skip to main content

Search for: All records

Creators/Authors contains: "Saito, Mak"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Abstract

    The colony-forming cyanobacteriaTrichodesmiumspp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describeTrichodesmiumpangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% completeTrichodesmiummetagenome-assembled genomes from hand-picked,Trichodesmiumcolonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2fixing clades ofTrichodesmiumacross the transect, withT. thiebautiidominating the colony-specific reads. Pangenomic analyses showed that allT. thiebautiiMAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in allT. erythraeumgenomes, vertically inherited byT. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limitedT. erythraeumis expected to be a ‘winner’ of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared toT. thiebautii, could put this outcome in question. Thus, the clear demarcation ofT. thiebautiimaintaining CRISPR-Cas systems, whileT. erythraeumdoes not, identifiesTrichodesmiumas an ecologically importantmore »CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmiuminteractions.

    « less
  2. Free, publicly-accessible full text available October 1, 2023
  3. Abstract Dissolved organic phosphorus (DOP) concentration distributions in the global surface ocean inform our understanding of marine biogeochemical processes such as nitrogen fixation and primary production. The spatial distribution of DOP concentrations in the surface ocean reflect production by primary producers and consumption as an organic nutrient by phytoplankton including diazotrophs and other microbes, as well as other loss processes such as photolysis. Compared to dissolved organic carbon and nitrogen, however, relatively few marine DOP concentration measurements have been made, largely due to the lack of automated analysis techniques. Here we present a database of marine DOP concentration measurements (DOPv2021) that includes new (n = 730) and previously published (n = 3140) observations made over the last ~30 years (1990–2021), including 1751 observations in the upper 50 m. This dataset encompasses observations from all major ocean basins including the poorly represented Indian, South Pacific, and Southern Oceans and provides insight into spatial distributions of DOP in the ocean. It is also valuable for researchers who work on marine primary production and nitrogen fixation.
    Free, publicly-accessible full text available December 1, 2023
  4. Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gasesmore »like CO, CO 2 , NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.« less
    Free, publicly-accessible full text available September 13, 2023
  5. Abstract

    Biological dinitrogen fixation is the major source of new nitrogen to marine systems and thus essential to the ocean’s biological pump. Constraining the distribution and global rate of dinitrogen fixation has proven challenging owing largely to uncertainty surrounding the controls thereon. Existing South Atlantic dinitrogen fixation rate estimates vary five-fold, with models attributing most dinitrogen fixation to the western basin. From hydrographic properties and nitrate isotope ratios, we show that the Angola Gyre in the eastern tropical South Atlantic supports the fixation of 1.4–5.4 Tg N.a−1, 28-108% of the existing (highly uncertain) estimates for the basin. Our observations contradict model diagnoses, revealing a substantial input of newly-fixed nitrogen to the tropical eastern basin and no dinitrogen fixation west of 7.5˚W. We propose that dinitrogen fixation in the South Atlantic occurs in hotspots controlled by the overlapping biogeography of excess phosphorus relative to nitrogen and bioavailable iron from margin sediments. Similar conditions may promote dinitrogen fixation in analogous ocean regions. Our analysis suggests that local iron availability causes the phosphorus-driven coupling of oceanic dinitrogen fixation to nitrogen loss to vary on a regional basis.

  6. Abstract. Over the past decade, the GEOTRACES and wider trace metalgeochemical community has made substantial contributions towardsconstraining the marine cobalt (Co) cycle and its major biogeochemicalprocesses. However, few Co speciation studies have been conducted in theNorth and equatorial Pacific Ocean, a vast portion of the world's oceans byvolume and an important end-member of deep thermohaline circulation.Dissolved Co (dCo) samples, including total dissolved and labile Co, weremeasured at-sea during the GEOTRACES Pacific Meridional Transect (GP15) expedition along the 152∘ W longitudinal from 56∘ N to20∘ S. Along this transect, upper-ocean dCo (σ0<26) was linearly correlated with dissolved phosphate (slope = 82±3, µmol : mol) due to phytoplankton uptake and remineralization.As depth increased, dCo concentrations became increasingly decoupled fromphosphate concentrations due to co-scavenging with manganese oxide particlesin the mesopelagic. The transect revealed an organically bound coastalsource of dCo to the Alaskan Stream associated with low-salinity waters. Anintermediate-depth hydrothermal flux of dCo was observed off the Hawaiiancoast at the Loihi Seamount, and the elevated dCo was correlated withpotential xs3He at and above the vent site; however, the Loihi Seamountlikely did not represent a major source of Co to the Pacific basin. Elevatedconcentrations of dCo within oxygen minimum zones (OMZs) in the equatorialNorth and South Pacific were consistent with the suppressionmore »of oxidativescavenging, and we estimate that future deoxygenation could increase the OMZdCo inventory by 18 % to 36 % over the next century. In Pacific Deep Water(PDW), a fraction of elevated ligand-bound dCo appeared protected fromscavenging by the high biogenic particle flux in the North Pacific basin.This finding is counter to previous expectations of low dCo concentrationsin the deep Pacific due to scavenging over thermohaline circulation.Compared to a Co global biogeochemical model, the observed transectdisplayed more extreme inventories and fluxes of dCo than predicted by themodel, suggesting a highly dynamic Pacific Co cycle.« less
  7. Abstract Pseudoalteromonas (BB2-AT2) is a ubiquitous marine heterotroph, often associated with labile organic carbon sources in the ocean (e.g. phytoplankton blooms and sinking particles). Heterotrophs hydrolyze exported photosynthetic materials, components of the biological carbon pump, with the use of diverse metalloenzymes containing zinc (Zn), manganese (Mn), cobalt (Co), and nickel (Ni). Studies on the metal requirements and cytosolic utilization of metals for marine heterotrophs are scarce, despite their relevance to global carbon cycling. Here, we characterized the Zn, Mn, Co, and Ni metallome of BB2-AT2. We found that the Zn metallome is complex and cytosolic Zn is associated with numerous proteins for transcription (47.2% of the metallome, obtained from singular value decomposition of the metalloproteomic data), translation (33.5%), proteolysis (12.8%), and alkaline phosphatase activity (6.4%). Numerous proteolytic enzymes also appear to be putatively associated with Mn, and to a lesser extent, Co. Putative identification of the Ni-associated proteins, phosphoglucomutase and a protein in the cupin superfamily, provides new insights for Ni utilization in marine heterotrophs. BB2-AT2 relies on numerous transition metals for proteolytic and phosphatase activities, inferring an adaptative potential to metal limitation. Our field observations of increased alkaline phosphatase activity upon addition of Zn in field incubations suggest thatmore »such metal limitation operates in sinking particulate material collected from sediment traps. Taken together, this study improves our understanding of the Zn, Mn, Co, and Ni metallome of marine heterotrophic bacteria and provides novel and mechanistic frameworks for understanding the influence of nutrient limitation on biogeochemical cycling.« less