Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere

Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.

Earthquake-enhanced dissolved carbon cycles in ultra-deep ocean sediments

Hadal trenches are unique geological and ecological systems located along subduction zones. Earthquake-triggered turbidites act as efficient transport pathways of organic carbon (OC), yet remineralization and transformation of OC in these systems are not comprehensively understood. Here we measure concentrations and stable- and radiocarbon isotope signatures of dissolved organic and inorganic carbon (DOC, DIC) in the subsurface sediment interstitial water along the Japan Trench axis collected during the IODP Expedition 386. We find accumulation and aging of DOC and DIC in the subsurface sediments, which we interpret as enhanced production of labile dissolved carbon owing to earthquake-triggered turbidites, which supports intensive microbial methanogenesis in the trench sediments. The residual dissolved carbon accumulates in deep subsurface sediments and may continue to fuel the deep biosphere. Tectonic events can therefore enhance carbon accumulation and stimulate carbon transformation in plate convergent trench systems, which may accelerate carbon export into the subduction zones.

Subseafloor sulphide deposit formed by pumice replacement mineralisation

Seafloor massive sulphide (SMS) deposits, modern analogues of volcanogenic massive sulphide (VMS) deposits on land, represent future resources of base and precious metals. Studies of VMS deposits have proposed two emplacement mechanisms for SMS deposits: exhalative deposition on the seafloor and mineral and void space replacement beneath the seafloor. The details of the latter mechanism are poorly characterised in detail, despite its potentially significant role in global metal cycling throughout Earth’s history, because in-situ studies require costly drilling campaigns to sample SMS deposits. Here, we interpret petrographic, geochemical and geophysical data from drill holes in a modern SMS deposit and demonstrate that it formed via subseafloor replacement of pumice. Samples from the sulphide body and overlying sediment at the Hakurei Site, Izena Hole, middle Okinawa Trough indicate that sulphides initially formed as aggregates of framboidal pyrite and matured into colloform and euhedral pyrite, which were replaced by chalcopyrite, sphalerite and galena. The initial framboidal pyrite is closely associated with altered material derived from pumice, and alternating layers of pumiceous and hemipelagic sediments functioned as a factory of sulphide mineralisation. We infer that anhydrite-rich layers within the hemipelagic sediment forced hydrothermal fluids to flow laterally, controlling precipitation of a sulphide body extending hundreds of meters.

Temperature limits to deep subseafloor life in the Nankai Trough subduction zone

Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.

Stress state in the largest displacement area of the 2011 Tohoku-Oki earthquake

The 2011 moment magnitude 9.0 Tohoku-Oki earthquake produced a maximum coseismic slip of more than 50 meters near the Japan trench, which could result in a completely reduced stress state in the region. We tested this hypothesis by determining the in situ stress state of the frontal prism from boreholes drilled by the Integrated Ocean Drilling Program approximately 1 year after the earthquake and by inferring the pre-earthquake stress state. On the basis of the horizontal stress orientations and magnitudes estimated from borehole breakouts and the increase in coseismic displacement during propagation of the rupture to the trench axis, in situ horizontal stress decreased during the earthquake. The stress change suggests an active slip of the frontal plate interface, which is consistent with coseismic fault weakening and a nearly total stress drop.

Tissue-specific regulation of IRS-2/PI 3-kinase association in aged rats

We have examined the insulin-stimulated IRS-2 association with PI 3-kinase and the phosphorylation of AKT/PKB, which is functionally located downstream of the PI 3-kinase, in aged (obese) rats. The IRS-2 protein levels were similar in 2 and 20 month-old rats in both tissues, liver and muscle. There were reductions in insulin-induced IRS-2 tyrosine phosphorylation in liver and muscle, accompanied by a decrease in IRS-2/PI 3-kinase association and in AKT/PKB phosphorylation only in muscle tissue of aged rats. This regulation may be important in the altered glucose metabolism observed in aged (obese) rats.

Defects in insulin signal transduction in liver and muscle of pregnant rats

Pregnancy is known to induce resistance, but the exact molecular mechanism involved is unknown. In the present study, we have examined the levels and phosphorylation state of the insulin receptor and of insulin receptor substrate 1 (IRS-1), as well as the association between IRS-1 and phosphatidylinositol 3-kinase (PI 3-kinase) in the liver and muscle of pregnant rats (day 20 of gestation) by immunoprecipitation and immunoblotting with anti-insulin receptor, anti-IRS-1, anti-PI 3-kinase and anti-phosphotyrosine antibodies. There were no changes in the insulin receptor concentration in the liver and muscle of pregnant rats. However, insulin stimulation of receptor autophosphorylation, as determined by immunoblotting with antiphosphotyrosine antibody, was reduced by 30 +/- 6% (p < 0.02) in muscle and 36 +/- 5% (p < 0.01) in liver at day 20 of gestation. IRS-1 protein levels decreased by 45 +/- 6% (p < 0.002) in liver and by 56 +/- 9% (p < 0.002) in muscle of pregnant rats. In samples previously immunoprecipitated with anti-IRS-1 antibody and blotted with antiphosphotyrosine antibody, the insulin-stimulated IRS-1 phosphorylation levels in the muscle and liver of pregnant rats decreased by 70 +/- 9% (p < 0.01) and 75 +/- 8% (p < 0.01), respectively. The insulin-stimulated IRS-1 association with PI 3-kinase decreased by 81 +/- 6% in muscle (p < 0.01) and 79 +/- 11% (p < 0.01) in the liver during pregnancy. These data suggest that changes in the early steps of insulin signal transduction may have a role in the insulin resistance observed in pregnancy.

