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Rainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum . In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout ( Oncorhynchus mykiss ) and searched for skin bacteria antagonistic to F. psychrophilum . By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947 T , and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon.

Rainbow trout (Oncorhynchus mykiss) is an important fish in global aquaculture. Various feed additives to suppress disease or reduce fish meal use have been studied. These manipulations influence the gut microbiome, which is considered to be linked to host health. However, a consensus remains to be established on the healthy gut microbiome composition. This study aimed to identify core genera in the gut of rainbow trout via a systematic review of 39 articles and determine candidate core species using long‐read amplicon sequencing targeting the full‐length 16S rRNA gene. Mycoplasma, Aeromonas, Clostridium, Deefgea, Streptococcus, Cetobacterium, Lactobacillus, Lactococcus, Methylobacterium, Corynebacterium, Shewanella and Staphylococcus were identified as core genera in the autochthonous gut microbiome of rainbow trout based on the systematic review. In addition, through long‐read amplicon sequencing, we identified candidate core species of the core genera of rainbow trout, such as Latilactobacillus sakei, Clostridium gasigeness, Deefgea piscis and Pseudomonas yamanorum. These findings may ultimately contribute to the development of manipulation technologies in aquaculture.

Non-methanotrophic bacteria such as methylotrophs often coexist with methane-oxidizing bacteria (methanotrophs) by cross-feeding on methane-derived carbon. Methanol has long been considered a major compound that mediates cross-feeding of methane-derived carbon. Despite the potential importance of cross-feeding in the global carbon cycle, only a few studies have actually explored metabolic responses of a bacteria when cross-feeding on a methanotroph. Recently, we isolated a novel facultative methylotroph, Methyloceanibacter caenitepidi Gela4, which grows syntrophically with the methanotroph, Methylocaldum marinum S8. To assess the potential metabolic pathways in M. caenitepidi Gela4 co-cultured with M. marinum S8, we conducted genomic analyses of the two strains, as well as RNA-Seq and chemical analyses of M. caenitepidi Gela4, both in pure culture with methanol and in co-culture with methanotrophs. Genes involved in the serine pathway were downregulated in M. caenitepidi Gela4 under co-culture conditions, and methanol was below the detection limit (< 310 nM) in both pure culture of M. marinum S8 and co-culture. In contrast, genes involved in the tricarboxylic acid cycle, as well as acetyl-CoA synthetase, were upregulated in M. caenitepidi Gela4 under co-culture conditions. Notably, a pure culture of M. marinum S8 produced acetate (< 16 μM) during growth. These results suggested that an organic compound other than methanol, possibly acetate, might be the major carbon source for M. caenitepidi Gela4 cross-fed by M. marinum S8. Co-culture of M. caenitepidi Gela4 and M. marinum S8 may represent a model system to further study methanol-independent cross-feeding from methanotrophs to non-methanotrophic bacteria.

[This corrects the article DOI: 10.1371/journal.pone.0213535.].

Deep subsurface formations (for example, high-temperature oil reservoirs) are candidate sites for carbon capture and storage technology. However, very little is known about how the subsurface microbial community would respond to an increase in CO 2 pressure resulting from carbon capture and storage. Here we construct microcosms mimicking reservoir conditions (55 °C, 5 MPa) using high-temperature oil reservoir samples. Methanogenesis occurs under both high and low CO 2 conditions in the microcosms. However, the increase in CO 2 pressure accelerates the rate of methanogenesis to more than twice than that under low CO 2 conditions. Isotope tracer and molecular analyses show that high CO 2 conditions invoke acetoclastic methanogenesis in place of syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis that typically occurs in this environment (low CO 2 conditions). Our results present a possibility of carbon capture and storage for enhanced microbial energy production in deep subsurface environments that can mitigate global warming and energy depletion. Deep subsurface formations are potential sites for carbon capture and storage but how subsurface microbial communities may respond to this is not clear. Here, Mayumi et al. construct microcosms and show that increasing CO 2 partial pressure via carbon capture and storage more than doubles the rate of methanogenesis.

The aquaculture industry is rapidly growing, yet sustainability remains a challenge. One crucial task is to reduce losses due to diseases. Monitoring fish health and detecting diseases early are key to establishing sustainable aquaculture. Using metagenomic and metabolomic analyses, we found that feces of ayu infected with Flavobacterium psychrophilum contain various specific biomarkers that increased 4 days post-challenge, at the earliest. Our findings are the first step in establishing a novel, non-invasive, and holistic monitoring method for fish diseases in aquaculture systems, especially in ayu, which is an important freshwater fish species in Asia, promoting a sustainable future.

