Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage 'Asgard' archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.

An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1T, was isolated as a pure co-culture with Methanogenium sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1T and propose Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300-750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1T grew at 4-30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H2-/formate-utilizing organisms. MK-D1T showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×106 16S rRNA gene copies ml-1. MK-D1T had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with 'Asgard' archaea and more specifically DHVC1/DSAG/MBG-B and 'Lokiarchaeota'/'Lokiarchaeia'. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were Infirmifilum lucidum 3507LTT (76.09 %) and Methanothermobacter tenebrarum RMAST (77.45 %) and the closest relative in enrichment culture was Candidatus 'Lokiarchaeum ossiferum' (95.39 %). The type strain of the type species is MK-D1T (JCM 39240T and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as Promethearchaeaceae fam. nov., Promethearchaeales ord. nov., Promethearchaeia class. nov., Promethearchaeota phyl. nov., and Promethearchaeati regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.

Comparison of early wound healing using modified papilla preservation technique between enamel matrix derivative and recombinant human fibroblast growth factor.

PURPOSE: Enamel matrix derivative (EMD) has demonstrated beneficial effects on wound healing following surgery. However, the effects of recombinant human fibroblast growth factor 2 (rhFGF-2) in periodontal regeneration therapy have not been extensively studied. This retrospective study was conducted to compare the wound healing outcomes of the modified papilla preservation technique (mPPT) between EMD and rhFGF-2 therapies. METHODS: A total of 79 sites were evaluated for early wound healing using the modified early wound healing index (mEHI), which included 6 items: incision, fibrin clotting, step, redness, swelling, and dehiscence. A numeric analog scale, along with postoperative images of the 6 mEHI items, was established and used for the evaluations. The inter-rater reliability of the mEHI was assessed via intraclass correlation coefficients (ICCs). After adjusting for factors influencing the mPPT, the differences in mEHI scores between the EMD and rhFGF-2 groups were statistically analyzed. Additionally, radiographic bone fill (RBF) was evaluated 6 months after surgery. RESULTS: The ICC of the mEHI was 0.575. The mEHI, redness score, and dehiscence scores were significantly higher in the rhFGF-2 group (n=33) than in the EMD group (n=46). Similar results were observed in the subgroup of patients aged 50 years or older, but not in those younger than 50 years. In the subgroup with non-contained bone defects, related results were noted, but not in the subgroup with contained bone defects. However, early wound healing did not correlate with RBF at 6 months after surgery. CONCLUSIONS: Within the limitations of this study, the findings suggest that early wound healing following the use of mPPT with rhFGF-2 is somewhat superior to that observed after mPPT with EMD. However, mEHI should be improved for use as a predictive tool for early wound healing and to reflect clinical outcomes after surgery.

Impact of COVID-19 spread on visit intervals and clinical parameters for patients with periodontitis in supportive periodontal therapy: a retrospective study.

PURPOSE: This study investigated the relationship between the number of days that hospital visits were postponed and changes in clinical parameters due to the spread of coronavirus disease 2019 (COVID-19), after the Japanese government declared a state of emergency in April 2020. METHODS: Regarding the status of postponement of appointments, we analyzed the patients who had visited the Nihon University Hospital at Matsudo for more than 1 year for supportive periodontal therapy (SPT) and classified them into low-, moderate- and high-risk subgroups according to the periodontal risk assessment (PRA). Clinical parameters for periodontal disease such as probing depth (PD), full-mouth bleeding score (FMBS), full-mouth plaque score, periodontal inflamed surface area (PISA), and periodontal epithelial surface area (PESA) were analyzed in 2 periods, from October 2019 to March 2020 and after April 2020. Correlation coefficients between days of deferral and the degree of changes in clinical parameters were calculated. RESULTS: The mean age of the 749 patients was 67.56±10.85 years, and 63.82% were female. Out of 749 patients, 33.24% deferred their SPT appointments after April 2020. The average total of postponement days was 109.49±88.84. The number of postponement days was positively correlated with changes in average PD (rs=0.474) and PESA (rs=0.443) in the high-risk subgroup of FMBS, and average PD (rs=0.293) and PESA (rs=0.253) in the high-risk subgroup of tooth number (TN). Patients belonging to the high-risk subgroups for both FMBS and TN had a positive correlation between postponement days and PISA (rs=0.56). CONCLUSIONS: The findings, the spread of COVID-19 appears to have extended the visit interval for some SPT patients. Moreover, longer visit intervals were correlated with the worsening of some clinical parameters for SPT patients with high PRA.

