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.

A storm-induced flood and associated nearshore dispersal of the river-derived suspended 137Cs

Accidental leakage of radionuclides from the Fukushima Nuclear Power Plant (FNPP1) took place in the aftermath of the catastrophic tsunamis associated with the Great East Japan Earthquake that occurred on March 11, 2011. Significant amount of radionuclides released into the atmosphere were reportedly transported and deposited on land located near FNPP1. The Niida River, Fukushima, Japan, has been recognized as a terrestrial source of highly contaminated suspended radiocesium adhering to sediment particles in the ocean through the river mouth as a result of hydrological processes. Remaining scientific questions include the oceanic dispersal and inventories of the sediments and suspended radiocesium in the ocean floor derived from the Niida River. Complementing limited in situ data, we developed a quadruple nested 3D ocean circulation and sediment transport model in an extremely high-resolution configuration to quantify the transport processes of the suspended radiocesium. Particularly, we investigated the storm and subsequent floods associated with Typhoon 201326 (Wipha) that passed off the Fukushima coast in October 2013, and subsequently promoted precipitation to a considerable extent and associated riverine freshwater discharge along with sediment outfluxes to the ocean. Using in situ bed sediment core data obtained from regions near the river mouth, we conducted a quantitative assessment of the accumulation and erosion of the sediments and explored the resultant suspended radiocesium distribution around the river mouth and nearshore areas along the Fukushima coast. We identified three major accumulative areas, near the river mouth within an area < 1 km, around the breakwaters in the north of the river mouth, and along the southern coastal area, while offshore and northward transports were minor. The present study clearly exhibits substantial retention of the land-derived radiocesium adsorbed to the sediments in the coastal areas, leading to possible long-term influences on the surrounding marine environment.

Multivariate Statistical and Multiproxy Constraints on Earthquake-Triggered Sediment Remobilization Processes in the Central Japan Trench

Understanding the impact of earthquakes on subaqueous environments is key for submarine paleoseismological investigations seeking to provide long-term records of past earthquakes. For this purpose, event deposits (e.g., turbidites) are, among others, identified and stratigraphically correlated over broad areas to test for synchronous occurrence of gravity flows. Hence, detailed spatiotemporal petrographic and geochemical fingerprints of such deposits are required to advance the knowledge about sediment source and the underlying remobilization processes induced by past earthquakes. In this study, we develop for the first time in paleoseismology a multivariate statistical approach using X-ray fluorescence core scanning, magnetic susceptibility, and wet bulk density data that allow to test, confirm, and enhance the previous visual and lithostratigraphic correlation across two isolated basins in the central Japan Trench. The statistical correlation is further confirmed by petrographic heavy grain analysis of the turbidites and additionally combined with our novel erosion model based on previously reported bulk organic carbon 14C dates. We find surficial sediment remobilization, a process whereby strong seismic shaking remobilizes the uppermost few centimeters of surficial slope sediment, to be a predominant remobilization process, which partly initiates deeper sediment remobilization downslope during strong earthquakes at the Japan Trench. These findings shed new light on source-to-sink transport processes in hadal trenches during earthquakes and help to assess the completeness of the turbidite paleoseismic record. Our results further suggest that shallow-buried tephra on the slope might significantly influence sediment remobilization and the geochemical and petrographic fingerprints of the resulting event deposits.

Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis

We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, alpha-helix, beta-sheet and beta-turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS- and GC-NSF(a)-0th order structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages.

