a top-down approach. We intend to inform the MERGE community of the initial results and encourage ongoing collaboration. Scientists from non-polar regions have also participated and are encouraged to remain involved in MERGE. MERGE is formed by scientists from Argentina, Australia, Austria, Belgium, Brazil, Bulgaria, Canada, Egypt, Finland, France, Germany, Italy, Japan, Korea, Malaysia, New Zealand, Philippines, Poland, Russia, Spain, UK, Uruguay, USA, and Vietnam, and associates from Chile, Denmark, Netherlands, and Norway.