New load transfer structure to reduce body deformation in side collisions.

OBJECTIVE: In this research, body technology was established for side collisions with new IIHS MDB as a representative case. In the conventional body structure, most of the load received from the barrier is absorbed by bending deformation of the door beam and B-pillar, etc. For that reason, the body is subjected to large deformation before reaching the maximum load, and the deformation increases further when subjected to a high-energy collision. Therefore, the objective of this research is to create a structure that increases the load from the initiation of impact and suppresses the deformation of the car body. METHOD: An arched door beam was developed to reduce the bending moment by the axial load in the longitudinal direction generated during the deformation and to increase the load in the lateral direction. A principle equation was developed that uses the shape of the door beam as a variable. A prototype of the arched door beam was fabricated, and its performance was evaluated by an impactor test. A full-car simulation was conducted using a mass-produced sedan as a base, to which the arched door beam was added to verify the performance of the complete vehicle. RESULTS: The results of the impactor tests were evaluated using the load gradient, which was defined as the generated load divided by the amount of deformation. Compared to conventional straight door beams, the load gradient was 7.1 times higher. Full-car simulation results showed that for a gasoline-powered vehicle body weight, the body load gradient of the proposed structure was 4.7 times higher, and the body deformation adjacent to the dummy shoulder was reduced by 210 mm. Spine acceleration of the dummy was reduced by 56%. CONCLUSION: The body structure proposed in this research has the effect of increasing the load gradient and reducing body deformation and spine acceleration. It is expected to be applicable to EVs and FCVs, which require more energy absorption due to their increased vehicle weight.

Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study.

In microbiology, cultivation is a central approach for uncovering novel physiology, ecology, and evolution of microorganisms, but conventional methods have left many microorganisms found in nature uncultured. To overcome the limitations of traditional methods and culture indigenous microorganisms, we applied a two-stage approach: enrichment/activation of indigenous organisms by using a continuous-flow down-flow hanging sponge bioreactor and subsequent selective batch cultivation. Here, we provide a protocol for this bioreactor-mediated technique using activation of deep marine sediment microorganisms and downstream isolation of a syntrophic co-culture containing an archaeon closely related to the eukaryote ancestor (Candidatus Promethearchaeum syntrophicum strain MK-D1) as an example. Both stages can easily be tailored to target other environments and organisms by modifying the inoculum, feed solution/gases, attachment material and/or cultivation media. We anaerobically incubate polyurethane sponges inoculated with deep-sea methane seep sediment in a reactor at 10 °C and feed anaerobic artificial seawater medium and methane. Once phylogenetically diverse and metabolically active microorganisms are adapted to synthetic conditions in the reactor, we transition to growing community samples in glass tubes with the above medium, simple substrates and selective compounds (e.g., antibiotics). To accommodate for the slow growth anticipated for target organisms, primary cultures can be incubated for ≥6-12 months and analyzed for community composition even when no cell turbidity is observed. One casamino acid- and antibiotic-amended culture prepared in this way led to the enrichment of uncultured archaea. Through successive transfer in vitro combined with molecular growth monitoring, we successfully obtained the target archaeon with its partner methanogen as a pure syntrophic co-culture.

Changes in halitosis value before and after Helicobacter pylori eradication: A single-institutional prospective study.