Transfer of heme oxygenase 1 cDNA by a replication-deficient adenovirus enhances interleukin 10 production from alveolar macrophages that attenuates lipopolysaccharide-induced acute lung injury in mice

By using a direct, intratracheal inoculation of an adenovirus encoding heme oxygenase 1 (Ad.HO-1), model gene therapy for acute lung injury induced by inhaled pathogen was performed. Data demonstrated that Ad.HO-1 administration is as effective as the pharmacologic upregulation of the endogenous HO-1 gene expression by hemin to attenuate neutrophilic inflammations of the lung after aerosolized lipopolysaccharide (LPS) exposure. Interestingly, immunohistochemical analysis revealed that the HO-1 gene was transferred not only to the airway epithelium, but to the alveolar macrophages (AMs). Moreover, overexpression of exogenous HO-1 in the macrophages provided a high level of endogenous interleukin 10 (IL-10) production from the macrophages, and additional experiments using IL-10 knockout mice demonstrated that the increase in IL-10 in the macrophages was critical for the resolution of neutrophilic migration in the lung after LPS exposure. These results suggest that AMs not only are barriers for efficient gene transfer to the respiratory epithelium, but also represent logical targets for Ad-mediated, direct, in vivo gene therapy strategies for inflammatory disorders in humans.

Longitudinal study of the mental health of caregivers caring for elderly patients with dementia: effect of institutional placement on mental health

One hundred and three family caregivers of relatives with dementia were longitudinally surveyed to examine the course of caregivers' mental health after the relatives had been placed in full-time care facilities. Mental health was assessed twice, with a 6-month interval, using the Japanese version of the 60-item General Health Questionnaire. The degree of social dysfunction was significantly reduced within 6 months after placement, while the other indicators of mental health (e.g. anxiety-insomnia, depression, somatic symptom and psychiatric morbidity) were not reduced within this term. However, anxiety-insomnia and psychiatric morbidity were significantly reduced more than 6 months after placement. Analyses by caregivers' lineal relations to the relatives indicated that only daughters-in-law showed a significant decrease in anxiety-insomnia and a marginal reduction in psychiatric morbidity. This study suggests that caregivers' social dysfunction was more greatly reduced than anxiety-insomnia and psychiatric morbidity within a relatively short term after placement, and that its effects on mental health might vary with the lineal relations.

[Pleural B cell lymphoma presenting as paraplegia]

A 54-year-old man felt pain on the right side of his chest. Two months later, paraplegia developed. A chest CT scan revealed a pleural effusion and a mass lesion along the right parietal pleura. The lesion extended directly into the adjacent part of the spinal canal and compressed the spinal cord. Cytologic examination of the pleural effusion revealed atypical lymphoid cells, and examination of a transcutaneous biopsy specimen showed monotonous atypical B lymphocytes. The diagnosis was pleural malignant lymphoma. Chemotherapy induced a partial remission, but 14 months after the first examination he died of central nervous system involvement. Pleural lymphoma can directly compress the spinal cord and cause paraplegia. Early diagnosis and therapy greatly affect the outcome in patients with spinal cord compression.

[Primary pulmonary lymphoma diagnosed from monoclonality of lymphocytes in a transbronchial biopsy specimen]

A 57-year-old man was found on a routine chest X-ray examination to have three infiltrative shadows: two in the right lung field and one in the left. Examination of a transbronchial biopsy specimen revealed infiltration of many small lymphocytes under the bronchial mucosa. In situ hybridization showed that they were monoclonal, and primary pulmonary lymphoma was diagnosed. The patient also had liver cirrhosis, diabetes mellitus, and hypertension. He was treated with a combination of pirarubein, cyclo-phosphamide, vindesine, prednisolone, and etoposide, but the tumors did not shrink. Therefore, as of the time of this writing he was being given only etoposide.

[Eosinophilic pneumonia presenting as a mass shadow]

A 35-year-old man underwent routine chest roentgenography and a mass shadow was seen in the left lung field. Examination of a transbronchial lung biopsy specimen revealed that many eosinophils had infiltrated under the bronchial mucosa and into the alveolar septum. The total serum IgE concentration was high, and skin tests with Aspergillus antigen and serum precipitating antibodies against Aspergillus were positive. The mass lesion disappeared without any therapy, and a cystic lesion remained. Mediators released from eosinophils were thought to have damaged the lung tissue. We should have administrated corticosteroids as soon as possible.