Anaerobic ammonium oxidation (anammox) is a novel biological nitrogen removal process that oxidizes NH4+ to N2 with NO2− as an electron acceptor. The purpose of this study was to examine the potential activity and characteristics of anammox in a conventional swine wastewater treatment facility, which uses an activated sludge system consisting of three cascade aeration tanks equipped with ceramic support material. Anammox activity was estimated by a 15N tracer assay method and was detected in all the sludge and biofilm samples in each aeration tank. Biofilm taken from the third aeration tank, in which the dissolved oxygen concentration was 7.5 mg/L and the wastewater included a high concentration of NO3−, showed by far the highest anammox activity. A clone library analysis showed the existence of anammox bacteria closely related to ‘Candidatus Jettenia asiatica’ and ‘Ca. Brocadia caroliniensis’. The optimum conditions for anammox activity were a pH of 6.7–7.2, a temperature of 35 °C, a NO2− concentration of 10 mmol/L or less, and an NH4+ concentration of 32 mmol/L or less.

The Pleistocene Kimitsu aquifer was selected for examination of the relationship between groundwater age and chemical evolution of Ca(HCO 3 ) 2 -type groundwater. For the most part, the aquifer is confined and composed mainly of quartz and feldspar with a small amount of calcite. The groundwater ages calculated by 14 C were adjusted by using a carbon mass-balance method and corrected for effects of 14 C diffusion. Groundwater ages in the Kimitsu aquifer vary from modern (upgradient) to approximately 2,400 years at 4.4 km from the edge of the recharge area. The 14 C age was verified by groundwater velocity calculated from the hydraulic gradient and hydraulic conductivity. The confined groundwater evolved to Ca(HCO 3 ) 2 -type around 50 years after recharge and this has been maintained for more than 8,300 years due to low chemical reactivity, derived from equilibrium with calcite, kaolinite and Ca-montmorillonite. In addition, high pH prevents the dissolution of Fe and Mn. Consequently, the rate of increase in electrical conductivity ranges from 10 to 30 μS/cm per 1,000 years. On the other hand, leakage from the deep region, which is recognized from high Cl – levels, causes remarkable increases in CH 4 and HCO 3 – concentrations, resulting in an apparent sulfidic zone at 500-m depth in most downgradient regions.

Purpose Axitinib is a selective tyrosine kinase inhibitor of VEGF receptors, approved for advanced renal cell carcinoma (RCC). Associations between axitinib plasma exposure, genetic polymorphisms of ABC transporters and axitinib-induced toxicities have not been adequately explored. Methods Twenty RCC patients treated with axitinib were enrolled in this study. Blood samples were collected 0, 0.5, 1, 2, 4, and 6 h after administration of axitinib on day 1 and at steady state. Plasma concentrations of axitinib were analyzed by UPLC–MS/MS. The ABCG2 (421C>A) and ABCB1 (1236C>T, 2677G>T/A, 3435C>T) genetic polymorphisms were determined by real-time PCR. Results ABCB1 haplotype was associated with increased dose-adjusted area under the plasma concentration–time curve (AUC) of axitinib at steady state. The incidence of fatigue during therapy was associated with high AUC 0–6 of axitinib ( P  = 0.013). The treatment period without discontinuation or dose reduction due to adverse events in patients with high AUC 0–6 of axitinib was significantly shorter than for those with low AUC 0–6 ( P  = 0.024). No significant differences were found in the frequency of adverse events among the ABCG2 genotype and ABCB1 haplotype groups. Conclusions Our results have demonstrated that adverse events leading to discontinuation or dose reduction in axitinib were associated with increased axitinib plasma exposure, but not directly with genetic polymorphisms of ABC transporters. Therefore, measurement of steady state axitinib plasma concentrations may be useful in avoiding adverse events in axitinib therapy.

The Pleistocene Kimitsu aquifer was selected for examination of the relationship between groundwater age and chemical evolution of Ca(HCO3)^sub 2^-type groundwater. For the most part, the aquifer is confined and composed mainly of quartz and feldspar with a small amount of calcite. The groundwater ages calculated by ^sup 14^C were adjusted by using a carbon mass-balance method and corrected for effects of ^sup 14^C diffusion. Groundwater ages in the Kimitsu aquifer vary from modern (upgradient) to approximately 2,400 years at 4.4 km from the edge of the recharge area. The ^sup 14^C age was verified by groundwater velocity calculated from the hydraulic gradient and hydraulic conductivity. The confined groundwater evolved to Ca(HCO3)^sub 2^-type around 50 years after recharge and this has been maintained for more than 8,300 years due to low chemical reactivity, derived from equilibrium with calcite, kaolinite and Ca-montmorillonite. In addition, high pH prevents the dissolution of Fe and Mn. Consequently, the rate of increase in electrical conductivity ranges from 10 to 30 [mu]S/cm per 1,000 years. On the other hand, leakage from the deep region, which is recognized from high Cl^sup -^ levels, causes remarkable increases in CH4 and HCO3 ^sup -^ concentrations, resulting in an apparent sulfidic zone at 500-m depth in most downgradient regions.[PUBLICATION ABSTRACT]