BACKGROUND AND AIM: Although patients report either improved or worsened halitosis after Helicobacter pylori eradication therapy, such complaints are subjective. Only a few studies have objectively evaluated reports of changes in halitosis after H. pylori eradication; thus, this study aimed to investigate these changes after a successful H. pylori eradication. METHODS: Between February 2015 and October 2018, 56 347 patients visited the clinic. Informed consent for participation in this study was obtained from 164 patients scheduled to undergo upper gastrointestinal endoscopy due to halitosis. Of the 91 patients with H. pylori infection, the halitosis values were evaluated as Refres breath (RB) values using a Total Gas Detector™ System and compared before and after successful H. pylori eradication, as confirmed with urea breath testing. RESULTS: Among the 91 patients treated, 77 patients were successfully eradicated of H. pylori and had their Refres values measured (21 men and 56 women; mean age, 64.2 ± 11.5 years, including 10 smokers); among these 77 patients, 27 showed RB values of > 60. Their RB values significantly improved from 73.5 Â (95% confidence interval [CI], 64.1-82.9) to 59.4 Â (95% CI, 50.0-68.8) (P = 0.038). Of the 30 patients who could be followed up for > 2 years after successful H. pylori eradication, 8 with an RB value ≥ 60 showed significant RB value improvements from 77.9 Â (95% CI, 59.4-96.4) to 30.1 Â (95% CI, 11.6-48.6) (P = 0.0016). CONCLUSIONS: Helicobacter pylori eradication therapy could improve halitosis, and such improvement could be maintained even 2 years after successful eradication.

False positive results in severe acute respiratory coronavirus 2 (SARS-CoV-2) rapid antigen tests for inpatients.

Severe acute respiratory syndrome coronavirus 2 rapid antigen detection (RAD) test kits are widely used as primary screening test in Japan because rapid diagnosis of coronavirus disease 2019 (COVID-19) is critical for infection control. We report cases with RAD test false-positive results in a ward for patients with disabilities. RAD tests potentially evoke hospital operational risk. It is desirable that performing PCR test appropriately when patients admitted to a medical treatment ward with COVID-19 symptoms instead of RAD test.

Preparation of Ordered Nanoporous Indium Tin Oxides with Large Crystallites and Individual Control over Their Thermal and Electrical Conductivities.

Metal oxides are considered suitable candidates for thermoelectric materials owing to their high chemical stabilities. The formation of ordered nanopores within these materials, which decreases thermal conductivity (κ), has attracted significant interest. However, the electrical conductivity (σ) of reported nanoporous metal oxides is low, owing to electron scattering at the thin pore walls and many grain boundaries formed by small crystallites. Therefore, a novel synthesis method that can control pore walls while forming relatively large crystallites to reduce κ and retain σ is required. In this study, we used indium tin oxide (ITO), which is a typical example among metal oxides with high σ. Nanoporous ITOs with large crystallite sizes of several hundred nanometers and larger were successfully prepared using indium chloride as a source of indium. The pore sizes were varied using colloidal silica nanoparticles with different particle sizes as templates. The crystal phase and nanoporous structure of ITO were preserved after spark plasma sintering at 723 K and 80 MPa. The κ was significantly lower than that reported for bulk ITO due to the phonon scattering caused by the nanoporous structure and thin pore walls. There was a limited decrease in σ even with high porosity. These findings show that κ and σ are independently controllable through the precise control of the structure. The control of the thickness of the pore walls at tens of nanometers was effective for the selective scattering of phonons, while almost retaining electron mobility. The remarkable preservation of σ was attributed to the large crystallites that maintained paths for electron conduction and decreased electron scattering at the grain boundaries.

Diverse mosquito-specific flaviviruses in the Bolivian Amazon basin.

The genus Flavivirus includes a range of mosquito-specific viruses in addition to well-known medically important arboviruses. Isolation and comprehensive genomic analyses of viruses in mosquitoes collected in Bolivia resulted in the identification of three novel flavivirus species. Psorophora flavivirus (PSFV) was isolated from Psorophora albigenu. The coding sequence of the PSFV polyprotein shares 60 % identity with that of the Aedes-associated lineage II insect-specific flavivirus (ISF), Marisma virus. Isolated PSFV replicates in both Aedes albopictus- and Aedes aegypti-derived cells, but not in mammalian Vero or BHK-21 cell lines. Two other flaviviruses, Ochlerotatus scapularis flavivirus (OSFV) and Mansonia flavivirus (MAFV), which were identified from Ochlerotatus scapularis and Mansonia titillans, respectively, group with the classical lineage I ISFs. The protein coding sequences of these viruses share only 60 and 40 % identity with the most closely related of known lineage I ISFs, including Xishuangbanna aedes flavivirus and Sabethes flavivirus, respectively. Phylogenetic analysis suggests that MAFV is clearly distinct from the groups of the current known Culicinae-associated lineage I ISFs. Interestingly, the predicted amino acid sequence of the MAFV capsid protein is approximately two times longer than that of any of the other known flaviviruses. Our results indicate that flaviviruses with distinct features can be found at the edge of the Bolivian Amazon basin at sites that are also home to dense populations of human-biting mosquitoes.