A possible origin of newly-born bacterial genes: significance of GC-rich nonstop frame on antisense strand

Base compositions were examined at every position in codons of more than 50 genes from taxonomically different bacteria and of the corresponding antisense sequences on the bacterial genes. We propose that the nonstop frame on antisense strand [NSF(a)] of GC-rich bacterial genes is the most promising sequence for newly-born genes. Reasons are: (i) NSF(a) frequently appears on the antisense strand of GC-rich bacterial genes; (ii) base compositions at three positions in the codon are nearly symmetrical between the gene having around 55% GC content and the corresponding NSF(a); (iii) amino acid compositions of actual proteins are also similar to those of hypothetical proteins from the GC-rich NSF(a); and (iv) proteins from NSF(a) of 60% or more GC content are flexible enough to adapt to various molecules encountered as novel substrates, due to the high glycine content. To support our proposition, using a computer we generated hypothetical antisense sequences with the same base compositions as of NSF(a) at each base position in the codon, and examined properties of resulting proteins encoded by the imaginary genes. It was confirmed that NSF(a) of GC-rich gene carrying about 60% GC content is competent enough for a newly-born gene.

[A case of cervico-mediastinal tuberculous lymphadenitis]

A 27-year-old female presented to our hospital because of anterior chest pain and left cervical tumor. Her chest X-ray film showed bilateral swelling of the superior mediastinum, which was composed of multiple mediastinal masses with obliteration of adjacent mediastinal fat on chest CT film. A specimen obtained from a left cervical lymph node histologically showed granuloma formation with central caseous necrosis, and the diagnosis of cervicomediastinal tuberculous lymphadenitis was therefore made. Both cervical tumor and mediastinal masses decreased in size following antituberculous chemotherapy. Mediastinal tuberculous lymphadenitis in young adults is rare. It is difficult to differentiate this condition from other mediastinal tumors, although its CT findings are characteristic.

Guanylate kinase of Escherichia coli K-12

We have identified the gene gmk, in the same operon as rpoZ, spoT, and recG at about 82 minutes on the Escherichia coli chromosome. The gmk (GMP kinase) gene encodes a peptide of 23,592 Da, possessing extensive similarity to the amino acid sequence of guanylate kinase from yeast. To confirm that gmk truly encodes guanylate kinase and to explore some of its enzymatic features, we have overproduced the product of gmk and purified it to homogeneity. Unlike guanylate kinases purified from eukaryotic sources, E. coli guanylate kinase is multimeric, and ionic conditions dictate its protomeric state; under low ionic conditions it appears to be a tetramer while under high ionic conditions it is a dimer. Kinetic analysis reveals that guanylate kinase, again, unlike eukaryotic guanylate kinases, binds GMP cooperatively and that the observed cooperatively changes with ionic strength. These results indicate that, despite extensive sequence similarity to its eukaryotic counterparts, E. coli guanylate kinase is structurally and enzymatically different.

Unusually biased nucleotide sequences on sense strands of Flavobacterium sp. genes produce nonstop frames on the corresponding antisense strands

From investigation of eight Flavobacterium sp. genes encoding enzyme proteins, it was found that six genes had nonstop frames (NSFs) on the antisense strands, and base sequences of the genes are mainly composed of repeating triplet sequence(s), 5'-GNC-3' (where G and C are guanine and cytosine, and N is either of the four bases), in the reading frames. Thus, we concluded that the biased nucleotide sequences on the sense strands produce NSFs on the corresponding antisense strands. Furthermore, from the precise alignments of both nucleotide and amino acid sequences of two related Flavobacterium sp. genes, nyIB and nyIB', it was found that base replacements might have occurred symmetrically in the codons. That is, transversions between G and C were observed at high frequencies at the first and third positions of codons, but not at the second positions. At the first position, AG base transitions were observed much more than similar CT transitions, whereas CT transitions were found at the third positions at a relatively high frequency. These suggest that symmetrical base replacements in codons might be the main contribution to evolution in Flavobacterium sp. genes.

Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations

It was known previously that 1) the relA gene of Escherichia coli encodes an enzyme capable of guanosine 3',5'-bispyrophosphate (ppGpp) synthesis, 2) an uncharacterized source of ppGpp synthesis exists in relA null strains, and 3) cellular degradation of ppGpp is mainly due to a manganese-dependent ppGpp 3'-pyrophosphohydrolase encoded by the spoT gene. Here, the effects of spoT gene insertions and deletions are compared with analogous alterations in neighboring genes in the spo operon and found to be lethal in relA+ strains as well as slower growing in relAl backgrounds than delta relA hosts. Cells with null alleles in both the relA and spoT genes are found no longer to accumulate ppGpp after glucose exhaustion or after chelation of manganese ions by picolinic acid addition; the inability to form ppGpp is reversed by a minimal spoT gene on a multicopy plasmid. Strains apparently lacking ppGpp show a complex phenotype including auxotrophy for several amino acids and morphological alterations. We propose that the SpoT protein can either catalyze or control the alternative pathway of ppGpp synthesis in addition to its known role as a (p)ppGpp 3'-pyrophosphohydrolase. We favor the possibility that the SpoT protein is a bifunctional enzyme capable of catalyzing either ppGpp synthesis or degradation.

Characterization of the spoT gene of Escherichia coli

The Escherichia coli spoT gene encodes a guanosine-3',5'-bispyrophosphate (ppGpp) 3'-pyrophosphohydrolase known to be responsible for cellular (ppGpp) degradation. The DNA sequence of the spoT region is presented. The spoT gene is deduced to be 702 codons long, with a probable UUG initiation codon, and a deduced mass of 79,342 daltons. Two spoT mutations (spoT202 and spoT203) have been localized to an open reading frame by complementation of function as well as by genetic marker rescue. The ability to overexpress the spoT gene is limited, but enough ppGppase activity can be made to reverse ppGpp accumulation during the stringent response to amino acid starvation. The spoT gene is located within a larger spo operon and is flanked by two smaller genes. The first gene in the operon encodes omega, a protein that copurifies with RNA polymerase (Gentry, D. R., and Burgess, R. R. (1986) Gene (Amst.) 48, 33-40). The spoT gene is the second gene in the operon; it is followed by a third open reading frame deduced to encode a protein with a mass of 25,343 daltons. Insertion of a kanamycin resistance gene in the omega gene reduces spoT gene expression as judged by lowered ppGppase activity, relA-dependent reduction of growth rate, and abolition of spoT mutant complementation activity. These effects are reversed by expression of the spoT gene, but not the omega gene, in trans. Transcription of the spo operon occurs in a clockwise direction on the E. coli chromosome and is probably directed by at least two promoters.

Induction of stringent response by streptomycin in Bacillus subtilis cells

A stringent response was induced in Bacillus subtilis vegetative cells by streptomycin. This was confirmed as follows: In B. subtilis stringent cells (BR16S), stable RNA synthesis was repressed, and pppGpp and ppGpp were transiently synthesized in the presence of required amino acids and streptomycin. However, these phenomena were not observed in the isogenic relaxed strain (BR16R) under the same conditions. On the other hand, tetracyclines did not induce the response, and, moreover, the stringent response to streptomycin upon pretreatment of the stringent cells with the antibiotics was released.

Accumulation of relA gene-independent ppGpp in Bacillus subtilis vegetative cells upon temperature shift-down

Both Bacillus subtilis BR16S (rel+) and BR16R (relA-) cells accumulated ppGpp after a temperature shift-down from 37 to 0 degree C. This indicates that a ppGpp accumulation system is present in B. subtilis vegetative cells, which is induced upon cold-shock treatment and is mediated by a relA gene-independent product.

