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Bernhard JM, Fisher LA, Murphy Q, Sen L, Yeh HD, Louyakis A, Gomaa F, Reilly M, Batta-Lona PG, Bucklin A, Le Roux V, Visscher PT. Transition from stromatolite to thrombolite fabric: potential role for reticulopodial protists in lake microbialites of a Proterozoic ecosystem analog. Front Microbiol 2023; 14:1210781. [PMID: 37965561 PMCID: PMC10642914 DOI: 10.3389/fmicb.2023.1210781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
Prior observations suggest that foraminiferan protists use their reticulopodia (anastomosing pseudopodia) to alter sediment fabric by disrupting laminations of subtidal marine stromatolites, erasing the layered structures in an experimental setting. Because microbialites and foraminifera are found in non-marine settings, we hypothesized that foraminifera living in lakes could also disrupt layered microbialite fabric. With this aim and using a variety of multidisciplinary approaches, we conducted field surveys and an experiment on microbialites from Green Lake (GL; Fayetteville, New York State, United States), which has been studied as a Proterozoic ecosystem analog. The lake is meromictic and alkaline, receiving calcium sulfate-rich water in the monimolimnion; it supports a well-developed carbonate platform that provides access to living and relict microbialites. The living microbialites grow from early spring to autumn, forming a laminated mat at their surface (top ~5 mm), but a clotted or massive structure exists at depth (> ~ 1 cm). We observed a morphotype of "naked" foraminiferan-like protist in samples from GL microbialites and sediments; thus, considered the possibility of freshwater foraminiferan impact on microbialite fabric. Results of an experiment that seeded the cultured freshwater foraminifer Haplomyxa saranae onto the GL microbialite surface indicates via micro-CT scanning and anisotropy analysis that the introduced foraminifer impacted uppermost microbialite layering (n = 3 cores); those cores with an added inhibitor lacked changes in anisotropy for two of those three cores. Thus, it remains plausible that the much smaller, relatively common, native free-form reticulate protist, which we identified as Chlamydomyxa labyrinthuloides, can disrupt microbialite fabrics on sub-millimeter scales. Our observations do not exclude contributions of other possible causal factors.
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Affiliation(s)
- Joan M. Bernhard
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Luke A. Fisher
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Quinne Murphy
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Leena Sen
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY, United States
| | - Heidi D. Yeh
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Artemis Louyakis
- Department of Marine Sciences, Northeastern University, Boston, MA, United States
| | - Fatma Gomaa
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Megan Reilly
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Department of Marine Sciences, Northeastern University, Boston, MA, United States
| | - Paola G. Batta-Lona
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Veronique Le Roux
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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2
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Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria. Proc Natl Acad Sci U S A 2022; 119:e2200198119. [PMID: 35704763 DOI: 10.1073/pnas.2200198119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
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3
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Gomaa F, Utter DR, Powers C, Beaudoin DJ, Edgcomb VP, Filipsson HL, Hansel CM, Wankel SD, Zhang Y, Bernhard JM. Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. SCIENCE ADVANCES 2021; 7:7/22/eabf1586. [PMID: 34039603 PMCID: PMC8153729 DOI: 10.1126/sciadv.abf1586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.
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Affiliation(s)
- Fatma Gomaa
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Powers
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - David J Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Joan M Bernhard
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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4
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Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle. PLANTS 2020; 9:plants9070903. [PMID: 32708782 PMCID: PMC7412212 DOI: 10.3390/plants9070903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH4+) and nitrate (NO3−) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N2O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N2O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.
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5
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Li Q, Lei Y, Morard R, Li T, Wang B. Diversity hotspot and unique community structure of foraminifera in the world's deepest marine blue hole - Sansha Yongle Blue Hole. Sci Rep 2020; 10:10257. [PMID: 32581270 PMCID: PMC7314809 DOI: 10.1038/s41598-020-67221-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/01/2020] [Indexed: 11/09/2022] Open
Abstract
Marine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole. Here, we generated the first DNA metabarcoding dataset from SYBH sediment focusing on foraminifera, a group of protists that have colonized various marine environments. We collected sediment samples from SYBH along a depth gradient to characterize the foraminiferal diversity and compared them with the foraminiferal diversity of the costal Jiaozhou Bay (JZB) and the abyssal Northwest Pacific Ocean (NWP). We amplified the SSU rDNA of foraminifera and sequenced them with high-throughput sequencing. The results showed that the foraminiferal assemblages in SYBH were vertically structured in response to the abiotic gradients and diversity was higher than in JZB and NWP. This study illustrates the capacity of foraminifera to colonize hostile environments and shows that blue holes are natural laboratories to explore physiological innovation associated with anoxia.