Isolation of an archaeon at the prokaryote-eukaryote interface.

The origin of eukaryotes remains unclear1-4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3) model.

Acoustical cues for perception of emotional vocalizations in rats.

The ultrasonic vocalizations of rats can transmit affective states to listeners. For example, rats typically produce shorter calls in a higher frequency range in social situations (pleasant call: PC), whereas they emit longer calls with lower frequency in distress situations (distress call: DC). Knowing what acoustical features contribute to auditory discrimination between these two calls will help to better characterize auditory perception of vocalized sounds in rats. In turn, this could lead to better estimation of models for processing vocalizations in sensory systems in general. Here, using an operant discrimination procedure, we examined the impact of various acoustical features on discriminating emotional ultrasonic vocalizations. We did this by systematically swapping three features (frequency range, time duration, and residual frequency-modulation pattern) between two emotional calls. After rats were trained to discriminate between PC and DC, we presented probe stimuli that were synthesized calls with one or two acoustical features swapped, and examined if the rats judged these calls as either PC or DC. The results revealed that all features were important for discrimination between the two call types, but frequency range provided the most information for discrimination. This supports the hypothesis that while rats utilize all acoustical features to perceive emotional vocalizations, they considerably rely on frequency cues.

Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation.

Recent explorations of scientific ocean drilling have revealed the presence of microbial communities persisting in sediments down to ~2.5 km below the ocean floor. However, our knowledge of these microbial populations in the deep subseafloor sedimentary biosphere remains limited. Here, we present a cultivation experiment of 2-km-deep subseafloor microbial communities in 20-million-year-old lignite coalbeds using a continuous-flow bioreactor operating at 40 °C for 1029 days with lignite particles as the major energy source. Chemical monitoring of effluent samples via fluorescence emission-excitation matrices spectroscopy and stable isotope analyses traced the transformation of coalbed-derived organic matter in the dissolved phase. Hereby, the production of acetate and 13C-depleted methane together with the increase and transformation of high molecular weight humics point to an active lignite-degrading methanogenic community present within the bioreactor. Electron microscopy revealed abundant microbial cells growing on the surface of lignite particles. Small subunit rRNA gene sequence analysis revealed that diverse microorganisms grew in the bioreactor (e.g., phyla Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Bacteroidetes, Spirochaetes, Tenericutes, Ignavibacteriae, and SBR1093). These results indicate that activation and adaptive growth of 2-km-deep microbes was successfully accomplished using a continuous-flow bioreactor, which lays the groundwork to explore networks of microbial communities of the deep biosphere and their physiologies.

Minor contribution of CYP3A5 to the metabolism of hepatitis C protease inhibitor paritaprevir in vitro.

Paritaprevir (PTV) is a non-structural protein 3/4A protease inhibitor developed for the treatment of hepatitis C disease as a fixed dose combination of ombitasvir (OBV) and ritonavir (RTV) with or without dasabuvir. The aim of this study was to evaluate the effects of cytochrome P450 (CYP) 3A5 on in vitro PTV metabolism using human recombinant CYP3A4, CYP3A5 (rCYP3A4, rCYP3A5) and human liver microsomes (HLMs) genotyped as either CYP3A5*1/*1, CYP3A5*1/*3 or CYP3A5*3/*3. The intrinsic clearance (CLint, Vmax/Km) for the production of a metabolite from PTV in rCYP3A4 was 1.5 times higher than that in rCYP3A5. The PTV metabolism in CYP3A5*1/*1 and CYP3A5*1/*3 HLMs expressing CYP3A5 was comparable to that in CYP3A5*3/*3 HLMs, which lack CYP3A5. CYP3A4 expression level was significantly correlated with PTV disappearance rate and metabolite formation. In contrast, there was no such correlation found for CYP3A5 expression level. This study represents that the major CYP isoform involved in PTV metabolism is CYP3A4, with CYP3A5 having a minor role in PTV metabolism. The findings of the present study may provide foundational information on PTV metabolism, and may further support dosing practices in HCV-infected patients prescribed PTV-based therapy.

