Population genetic structure of the deep‐sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Evolutionary Applications 11 (2018): 1915-1930, doi:10.1111/eva.12696.Studying population genetics of deep‐sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep‐sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis‐based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6, cox1, and nad4) and 6,398 genomewide single nucleotide polymorphisms (SNPs) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea (SCS) and three individuals in Sagami Bay (SB) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co‐occurrence of two cryptic semi‐isolated lineages. When using 125 outlier SNPs identified focusing on individuals in the Okinawa Trough (OT) and SB, a minor genetic subdivision was detected between individuals in the southern OT (S‐OT) and those in the middle OT (M‐OT) and SB. This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S‐OT and the M‐OT. Introgression analyses based on these outlier SNPs revealed that Hatoma Knoll in the S‐OT represents a possible contact zone for individuals in the OT‐SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai‐yon Yonaguni Knoll in the S‐OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific.General Research Fund Grant Number: HKBU12302917; Hong Kong Baptist University Grant Number: 15‐1012‐P0

Nutritional sources of meio- and macrofauna at hydrothermal vents and adjacent areas: Natural-abundance radiocarbon and stable isotope analyses

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nomaki, H., Uejima, Y., Ogawa, N. O., Yamane, M., Watanabe, H. K., Senokuchi, R., Bernhard, J. M., Kitahashi, T., Miyairi, Y., Yokoyama, Y., Ohkouchi, N., & Shimanaga, M. Nutritional sources of meio- and macrofauna at hydrothermal vents and adjacent areas: Natural-abundance radiocarbon and stable isotope analyses. Marine Ecology Progress Series, 622, (2019): 49-65, doi:10.3354/meps13053.Deep-sea hydrothermal vents host unique marine ecosystems that rely on organic matter produced by chemoautotrophic microbes together with phytodetritus. Although meiofauna can be abundant at such vents, the small size of meiofauna limits studies on nutritional sources. Here we investigated dietary sources of meio- and macrofauna at hydrothermal vent fields in the western North Pacific using stable carbon and nitrogen isotope ratios (δ13C, δ15N) and natural-abundance radiocarbon (Δ14C). Bacterial mats and Paralvinella spp. (polychaetes) collected from hydrothermal vent chimneys were enriched in 13C (up to -10‰) and depleted in 14C (-700 to -580‰). The δ13C and Δ14C values of dirivultid copepods, endemic to hydrothermal vent chimneys, were -11‰ and -661‰, respectively, and were similar to the values in the bacterial mats and Paralvinella spp. but distinct from those of nearby non-vent sediments (δ13C: ~-24‰) and water-column plankton (Δ14C: ~40‰). In contrast, δ13C values of nematodes from vent chimneys were similar to those of non-vent sites (ca. -25‰). Results suggest that dirivultids relied on vent chimney bacterial mats as their nutritional source, whereas vent nematodes did not obtain significant nutrient amounts from the chemolithoautotrophic microbes. The Δ14C values of Neoverruca intermedia (vent barnacle) suggest they gain nutrition from chemoautotrophic microbes, but the source of inorganic carbon was diluted with bottom water much more than those of the Paralvinella habitat, reflecting Neoverruca’s more distant distribution from active venting. The combination of stable and radioisotope analyses on hydrothermal vent organisms provides valuable information on their nutritional sources and, hence, their adaptive ecology to chemosynthesis-based ecosystems.We are grateful to the crews and scientists of the R/V ‘Natsushima’ and the ROV ‘Hyper-Dolphin’ of the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) during the NT12-10, NT13-09 and NT14-06 cruises, and the R/V ‘Kaimei’ and the KM-ROV of JAMSTEC during the KM-ROV training cruise. We thank Yuki Iwadate for her help on sample preparations and 2 anonymous reviewers and the editor, who provided helpful comments on an earlier version of this manuscript. This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Scientific Research C 26440246 to M.S.), the Japan Society for the Promotion of Science (Invitational fellowships for research in Japan, S14032 to J.M.B.), the WHOI Robert W. Morse Chair for Excellence in Oceanography, and The Investment in Science Fund at WHOI

Transcriptional Characteristics and Differences in Arabidopsis Stigmatic Papilla Cells Pre- and Post-Pollination