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Affiliation(s)
- Qingxia Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanli Lei
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Raphaёl Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany
| | - Tiegang Li
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Baodong Wang
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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6
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Zhang X, Ward BB, Sigman DM. Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 2020; 120:5308-5351. [DOI: 10.1021/acs.chemrev.9b00613] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel M. Sigman
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
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7
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Gooday AJ, Schoenle A, Dolan JR, Arndt H. Protist diversity and function in the dark ocean - Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists. Eur J Protistol 2020; 75:125721. [PMID: 32575029 DOI: 10.1016/j.ejop.2020.125721] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/27/2022]
Abstract
The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.
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Affiliation(s)
- Andrew J Gooday
- National Oceanography Centre, University of Southampton Waterfront Campus, Southampton, UK; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - John R Dolan
- Sorbonne Université, CNRS UMR 7093, Laboratoroire d'Océanographie de Villefranche-sur-Mer, Villefranche-sur-Mer, France
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
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8
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Suokhrie T, Saraswat R, Nigam R. Lack of denitrification causes a difference in benthic foraminifera living in the oxygen deficient zones of the Bay of Bengal and the Arabian Sea. MARINE POLLUTION BULLETIN 2020; 153:110992. [PMID: 32275541 DOI: 10.1016/j.marpolbul.2020.110992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 06/11/2023]
Abstract
Despite being located at the same latitudes, the Bay of Bengal oxygen deficient zone (ODZ) is markedly different than the Arabian Sea ODZ. The uptake of oxygen in the Bay of Bengal does not lead to denitrification as in the Arabian Sea. This difference in ODZ of the Bay of Bengal and the Arabian Sea is expected to support different benthic fauna. We report that the living benthic foraminifera in the Bay of Bengal ODZ are markedly different than that in the Arabian Sea ODZ. Only four species (Brizalina spathulata, Eubuliminella exilis, Uvigerina peregrina and Rotaliatinopsis semiinvoluta) dominant in the Bay of Bengal ODZ have also been reported from the Arabian Sea oxygen deficient waters. The difference in living benthic foraminifera dominant in the ODZ of the Bay of Bengal and the Arabian Sea, is attributed to the lack of denitrification and associated processes in the Bay of Bengal.
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Affiliation(s)
- Thejasino Suokhrie
- Oceanography Orientation Division, CSIR-National Institute of Oceanography, Goa, India.
| | - Rajeev Saraswat
- Micropaleontology Laboratory, Geological Oceanography Division, CSIR-National Institute of Oceanography, Goa, India.
| | - R Nigam
- Micropaleontology Laboratory, Geological Oceanography Division, CSIR-National Institute of Oceanography, Goa, India
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9
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Enrichment of intracellular sulphur cycle -associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis. Sci Rep 2019; 9:11692. [PMID: 31406214 PMCID: PMC6690927 DOI: 10.1038/s41598-019-48166-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA -gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.
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10
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Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone. Proc Natl Acad Sci U S A 2019; 116:2860-2865. [PMID: 30728294 DOI: 10.1073/pnas.1813887116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors-nitrate (NO3 -) or oxygen (O2)-makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O2 respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O2 respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O2 respiration than for denitrification, indicating that NO3 - metabolism during denitrification is more efficient than O2 metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O2 respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO3 - storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO3 - availability. This suggests that the cell size of denitrifying foraminifera is not limited by O2 but rather by NO3 - availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO3 - is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO3 - and O2.