High prevalence of anemia in 10-month-old breast-fed Japanese infants.

BACKGROUND: Anemia in infancy is still prevalent in developing countries. Commercial iron-fortified complementary foods or iron drops are not available in Japan, and breast-fed infants have a higher risk of anemia. We studied anemia screening in 10-month-old infants to determine whether breast-feeding is a risk factor for anemia. METHODS: Anemia screening was performed during regular health check for 10-month-old children at four local pediatric clinics in Shimane Prefecture, Japan. Venous blood was obtained for complete blood count. The clinical characteristics of each child were obtained via questionnaire. Anemia was defined as hemoglobin <11.0 g/dL. Children were categorized into anemia and no-anemia groups, and univariate analysis was conducted on comparison of the clinical variables. Multivariate logistic regression analysis for anemia was performed to adjust for several clinical variables. RESULTS: We analyzed data in 325 children. On univariate analysis, anemia was associated with breast-feeding, monthly bodyweight gain and gestational week. On multivariate logistic regression analysis, anemia was associated with feeding type and gestational week (OR of partial breast-feeding and formula feeding, 0.446; 95%CI: 0.208-0.957; and 0.223; 95%CI: 0.075-0.660, respectively, compared with exclusive breast-feeding, OR, 1.0; and gestational week, OR, 0.753; 95%CI: 0583-0.972). CONCLUSION: Breast-feeding is an important factor for anemia in 10-month-old Japanese infants. Breast-fed infants after 6 months of age may need iron supplements or iron-fortified complimentary foods.

Biotic manganese oxidation coupled with methane oxidation using a continuous-flow bioreactor system under marine conditions.

Biogenic manganese oxides (BioMnOx) can be applied for the effective removal and recovery of trace metals from wastewater because of their high adsorption capacity. Although a freshwater continuous-flow system for a nitrifier-based Mn-oxidizing microbial community for producing BioMnOx has been developed so far, a seawater continuous-flow bioreactor system for BioMnOx production has not been established. Here, we report BioMnOx production by a methanotroph-based microbial community by using a continuous-flow bioreactor system. The bioreactor system was operated using a deep-sea sediment sample as the inoculum with methane as the energy source for over 2 years. The BioMnOx production became evident after 370 days of reactor operation. The maximum Mn oxidation rate was 11.4 mg L-1 day-1. An X-ray diffraction analysis showed that the accumulated BioMnOx was birnessite. 16S rRNA gene-based clone analyses indicated that methanotrophic bacterial members were relatively abundant in the system; however, none of the known Mn-oxidizing bacteria were detected. A continuous-flow bioreactor system coupled with nitrification was also run in parallel for 636 days, but no BioMnOx production was observed in this bioreactor system. The comparative experiments indicated that the methanotroph-based microbial community, rather than the nitrifier-based community, was effective for BioMnOx production under the marine environmental conditions.

Response characteristics of the rat anterior cingulate cortex to ultrasonic communicative vocalizations.

Emotional communication involves transmitting information on affective states. Rat 50- and 22-kHz ultrasonic vocalizations (USVs) are emotional communication signals that reflect positive or negative states, respectively. In general, emotional communication signals that elicit changes in event-related potentials (ERPs), suggesting a specific mechanism for processing these signals. As this is observed in several communication systems including humans, we hypothesized that rat USVs can also trigger such changes. In this study, we measured rat local field potentials and used them to calculate ERPs from the anterior cingulate cortex (ACC), an area related to motor production of USVs. In Experiment 1, we measured ERPs to pure tones with peak frequencies around 50 or 22 kHz to examine whether the ACC is involved in auditory sensory processing related to pitch. The results showed that pure tones around 50 kHz elicited large amplitude ERPs, whereas those around 22 kHz resulted in smaller ERPs. In Experiment 2, we compared ERPs in response to rat USVs (emotional stimuli) with ERPs to pure tones modeled after USVs (neutral stimuli). The peak frequencies were the same between USVs and neutral sounds, but USVs showed more frequency modulation than neutral sounds. USVs elicited larger changes in the amplitude of ERP components than neutral stimuli did. These experiments suggest that the rat ACC is sensitive to frequencies around 50 and 22 kHz, and is especially tuned to frequency modulation around these frequencies. Taken together, the rat ACC may process the emotional content of communication signals on the basis of pitch and frequency modulation.