Pollination is an important early step in sexual plant reproduction. In Arabidopsis thaliana, sequential pollination events, from pollen adhesion onto the stigma surface to pollen tube germination and elongation, occur on the stigmatic papilla cells. Following successful completion of these events, the pollen tube penetrates the stigma and finally fertilizes a female gametophyte. The pollination events are thought to be initiated and regulated by interactions between papilla cells and pollen. Here, we report the characterization of gene expression profiles of unpollinated (UP), compatible pollinated (CP) and incompatible pollinated (IP) papilla cells in A. thaliana. Based on cell type-specific transcriptome analysis from a combination of laser microdissection and RNA sequencing, 15,475, 17,360 and 16,918 genes were identified as expressed in UP, CP and IP papilla cells, respectively, and, of these, 14,392 genes were present in all three data sets. Differentially expressed gene (DEG) analyses identified 147 and 71 genes up-regulated in CP and IP papilla cells, respectively, and 115 and 46 genes down-regulated. Gene Ontology and metabolic pathway analyses revealed that papilla cells play an active role as the female reproductive component in pollination, particularly in information exchange, signal transduction, internal physiological changes and external morphological modification. This study provides fundamental information on the molecular mechanisms involved in pollination in papilla cells, furthering our understanding of the reproductive role of papilla cell

Cell Type-Specific Transcriptome of Brassicaceae Stigmatic Papilla Cells From a Combination of Laser Microdissection and RNA Sequencing

Pollination is an early and critical step in plant reproduction, leading to successful fertilization. It consists of many sequential processes, including adhesion of pollen grains onto the surface of stigmatic papilla cells, foot formation to strengthen pollen-stigma interaction, pollen hydration and germination, and pollen tube elongation and penetration. We have focused on an examination of the expressed genes in papilla cells, to increase understanding of the molecular systems of pollination. From three representative species of Brassicaceae (Arabidopsis thaliana, A. halleri and Brassica rapa), stigmatic papilla cells were isolated precisely by laser microdissection, and cell type-specific gene expression in papilla cells was determined by RNA sequencing. As a result, 17,240, 19,260 and 21,026 unigenes were defined in papilla cells of A. thaliana, A. halleri and B. rapa, respectively, and, among these, 12,311 genes were common to all three species. Among the17,240 genes predicted in A. thaliana, one-third were papilla specific while approximately half of the genes were detected in all tissues examined. Bioinformatics analysis revealed that genes related to a wide range of reproduction and development functions are expressed in papilla cells, particularly metabolism, transcription and membrane-mediated information exchange. These results reflect the conserved features of general cellular function and also the specific reproductive role of papilla cells, highlighting a complex cellular system regulated by a diverse range of molecules in these cells. This study provides fundamental biological knowledge to dissect the molecular mechanisms of pollination in papilla cells and will shed light on our understanding of plant reproduction mechanism

Exploring the ecology of deep-sea hydrothermal vents in a metacommunity framework

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 49, doi:10.3389/fmars.2018.00049.Species inhabiting deep-sea hydrothermal vents are strongly influenced by the geological setting, as it provides the chemical-rich fluids supporting the food web, creates the patchwork of seafloor habitat, and generates catastrophic disturbances that can eradicate entire communities. The patches of vent habitat host a network of communities (a metacommunity) connected by dispersal of planktonic larvae. The dynamics of the metacommunity are influenced not only by birth rates, death rates and interactions of populations at the local site, but also by regional influences on dispersal from different sites. The connections to other communities provide a mechanism for dynamics at a local site to affect features of the regional biota. In this paper, we explore the challenges and potential benefits of applying metacommunity theory to vent communities, with a particular focus on effects of disturbance. We synthesize field observations to inform models and identify data gaps that need to be addressed to answer key questions including: (1) what is the influence of the magnitude and rate of disturbance on ecological attributes, such as time to extinction or resilience in a metacommunity; (2) what interactions between local and regional processes control species diversity, and (3) which communities are “hot spots” of key ecological significance. We conclude by assessing our ability to evaluate resilience of vent metacommunities to human disturbance (e.g., deep-sea mining). Although the resilience of a few highly disturbed vent systems in the eastern Pacific has been quantified, these values cannot be generalized to remote locales in the western Pacific or mid Atlantic where disturbance rates are different and information on local controls is missing.LM was supported by NSF OCE 1356738 and DEB 1558904. SB was supported by the NSF DEB 1558904 and the Investment in Science Fund at Woods Hole Oceanographic Institution. MB was supported by the Austrian Science Fund grants P20190-B17 and P16774-B03. LL was supported by NSF OCE 1634172 and the JM Kaplan Fund. MN was supported by NSF DEB 1558904. Y-JW was supported by a Korean Institute of Ocean Science and Technology (KIOST) grant PM60210

