Takeshi Kakegawa

A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring

A novel type of a sulfate-reducing microorganism, represented by strain Na82T, was isolated from a hot spring in Narugo, Japan. The isolate was a moderate thermophilic autotroph that was able to grow on H2/CO2 by sulfate respiration. The isolate could grow with nitrate in place of sulfate, and possessed menaquinone-7 and menaquinone-7(H2) as respiratory quinones. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Na82T was a member of the domain Bacteria and distant from any known bacteria, as well as from other sulfate-reducing bacteria (sequence similarities less than 80%). The phylogenetic analysis of the dsrAB gene (alpha and beta subunits of dissimilatory sulfite reductase) sequence also suggested that strain Na82T was not closely related to other sulfate reducers. On the basis of the phenotypic and phylogenetic data, a new taxon is established for the isolate. We proposed the name Thermodesulfobium narugense gen. nov., sp. nov. with strain Na82T (=DSM 14796T=JCM 11510T) as the type strain. Furthermore, a new family, Thermodesulfobiaceae fam. nov., is proposed for the genus.

Microbial communities in iron‐silica‐rich microbial mats at deep‐sea hydrothermal fields of the Southern Mariana Trough

The abundance, diversity and composition of bacterial and archaeal communities in the microbial mats at deep-sea hydrothermal fields were investigated, using culture-independent 16S rRNA and functional gene analyses combined with mineralogical analysis. Microbial mats were collected at two hydrothermal areas on the ridge of the back-arc spreading centre in the Southern Mariana Trough. Scanning electron microscope and energy dispersive X-ray spectroscopic (SEM-EDS) analyses revealed that the mats were mainly composed of amorphous silica and contained numerous filamentous structures of iron hydroxides. Direct cell counting with SYBR Green I staining showed that the prokaryotic cell densities were more than 10(8) cells g(-1). Quantitative polymerase chain reaction (Q-PCR) analysis revealed that Bacteria are more abundant than Archaea in the microbial communities. Furthermore, zetaproteobacterial cells accounted for 6% and 22% of the prokaryotic cells in each mat estimated by Q-PCR with newly designed primers and TaqMan probe. Phylotypes related to iron-oxidizers, methanotrophs/methylotrophs, ammonia-oxidizers and sulfate-reducers were found in the 16S rRNA gene clone libraries constructed from each mat sample. A variety of unique archaeal 16S rRNA gene phylotypes, several pmoA, dsrAB and archaeal amoA gene phylotypes were also recovered from the microbial mats. Our results provide insights into the diversity and abundance of microbial communities within microbial mats in deep-sea hydrothermal fields.

New perspective on Aptian carbon isotope stratigraphy: Data from δ13C records of terrestrial organic matter

Carbon isotope analyses were performed on detrital woody materials in Aptian (mid- Cretaceous) marine sediments of central Hokkaido, northern Japan. A positive δ13Cwood excursion (from −25.4‰ to −21.8‰) following a remarkable negative isotope shift is recognized in the early Aptian, and a small positive anomaly is also found in the latest Aptian. This δ13Cwood profile is exactly in phase with the δ13Ccarbonate curve from a Pacific guyot when the age of the guyot carbonates is revised using published Sr isotope stratigraphies. The highly conformable δ13C profiles of Pacific and Hokkaido sections suggest that δ13C compositions of Aptian marine and terrestrial carbon reservoirs changed simultaneously by the same amplitude within the ocean-atmosphere-biosphere system. Fluctuation patterns of Tethyan δ13Ccarbonate curves are slightly different from those of Pacific and Hokkaido sections. Such differences in δ13C profiles may be attributed to the local paleoceanographic setting of the Aptian Mediterranean Tethys.

Biogeography and biodiversity in sulfide structures of active and inactive vents at deep-sea hydrothermal fields of the Southern Mariana Trough.

ABSTRACT The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments.

