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  • Bacteria  (2)
  • Denitrification  (2)
  • 1
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    Inter-­comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins (2015)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Extremophiles 19 (2015): 949-960, doi:10.1007/s00792-015-0770-1.
    Description: The sediment microbiota of the Mediterranean deep-sea anoxic hypersaline basins (DHABs) are understudied relative to communities in the brines and halocline waters. In this study, the active fraction of the prokaryotic community in the halocline sediments of L’ Atalante, Urania, and Discovery DHABs was investigated based on extracted total RNA and 454 pyrosequencing of the 16S rRNA gene. Bacterial and archaeal communities were different in the sediments underlying the halocline waters of the three habitats, reflecting the unique chemical settings of each basin. The relative abundance of unique operational taxonomic units (OTUs) was also different between deep-sea control sediments and sediments underlying DHAB haloclines, suggesting adaptation to the steep DHAB chemical gradients. Only a few OTUs were affiliated to known bacterial halophilic and/or anaerobic groups. Many OTUs, including some of the dominant ones, were related to aerobic taxa. Archaea were detected only in few halocline samples, with lower OTU richness relative to Bacteria, and were dominated by taxa associated with methane cycling. This study suggests that, while metabolically active prokaryotic communities appear to be present in sediments underlying the three DHABs investigated, their diversity and activity are likely to be more reduced in sediments underlying the brines.
    Description: This work was supported by NSF OCE- 0849578 to VE and JB and OCE-1061391 to JB and VE. MP was supported by the WHOI postdoctoral scholarship program. KAK was partially supported by the University of Thessaly through a sabbatical in 2013.
    Description: 2016-07-16
    Keywords: Bacteria ; Archaea ; cDNA ; Activity ; L’ Atalante ; Urania ; Discovery ; Anoxic
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 2
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    Potential importance of physiologically diverse benthic foraminifera in sedimentary nitrate storage and respiration (2012)
    American Geophysical Union
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 117 (2012): G03002, doi:10.1029/2012JG001949.
    Description: Until recently, the process of denitrification (conversion of nitrate or nitrite to gaseous products) was thought to be performed exclusively by prokaryotes and fungi. The finding that foraminifera perform complete denitrification could impact our understanding of nitrate removal in sediments as well as our understanding of eukaryotic respiration, especially if it is widespread. However, details of this process and the subcellular location of these reactions in foraminifera remain uncertain. For example, prokaryotic endobionts, rather than the foraminifer proper, could perform denitrification, as has been shown recently in an allogromiid foraminifer. Here, intracellular nitrate concentrations and isotope ratios (δ15NNO3 and δ18ONO3) were measured to assess the nitrate dynamics in four benthic foraminiferal species (Bolivina argentea, Buliminella tenuata, Fursenkoina cornuta, Nonionella stella) with differing cellular architecture and associations with microbial endobionts, recovered from Santa Barbara Basin, California. Cellular nitrate concentrations were high (12–217 mM) in each species, and intracellular nitrate often had elevated δ15NNO3 and δ18ONO3 values. Experiments including suboxic and anoxic incubations of B. argentea revealed a decrease in intracellular nitrate concentration and an increase in δ15NNO3 and δ18ONO3 over time, indicating nitrate respiration and/or denitrification within the foraminifera. Results illustrate that nitrate reduction occurs in a range of foraminiferal species, including some possessing endobionts (including a chloroplast-sequestering species) and others lacking endobionts, implying that microbial associates may not solely be responsible for this process in foraminifera. Furthermore, we show that benthic foraminifera may represent important reservoirs of nitrate storage in sediments, as well as mediators of its removal.
    Description: This research was supported by NSF grant EF-0702491 to JMB, KLC, and VPE.
    Description: 2013-01-03
    Keywords: SSU rRNA ; Santa Barbara Basin ; Denitrification ; NirK ; NirS ; Symbiosis
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Intracellular isotope localization in Ammonia sp. (Foraminifera) of oxygen-depleted environments : results of nitrate and sulfate labeling experiments (2016)
    Frontiers Media
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 163, doi:10.3389/fmicb.2016.00163.
    Description: Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much 15N or 34S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200–500 nm in diameter and co-occurred with possible endobionts, were labeled with 15N originated from 15N-labeled nitrate under anoxia and were labeled with both 15N and 34S under dysoxia. The labeling with 15N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.
    Description: This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Young Scientists B No. 22740340 and Scientific Research C No. 24540504 to HN), an Invitation Fellowship for Research in Japan to JB by Japan Society for the Promotion of Science (JSPS), the Robert W. Morse Chair for Excellence in Oceanography at WHOI to JB, and The Investment in Science Fund at WHOI to JB.
    Keywords: Foraminifer ; Nitrate ; NanoSIMS ; Electron dense body ; Endobionts ; Ultrastructure ; Denitrification
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
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    Ultrastructural observations on prokaryotic associates of benthic foraminifera : food, mutualistic symbionts, or parasites? (2018)
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Micropaleontology 138 (2018): 33-45, doi:10.1016/j.marmicro.2017.09.001.
    Description: Because prokaryotes (Eubacteria, Archaea) are ubiquitous in the marine realm, it may not be surprising that they are important to the diet of at least some foraminifera. Over recent decades, Transmission Electron Microscopy (TEM) has revealed that, at the ultrastructural level, additional intimate relationships exist between prokaryotes and foraminifera. For example, the cytoplasm of a variety of benthic foraminiferal species contains intact prokaryotes. Other benthic foraminiferal species support prokaryotic populations on their exterior. Some of these prokaryote-foraminifera associations are sufficiently consistent to be considered symbioses. Symbiotic relationships include beneficial associations (mutualism; commensalism) to detrimental associations (parasitism). Here, we provide a synopsis of known foraminiferal- prokaryotic symbioses and TEM micrographs illustrating many specific associations. We further comment on and illustrate additional interactions such as bacterial scavenging on foraminifera and foraminiferal feeding on prokaryotes. Documenting and understanding all of these microbial interactions will contribute to a more comprehensive knowledge of benthic marine ecology and biology.
    Description: JMB’s contributions were funded by US NSF funding over many years, most recently NSF grant OCE-1634469, as well as the WHOI Robert W. Morse Chair for Excellence in Oceanography and The Investment in Science Fund at WHOI. MT and HN’s contributions were funded by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (no. 24340131 to MT and no. 22740340 to HN).
    Keywords: Transmission Electron Microscopy ; Rhizarian protist ; Commensalism ; Microbiome ; Oxygen depletion ; Bacteria
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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