Deoxymugineic acid increases Zn translocation in Zn-deficient rice plants

Deoxymugineic acid (DMA) is a member of the mugineic acid family phytosiderophores (MAs), which are natural metal chelators produced by graminaceous plants. Rice secretes DMA in response to Fe deficiency to take up Fe in the form of Fe(III)–MAs complex. In contrast with barley, the roots of which secrete MAs in response to Zn deficiency, the amount of DMA secreted by rice roots was slightly decreased under conditions of low Zn supply. There was a concomitant increase in endogenous DMA in rice shoots, suggesting that DMA plays a role in the translocation of Zn within Zn-deficient rice plants. The expression of OsNAS1 and OsNAS2 was not increased in Zn-deficient roots but that of OsNAS3 was increased in Zn-deficient roots and shoots. The expression of OsNAAT1 was also increased in Zn-deficient roots and dramatically increased in shoots; correspondingly, HPLC analysis was unable to detect nicotianamine in Zn-deficient shoots. The expression of OsDMAS1 was increased in Zn-deficient shoots. Analyses using the positron-emitting tracer imaging system (PETIS) showed that Zn-deficient rice roots absorbed less 62Zn-DMA than 62Zn2+. Importantly, supply of 62Zn-DMA rather than 62Zn2+ increased the translocation of 62Zn into the leaves of Zn-deficient plants. This was especially evident in the discrimination center (DC). These results suggest that DMA in Zn-deficient rice plants has an important role in the distribution of Zn within the plant rather than in the absorption of Zn from the soil

Development of a mugineic acid family phytosiderophore analog as an iron fertilizer

Iron (Fe) is an essential nutrient, but is poorly bioavailable because of its low solubility in alkaline soils; this leads to reduced agricultural productivity. To overcome this problem, we first showed that the soil application of synthetic 2′-deoxymugineic acid, a natural phytosiderophore from the Poaceae, can recover Fe deficiency in rice grown in calcareous soil. However, the high cost and poor stability of synthetic 2′-deoxymugineic acid preclude its agricultural use. In this work, we develop a more stable and less expensive analog, proline-2′-deoxymugineic acid, and demonstrate its practical synthesis and transport of its Fe-chelated form across the plasma membrane by Fe(III)•2’-deoxymugineic acid transporters. Possibility of its use as an iron fertilizer on alkaline soils is supported by promotion of rice growth in a calcareous soil by soil application of metal free proline-2’-deoxymugineic acid

Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors

AK2 is an adenylate phosphotransferase that localizes at the intermembrane spaces of the mitochondria, and its mutations cause a severe combined immunodeficiency with neutrophil maturation arrest named reticular dysgenesis (RD). Although the dysfunction of hematopoietic stem cells (HSCs) has been implicated, earlier developmental events that affect the fate of HSCs and/or hematopoietic progenitors have not been reported. Here, we used RD-patient-derived induced pluripotent stem cells (iPSCs) as a model of AK2-deficient human cells. Hematopoietic differentiation from RD-iPSCs was profoundly impaired. RD-iPSC-derived hemoangiogenic progenitor cells (HAPCs) showed decreased ATP distribution in the nucleus and altered global transcriptional profiles. Thus, AK2 has a stage-specific role in maintaining the ATP supply to the nucleus during hematopoietic differentiation, which affects the transcriptional profiles necessary for controlling the fate of multipotential HAPCs. Our data suggest that maintaining the appropriate energy level of each organelle by the intracellular redistribution of ATP is important for controlling the fate of progenitor cells

52Fe Translocation in Barley as Monitored by a Positron-Emitting Tracer Imaging System (PETIS): Evidence for the Direct Translocation of Fe from Roots to Young Leaves via Phloem

The real-time translocation of iron (Fe) in barley (Hordeum vulgare L. cv. Ehimehadaka no. 1) was visualized using the positron-emitting tracer 52Fe and a positron-emitting tracer imaging system (PETIS). PETIS allowed us to monitor Fe translocation in barley non-destructively under various conditions. In all cases, 52Fe first accumulated at the basal part of the shoot, suggesting that this region may play an important role in Fe distribution in graminaceous plants. Fe-deficient barley showed greater translocation of 52Fe from roots to shoots than did Fe-sufficient barley, demonstrating that Fe deficiency causes enhanced 52Fe uptake and translocation to shoots. In the dark, translocation of 52Fe to the youngest leaf was equivalent to or higher than that under the light condition, while the translocation of 52Fe to the older leaves was decreased, in both Fe-deficient and Fe-sufficient barley. This suggests the possibility that the mechanism and/or pathway of Fe translocation to the youngest leaf may be different from that to the older leaves. When phloem transport in the leaf was blocked by steam treatment, 52Fe translocation from the roots to older leaves was not affected, while 52Fe translocation to the youngest leaf was reduced, indicating that Fe is translocated to the youngest leaf via phloem in addition to xylem. We propose a novel model in which root-absorbed Fe is translocated from the basal part of the shoots and/or roots to the youngest leaf via phloem in graminaceous plants