Abundance of Zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough

To extend knowledge of subseafloor microbial communities within the oceanic crust, the abundance, diversity and composition of microbial communities in crustal fluids at back-arc hydrothermal fields of the Southern Mariana Trough (SMT) were investigated using culture-independent molecular techniques based on 16S rRNA gene sequences. Seafloor drilling was carried out at two hydrothermal fields, on- and off-ridge of the back-arc spreading centre of the SMT. 16S rRNA gene clone libraries for bacterial and archaeal communities were constructed from the fluid samples collected from the boreholes. Phylotypes related to Thiomicrospira in the Gammaproteobacteria (putative sulfide-oxidizers) and Mariprofundus in the Zetaproteobacteria (putative iron-oxidizers) were recovered from the fluid samples. A number of unique archaeal phylotypes were also recovered. Fluorescence in situ hybridization (FISH) analysis indicated the presence of active bacterial and archaeal populations in the fluids. The Zetaproteobacteria accounted for up to 32% of the total prokaryotic cell number as shown by FISH analysis using a specific probe designed in this study. Our results lead to the hypothesis that the Zetaproteobacteria play a role in iron oxidation within the oceanic crust.

Stability of Amino Acids and Their Oligomerization Under High-Pressure Conditions: Implications for Prebiotic Chemistry

The polymerization of amino acids leading to the formation of peptides and proteins is a significant problem for the origin of life. This problem stems from the instability of amino acids and the difficulty of their oligomerization in aqueous environments, such as seafloor hydrothermal systems. We investigated the stability of amino acids and their oligomerization reactions under high-temperature (180-400°C) and high-pressure (1.0-5.5 GPa) conditions, based on the hypothesis that the polymerization of amino acids occurred in marine sediments during diagenesis and metamorphism, at convergent margins on early Earth. Our results show that the amino acids glycine and alanine are stabilized by high pressure. Oligomers up to pentamers were formed, which has never been reported for alanine in the absence of a catalyst. The yields of peptides at a given temperature and reaction time were higher under higher-pressure conditions. Elemental, infrared, and isotopic analyses of the reaction products indicated that deamination is a key degradation process for amino acids and peptides under high-pressure conditions. A possible NH(3)-rich environment in marine sediments on early Earth may have further stabilized amino acids and peptides by inhibiting their deamination.

Stratigraphic carbon isotope fluctuations of detrital woody materials during the Aptian Stage in Hokkaido, Japan: Comprehensive δ13C data from four sections of the Ashibetsu area

Abstract Geological and organic geochemical studies were performed on an Aptian (mid-Cretaceous) sedimentary succession of the Sorachi and Yezo groups in the Ashibetsu area, central Hokkaido, northern Japan. Microscopic observations of kerogen samples indicate that the constituents of sedimentary organic matter (SOM) are predominantly detrital woody materials (opaque and translucent phytoclasts). Hydrogen/carbon atomic ratios of the kerogen samples indicate that the SOM have not been affected by thermal alteration significantly and thus preserved the original δ13C compositions. It is found that δ13Cwood profiles of four sections from the Ashibetsu area fluctuate systematically with stratigraphy. The δ13Cwood profiles show a remarkable negative shift followed by a positive excursion of ∼3.6‰ (from −25.4 to −21.8‰) exhibiting a bifurcate shape in the early Aptian. δ13Cwood values become nearly constant between −23.0 and −23.5‰ and then approximate to ∼−24.0‰ in the late Aptian. A relatively small positive anomaly is also identified in the latest Aptian. The similarity in δ13Cwood profiles among different sections suggests that SOM with homogenized δ13C values of C3 plants were deposited in sediments. Transportation for a long distance from the sufficiently large provenance is postulated to mix C3 plant materials, resulting in the homogenization of δ13Cwood values. The δ13Cwood profile is essentially conformable with that of Pacific marine carbonates, with their isotopic difference almost constant at all times. Such conformable marine and terrestrial δ13C variations support the previous hypothesis that the temporal δ13C change of the Aptian ocean–atmosphere–biosphere system is precisely traced by bulk isotopic analyses of detrital woody materials, and the supplemental paleoenvironmental effects onto δ13Cwood composition, such as pCO2 changes, are probably negligible.