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11
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Prazeres M. Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia. Front Microbiol 2018; 9:2404. [PMID: 30356788 PMCID: PMC6189564 DOI: 10.3389/fmicb.2018.02404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/19/2018] [Indexed: 12/24/2022] Open
Abstract
Ocean warming is known to cause detrimental effects in coral reef fauna that rely on photo-symbiosis for survival. Microbial associations can facilitate the success of species across a range of environmental conditions, and play a role in the capacity of organisms to respond to climate change. In 2016, the Great Barrier Reef experienced its third mass bleaching event, with sea surface temperature rising to 1.3°C above long-term monthly summer averages. Here, I investigate the effects of ocean warming on the chlorophyll a (chl a) content and microbiome of the large benthic Foraminifera Amphistegina radiata. Samples were collected in January and April 2016, before and after the mass bleaching event. In total, 71 specimens were collected from two different depths (6- and 18-m) to investigate depth-dependant responses associated with changes in chl a and microbiome. Pigment analysis showed a significant reduction in chl a between time points in specimens collected at both depths. Reduction in pigmentation was accompanied by changes in the microbiome, and a significant interaction of depth and time was observed. Genus-level bacterial community associated with A. radiata was significantly different across depth and time. However, ocean warming affected populations at both depths to a similar extent, and resulted in change from a Betaproteobacteria-dominated assemblage in January to a more diverse bacterial community by April. Analysis of presence/absence and relative abundance of bacterial taxa revealed significant differences between time points at both depths analyzed. OTUs classified as Firmicutes, which were either absent, or present in very low relative abundances (<0.1%) across all sample groups in January, were identified in abundances as high as ∼20% in specimens collected from 18-m depth in April. Class-level shifts were observed in shallow-dwelling specimens, from high abundances of Betaproteobacteria to a high abundance and diversity of Actinobacteria. These results demonstrate the sensitivity of LBF to the effects of ocean warming, for which depth did not provide protection, and highlights the capacity of LBF to re-assemble bacterial communities after a disturbance. This study provides the first molecular-based demonstration of changes in foraminifera-associated bacterial assemblages during a bleaching event on a natural reef system.
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Affiliation(s)
- Martina Prazeres
- Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, Netherlands
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12
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Woehle C, Roy AS, Glock N, Wein T, Weissenbach J, Rosenstiel P, Hiebenthal C, Michels J, Schönfeld J, Dagan T. A Novel Eukaryotic Denitrification Pathway in Foraminifera. Curr Biol 2018; 28:2536-2543.e5. [PMID: 30078568 PMCID: PMC6783311 DOI: 10.1016/j.cub.2018.06.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/22/2018] [Accepted: 06/14/2018] [Indexed: 12/25/2022]
Abstract
Benthic foraminifera are unicellular eukaryotes inhabiting sediments of aquatic environments. Several species were shown to store and use nitrate for complete denitrification, a unique energy metabolism among eukaryotes. The population of benthic foraminifera reaches high densities in oxygen-depleted marine habitats, where they play a key role in the marine nitrogen cycle. However, the mechanisms of denitrification in foraminifera are still unknown, and the possibility of a contribution of associated bacteria is debated. Here, we present evidence for a novel eukaryotic denitrification pathway that is encoded in foraminiferal genomes. Large-scale genome and transcriptomes analyses reveal the presence of a denitrification pathway in foraminifera species of the genus Globobulimina. This includes the enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) as well as a wide range of nitrate transporters (Nrt). A phylogenetic reconstruction of the enzymes' evolutionary history uncovers evidence for an ancient acquisition of the foraminiferal denitrification pathway from prokaryotes. We propose a model for denitrification in foraminifera, where a common electron transport chain is used for anaerobic and aerobic respiration. The evolution of hybrid respiration in foraminifera likely contributed to their ecological success, which is well documented in palaeontological records since the Cambrian period.
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Affiliation(s)
- Christian Woehle
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany.
| | - Alexandra-Sophie Roy
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany.
| | - Nicolaas Glock
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse, Kiel 24148, Germany
| | - Tanita Wein
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
| | - Julia Weissenbach
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
| | - Claas Hiebenthal
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse, Kiel 24148, Germany
| | - Jan Michels
- Institute of Zoology, Kiel University, Am Botanischen Garten 1-9, Kiel 24118, Germany
| | - Joachim Schönfeld
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse, Kiel 24148, Germany
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
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13
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Coupling of oceanic carbon and nitrogen facilitates spatially resolved quantitative reconstruction of nitrate inventories. Nat Commun 2018; 9:1217. [PMID: 29572447 PMCID: PMC5865207 DOI: 10.1038/s41467-018-03647-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/02/2018] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic impacts are perturbing the global nitrogen cycle via warming effects and pollutant sources such as chemical fertilizers and burning of fossil fuels. Understanding controls on past nitrogen inventories might improve predictions for future global biogeochemical cycling. Here we show the quantitative reconstruction of deglacial bottom water nitrate concentrations from intermediate depths of the Peruvian upwelling region, using foraminiferal pore density. Deglacial nitrate concentrations correlate strongly with downcore δ13C, consistent with modern water column observations in the intermediate Pacific, facilitating the use of δ13C records as a paleo-nitrate-proxy at intermediate depths and suggesting that the carbon and nitrogen cycles were closely coupled throughout the last deglaciation in the Peruvian upwelling region. Combining the pore density and intermediate Pacific δ13C records shows an elevated nitrate inventory of >10% during the Last Glacial Maximum relative to the Holocene, consistent with a δ13C-based and δ15N-based 3D ocean biogeochemical model and previous box modeling studies. Understanding controls on past nitrogen budgets can improve predictions for future global biogeochemical cycling. Here, using foraminiferal pore density and δ13C, the authors present a quantitative record of deglacial nitrate from the intermediate Pacific and infer close coupling between carbon and nitrogen cycles.