[Neonatal apnea after general anesthesia--effects of intraoperative hyperventilation and serum ionized Ca concentration]

The relationship between neonatal apnea following general anesthesia and serum ionized calcium (Ca2+) concentration was examined in 13 neonates who had received intraoperative hyperventilation. In all cases, preoperative serum Ca2+ concentration was within normal limits. The anesthesia was maintained by nitrous oxide and oxygen. At the end of anesthesia, the incidence of abnormal breathing such as apnea, periodic breathing or subcostal retraction and their activity were investigated. Five minutes after intravenous administration of 2% CaCl2 solution (16 mg.kg-1), the same parameters were compared with the values before CaCl2 administration. As we used only Ca2+ free solution for fluid therapy during operation, serum Ca2+ concentration decreased gradually under general anesthesia, but after CaCl2 administration, it increased and the incidence of abnormal breathing decreased. To determine the relationship between hyperventilation and the incidence of abnormal breathing, the data were analyzed by dividing the patients into two groups based on PaCO2 level, a lower PaCO2 group (intraoperative PaCO2 < 30 mmHg, n = 5) and a higher PaCO2 group (PaCO2 > or = 30 mmHg, n = 8). But there was no significant relationship between them. In conclusion, this study demonstrates that the Ca administration has a favorable effect on respiratory system and motor activity, but we cannot relate the incidence of postoperative abnormal breathing to the degree of hyperventilation.

[Two cases of tension pneumothorax caused by tracheal suction during the operation of pectus excavatum]

Rehbein's method is one of the surgical procedures for pediatric pectus excavatum, which constructs thorax by lifting and fixating the sternum using metal strut inserted into bone marrow of bilateral ribs. We experienced two pediatric cases of tension pneumothorax caused by tracheal suctioning during the operation by this method. The etiology of tension pneumothorax was thought to be as follows. A small pleural hole was made during separation of ribs from surrounding tissues and a large amount of air entered into the pleural space and check valve mechanism worked at the pleural hole when the lung was collapsed on tracheal suctioning. In anesthetic management of pectus excavatum by Rehbein's method, we should always be cautious of the possible occurrence of tension pneumothorax.

[Anesthetic management of a neonate with esophageal atresia with double tracheoesophageal fistulae]

We reported the anesthetic management of a 1-day-old female neonate (2,110 gm) with esophageal atresia combined with double tracheoesophageal fistulae, which is classified as Gross type D. Though Gross type C was suspected preoperatively, the proximal fistula was found coincidentally during the preparation of the upper pouch. Because, for one thing, the origin of the proximal fistula was close to the end of the upper pouch (1cm), and for another, the distance between the both fistulae was short (1cm). As for the proximal fistula, it was 2 mm in diameter, and it was easily sealed with the side of the endotracheal tube. No other respiratory managements were needed except frequent suctionings of copious intratracheal secretions. On the other hand, the distal fistula, 10 mm in diameter, caused hypercapnea due to hypoventilation before gastrostomy. It was so big that it is easily intubated. This type of tracheoesophageal fistula is extraordinarily rare and its proximal fistula is difficult to find before, during, and even after operation. The missing of the proximal fistula often provokes severe respiratory infections and furthermore, sepsis postoperatively. It is concluded that in all the cases of tracheoesophageal fistula, the existence of the proximal fistula should be considered without fail and managed accordingly. To diagnose correctly, the use of preoperative bronchofiberscopy is also recommended.

[Serum catecholamine concentrations and hemodynamics during operations on 23 children with neuroblastoma]

The purpose of the present report is to reveal the relation between hemodynamic changes and serum catecholamine concentrations during operation of 23 neuroblastoma patients. The patients were aged from 6 months to 7 years (mean 1.2 year), and 20 patients (86%) were under 1 year of age. All the patients were in early stage of tumor development because they were diagnosed as neuroblastoma mainly by mass screening test for VMA and HVA in urine utilizing HPLC. This urinary mass screening test for infants is performed routinely in Japan. Operative manipulation of tumor provoked the significant elevation of blood pressure, and the increasing tendency of heart rate and rectal temperature. The mean concentrations of three kinds of serum catecholamine, epinephrine, norepinephrine and dopamine, were all very high during manipulation of tumor. Especially, the norepinephrine concentration was 90.2 times higher than the preoperative value. The children who showed high blood pressure, over 70% of the control level, showed high urinary VMA and VMA/HVA ratio preoperatively and a high norepinephrine secretion during operation. We conclude that for the anesthetic management of neuroblastoma, it is necessary to control the elevation of blood pressure even in small children, especially in the patients who have showed high values of urinary VMA and VMA/HVA ratio preoperatively.