Cognitive bias in rats evoked by ultrasonic vocalizations suggests emotional contagion.

Emotional contagion occurs when an individual acquires the emotional state of another via social cues, and is an important component of empathy. Empathic responses seen in rodents are often explained by emotional contagion. Rats emit 50kHz ultrasonic vocalizations (USVs) in positive contexts, and emit 22kHz USVs in negative contexts. We tested whether rats show positive or negative emotional contagion after hearing conspecific USVs via a cognitive bias task. We hypothesized that animals in positive emotional states would perceive an ambiguous cue as being good (optimistic bias) whereas animals in negative states would perceive the same cue as being bad (pessimistic bias). Rats were trained to respond differently to two sounds with distinct pitches, each of which signaled either a positive or a negative outcome. An ambiguous cue with a frequency falling between the two stimuli tested whether rats interpreted it as positive or negative. Results showed that rats responded to ambiguous cues as positive when they heard the 50kHz USV (positive vocalizations) and negative when they heard the 22kHz USV (negative vocalizations). This suggests that conspecific USVs can evoke emotional contagion, both for positive and negative emotions, to change the affective states in receivers.

Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream.

UNLABELLED: Ammonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in the in situ quantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (δ(15)NNO2- and δ(18)ONO2-, respectively) are geochemical tracers for evaluating the sources and the in situ rate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilic Thaumarchaeota populations composed almost entirely of "Candidatus Nitrosocaldus." The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The δ(18)O value of nitrite produced from ammonia oxidation varied with the δ(18)O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH ≥6.6, the rate of ammonia oxidation by thermophilic Thaumarchaeota could be estimated using δ(18)ONO2- in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments. IMPORTANCE: Because ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying the regulation of the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilic Thaumarchaeota and elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation.

Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta.

An anaerobic, psychrophilic bacterium, strain MO-SPC2(T), was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediments collected from off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. Cells were pleomorphic: spherical, annular, curved rod, helical and coccoid cell morphologies were observed. Motility only occurred in helical cells. Strain MO-SPC2(T) grew at 0-17 °C (optimally at 9 °C), at pH 6.0-8.0 (optimally at pH 6.8-7.2) and in 20-40 g NaCl l(-1) (optimally at 20-30 NaCl l(-1)). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC2(T) were phosphatidylglycolipids, phospholipids and glycolipids. The major cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9. Isoprenoid quinones were not detected. The G+C content of the DNA was 32.3 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-SPC2(T) was affiliated with the genus Sphaerochaeta within the phylum Spirochaetes, and its closest relatives were Sphaerochaeta pleomorpha Grapes(T) (88.4 % sequence identity), Sphaerochaeta globosa Buddy(T) (86.7 %) and Sphaerochaeta coccoides SPN1(T) (85.4 %). Based on phenotypic characteristics and phylogenetic traits, strain MO-SPC2(T) is considered to represent a novel species of the genus Sphaerochaeta, for which the name Sphaerochaeta multiformis sp. nov. is proposed. The type strain is MO-SPC2(T) ( = JCM 17281(T) = DSM 23952(T)). An emended description of the genus Sphaerochaeta is also proposed.

A long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor.

Anaerobic oxidation of methane (AOM) in marine sediments is an important global methane sink, but the physiological characteristics of AOM-associated microorganisms remain poorly understood. Here we report the cultivation of an AOM microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor with polyurethane sponges, called the down-flow hanging sponge (DHS) bioreactor. We anaerobically incubated deep-sea methane-seep sediment collected from the Nankai Trough, Japan, for 2,013 days in the bioreactor at 10°C. Following incubation, an active AOM activity was confirmed by a tracer experiment using 13C-labeled methane. Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor. After 2,013 days of incubation, the predominant archaeal components were anaerobic methanotroph (ANME)-2a, Deep-Sea Archaeal Group, and Marine Benthic Group-D, and Gammaproteobacteria was the dominant bacterial lineage. Fluorescence in situ hybridization analysis showed that ANME-1 and -2a, and most ANME-2c cells occurred without close physical interaction with potential bacterial partners. Our data demonstrate that the DHS bioreactor system is a useful system for cultivating fastidious methane-seep-associated sedimentary microorganisms.