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14
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Høgslund S, Cedhagen T, Bowser SS, Risgaard-Petersen N. Sinks and Sources of Intracellular Nitrate in Gromiids. Front Microbiol 2017; 8:617. [PMID: 28473806 PMCID: PMC5397464 DOI: 10.3389/fmicb.2017.00617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/27/2017] [Indexed: 11/27/2022] Open
Abstract
A substantial nitrate pool is stored within living cells in various benthic marine environments. The fate of this bioavailable nitrogen differs according to the organisms managing the intracellular nitrate (ICN). While some light has been shed on the nitrate carried by diatoms and foraminiferans, no study has so far followed the nitrate kept by gromiids. Gromiids are large protists and their ICN concentration can exceed 1000x the ambient nitrate concentration. In the present study we investigated gromiids from diverse habitats and showed that they contained nitrate at concentrations ranging from 1 to 370 mM. We used 15N tracer techniques to investigate the source of this ICN, and found that it originated both from active nitrate uptake from the environment and from intracellular production, most likely through bacterial nitrification. Microsensor measurements showed that part of the ICN was denitrified to N2 when gromiids were exposed to anoxia. Denitrification seemed to be mediated by endobiotic bacteria because antibiotics inhibited denitrification activity. The active uptake of nitrate suggests that ICN plays a role in gromiid physiology and is not merely a consequence of the gromiid hosting a diverse bacterial community. Measurements of aerobic respiration rates and modeling of oxygen consumption by individual gromiid cells suggested that gromiids may occasionally turn anoxic by their own respiration activity and thus need strategies for coping with this self-inflicted anoxia.
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Affiliation(s)
- Signe Høgslund
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | - Tomas Cedhagen
- Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | - Samuel S Bowser
- Wadsworth Center, New York State Department of Health, AlbanyNY, USA
| | - Nils Risgaard-Petersen
- Department of Bioscience, Aarhus UniversityAarhus, Denmark.,Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
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15
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Kamp A, Stief P, Bristow LA, Thamdrup B, Glud RN. Intracellular Nitrate of Marine Diatoms as a Driver of Anaerobic Nitrogen Cycling in Sinking Aggregates. Front Microbiol 2016; 7:1669. [PMID: 27847498 PMCID: PMC5088207 DOI: 10.3389/fmicb.2016.01669] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/06/2016] [Indexed: 01/20/2023] Open
Abstract
Diatom-bacteria aggregates are key for the vertical transport of organic carbon in the ocean. Sinking aggregates also represent pelagic microniches with intensified microbial activity, oxygen depletion in the center, and anaerobic nitrogen cycling. Since some of the aggregate-forming diatom species store nitrate intracellularly, we explored the fate of intracellular nitrate and its availability for microbial metabolism within anoxic diatom-bacteria aggregates. The ubiquitous nitrate-storing diatom Skeletonema marinoi was studied as both axenic cultures and laboratory-produced diatom-bacteria aggregates. Stable 15N isotope incubations under dark and anoxic conditions revealed that axenic S. marinoi is able to reduce intracellular nitrate to ammonium that is immediately excreted by the cells. When exposed to a light:dark cycle and oxic conditions, S. marinoi stored nitrate intracellularly in concentrations >60 mmol L-1 both as free-living cells and associated to aggregates. Intracellular nitrate concentrations exceeded extracellular concentrations by three orders of magnitude. Intracellular nitrate was used up within 2-3 days after shifting diatom-bacteria aggregates to dark and anoxic conditions. Thirty-one percent of the diatom-derived nitrate was converted to nitrogen gas, indicating that a substantial fraction of the intracellular nitrate pool of S. marinoi becomes available to the aggregate-associated bacterial community. Only 5% of the intracellular nitrate was reduced to ammonium, while 59% was recovered as nitrite. Hence, aggregate-associated diatoms accumulate nitrate from the surrounding water and sustain complex nitrogen transformations, including loss of fixed nitrogen, in anoxic, pelagic microniches. Additionally, it may be expected that intracellular nitrate not converted before the aggregates have settled onto the seafloor could fuel benthic nitrogen transformations.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies, Aarhus UniversityAarhus, Denmark