Induction of Bacillus subtilis sporulation by decoyinine and the concomitant disappearance of ppGpp in vegetative cells

Sporulation of Bacillus subtilis, growing exponentially in the presence of rapidly metabolizable nutrients, was induced by addition of decoyinine (an antibiotic inhibitor of GMP synthesis), and intracellular amounts of ppGpp were determined after 2 M formic acid extraction by polyethyleneimine (PEI)-cellulose thin-layer chromatography. Consequently, it was found that the ppGpp in vegetative cells abruptly disappeared after the addition of decoyinine. This indicates that the disappearance of ppGpp is closely correlated to the initiation of B. subtilis sporulation.

Disappearance of guanosine 5'-diphosphate 3'-diphosphate in Bacillus subtilis vegetative cells upon carbon source deprivation

Bacillus subtilis was grown in a nutrient medium, mNSMP, and a synthetic medium, mS6(C), in which spore formation was initiated after vegetative growth and exhaustion of carbon source or glucose. The amounts of intracellular phosphorylated compounds were analyzed at intervals by 2 M formic acid extraction and polyethyleneimine (PEI)-cellulose thin-layer chromatography followed by autoradiography. A hyperphosphorylated nucleotide, guanosine 5'-diphosphate 3'-diphosphate (ppGpp), was accumulated in cells during vegetative growth in both mNSMP and mS6(C), and then the nucleotide was degraded upon initiation of sporulation in both cases. Furthermore, after the nucleotide had disappeared in cells cultivated in mS6(C) upon exhaustion of the carbon source, it could be reformed in the sporulating cells by addition of glucose to the medium. These results suggest that the ppGpp in vegetative cells may function in the regulation of B. subtilis sporulation.

Presence of guanosine 5'-diphosphate 3'-diphosphate in Bacillus subtilis vegetative cells

Extracts of Bacillus subtilis vegetative cells with 2 M formic acid contained a large amount of a hyperphosphorylated nucleotide ("spot 4" nucleotide). The compound always comigrated with authentic guanosine 5'-diphosphate 3'-diphosphate (ppGpp) on two-dimensional polyethyleneimine (PEI)-cellulose thin-layer chromatography performed with three different solvent systems. Furthermore, all dephosphorylated 32P-labeled derivatives from the "spot 4" nucleotide comigrated on a one-dimensional PEI-cellulose plate with those from authentic ppGpp present in the same reaction mixture, when the compounds were hydrolyzed with snake venom phosphodiesterase or alkali. The level of the "spot 4" nucleotide (ppGpp) in the cell extracts was 0.14 nmol P/A660, corresponding to about one-third of the guanosine 5'-triphosphate (GTP) level and about 10% of the adenosine 5'-triphosphate (ATP) level. These results indicate that a "magic spot" nucleotide, ppGpp, is present at a high level in B. subtilis cells vegetatively growing in mNSMP.

Properties of unprimed poly(A)-poly(U) synthesis by Caulobacter crescentus RNA polymerase

Some properties of unprimed poly(A)-poly(U) synthesis by DNA-dependent RNA polymerase from Caulobacter crescentus were examined. The reaction required ATP and UTP as substrates and manganese as a divalent cation. Rifampicin completely inhibited the reaction at a concentration of 1 micron/ml, and the enzyme catalyzed the polymer synthesis well regardless of the presence of GTP, CTP or both. The chain length of the poly(A)-poly(U) synthesized was about one hundred base pairs, as estimated from a sedimentation velocity and the molar ratio of [3H]AMP to [gamma-32P]ATP incorporated into the poly(A)-poly(U). The reaction was dependent on the square of the enzyme concentration and the enzyme dimers formed complexes with poly(A)-poly(U) during the reaction.

Isolation and chemcial properties of A-protein from filamentous phage Fd

A-Protein was isolated from a purified male-specific filamentous phage fd particle. A-Protein has a molecular weight of approximately 60,000 daltons, as estimated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The amino-terminal residue was glycine as determined by the dansylation technique. Amino acid analysis showed that histidine, arginine, and cysteine, which are not contained in B-protein, are present in A-protein.