CARBON ISOTOPE RECORDS OF TERRESTRIAL ORGANIC MATTER AND OCCURRENCE OF PLANKTONIC FORAMINIFERA FROM THE ALBIAN STAGE OF HOKKAIDO, JAPAN: OCEAN-ATMOSPHERE δ13C TRENDS AND CHRONOSTRATIGRAPHIC IMPLICATIONS

Abstract Carbon isotope compositions of sedimentary organic matter (average −24.1‰) from an Albian marine siliciclastic succession in Hokkaido, Japan, exhibit a distinct anomaly by ∼+1.2‰ with a trifurcate shape across the Albian–Cenomanian boundary and two relatively small shifts (<+1‰) in the middle and upper Albian, respectively. The organic matter consist predominantly of woody materials with an insignificant degree of thermal alteration, judged from the visual and elemental characteristics of kerogen; the stratigraphic δ13Corg fluctuations are independent of lithological or total organic carbon variations. Thus, the Hokkaido δ13Corg profile is interpreted as representing the temporal δ13C changes in whole C3 plant vegetation in the provenance of East Asia during Albian time. The patterns and amplitudes in δ13Cwood values and their relationship with planktonic foraminiferal zones are conformable with coeval Tethyan δ13C records of pelagic carbonates. This observation reinforces the view that δ13C compositions of marine and terrestrial carbon reservoirs fluctuated simultaneously by the same amplitude within the ocean-atmosphere-biosphere system regardless of changes in such paleoenvironmental parameters as pCO2. From a chemostratigraphic viewpoint, time-equivalent levels of Oceanic Anoxic Events and stage boundaries are constrained for the Hokkaido sections, allowing for the proposal of a detailed chronostratigraphic framework for future advanced paleoceanographic research in the mid-Cretaceous northwestern Pacific region.

Selective stabilization of ribose by borate.

In this study, borate was found to selectively increase the stability of ribose over other aldopentoses. Ribose is the only sugar present in both early RNA-based biochemistry and contemporary DNA-based life, and the stability of ribose is of fundamental concern for determining the origin of early RNA-based biochemistry. The formose reaction is a potential process in the prebiotic synthesis of ribose and its stereoisomers arabinose, xylose, and lyxose. Ribose is the least stable of these aldopentoses, raising the fundamental question of whether it was originally a component of primitive RNA or was selected through biotic processes. Borate is known to increase the stability of aldopentoses, but the specific differences in the stabilization achieved among different stereoisomers remain unclear. In this study, it was found that the stabilities of all of the tested pentoses increased with the concentration of added borate, but notably, the stability of ribose increased the most. The predominant formation of complexes between borate and ribose was verified, in agreement with previous studies. This borate complex formation might have sequestered ribose from the isomerization and decomposition reactions, resulting in its selective stabilization. These findings indicate that ribose could have accumulated in borate-rich environments on the early Earth and suggest that ribose-based nucleotides combined with phosphate and nucleobases formed abiotically.

A New 14C Data Set of the PY608W-PC Sediment Core from Lake Pumoyum Co (Southeastern Tibetan Plateau) over the Last 19 kyr

A new continuous sediment core (PY608W-PC; 3.8 m length) for reconstruction of climatic and environmental changes in the southeastern Tibetan Plateau was taken from the eastern part of Lake Pumoyum Co in August 2006. Sediment layers of the lower part of PY608W-PC (380-300 cm depth) were composed mainly of relatively large plant residues (up to ~3 cm in length) with an admixture of fine sand and sandy silt. The large plant residues disappeared at ~300-290 cm depth in core PY608W-PC and were replaced by silt-silty clay. The large plant residues from the lower part of PY608W-PC could be aquatic, because the plant residues were extremely enriched in 13C (up to -3.0‰, -5.6 ± 2.3‰ on average). On the other hand, the plant residue concentrates (PRC fractions) from the upper part of the core (290-0 cm in depth) could be terrestrial C3 plants (?13C = -21.8 ± 1.7‰ on average). Radiocarbon dating was performed on the large plant residues and PRC fractions from the PY608W-PC sediment core, which represented the chronology from ~19,000 cal BP to present.