| | - Peter Stief
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
| | - Laura A. Bristow
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
- Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
| | - Ronnie N. Glud
- Department of Biology and Nordic Center for Earth Evolution, University of Southern DenmarkOdense, Denmark
- Department of Biogeochemistry and Earth Science, Scottish Association for Marine ScienceOban, UK
- Department of Bioscience, Arctic Research Centre, Aarhus UniversityAarhus, Denmark
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16
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Nomaki H, Bernhard JM, Ishida A, Tsuchiya M, Uematsu K, Tame A, Kitahashi T, Takahata N, Sano Y, Toyofuku T. Intracellular Isotope Localization in Ammonia sp. (Foraminifera) of Oxygen-Depleted Environments: Results of Nitrate and Sulfate Labeling Experiments. Front Microbiol 2016; 7:163. [PMID: 26925038 PMCID: PMC4759270 DOI: 10.3389/fmicb.2016.00163] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
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 (15)N or (34)S 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 (15)N originated from (15)N-labeled nitrate under anoxia and were labeled with both (15)N and (34)S under dysoxia. The labeling with (15)N 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.
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Affiliation(s)
- Hidetaka Nomaki
- Department of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Joan M Bernhard
- Geology and Geophysics Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Akizumi Ishida
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Masashi Tsuchiya
- Department of Marine Biodiversity, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | | | | | - Tomo Kitahashi
- Project Team for Research and Development of Next-generation Technology for Ocean Resources Exploration, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Naoto Takahata
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Yuji Sano
- Department of Chemical Oceanography, Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Takashi Toyofuku
- Department of Marine Biodiversity, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
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17
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Enge AJ, Wukovits J, Wanek W, Watzka M, Witte UFM, Hunter WR, Heinz P. Carbon and Nitrogen Uptake of Calcareous Benthic Foraminifera along a Depth-Related Oxygen Gradient in the OMZ of the Arabian Sea. Front Microbiol 2016; 7:71. [PMID: 26903959 PMCID: PMC4749719 DOI: 10.3389/fmicb.2016.00071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Abstract
Foraminifera are an important faunal element of the benthos in oxygen-depleted settings such as Oxygen Minimum Zones (OMZs) where they can play a relevant role in the processing of phytodetritus. We investigated the uptake of phytodetritus (labeled with (13)C and (15)N) by calcareous foraminifera in the 0-1 cm sediment horizon under different oxygen concentrations within the OMZ in the eastern Arabian Sea. The in situ tracer experiments were carried out along a depth transect on the Indian margin over a period of 4 to 10 days. The uptake of phytodetrital carbon within 4 days by all investigated species shows that phytodetritus is a relevant food source for foraminifera in OMZ sediments. The decrease of total carbon uptake from 540 to 1100 m suggests a higher demand for carbon by species in the low-oxygen core region of the OMZ or less food competition with macrofauna. Especially Uvigerinids showed high uptake of phytodetrital carbon at the lowest oxygenated site. Variation in the ratio of phytodetrital carbon to nitrogen between species and sites indicates that foraminiferal carbon and nitrogen use can be decoupled and different nutritional demands are found between species. Lower ratio of phytodetrital carbon and nitrogen at 540 m could hint for greater demand or storage of food-based nitrogen, ingestion, or hosting of bacteria under almost anoxic conditions. Shifts in the foraminiferal assemblage structure (controlled by oxygen or food availability) and in the presence of other benthic organisms are likely to account for observed changes in the processing of phytodetritus in the different OMZ habitats. Foraminifera dominate the short-term processing of phytodetritus in the OMZ core but are less important in the lower OMZ boundary region of the Indian margin as biological interactions and species distribution of foraminifera change with depth and oxygen levels.
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Affiliation(s)
| | - Julia Wukovits
- Department of Palaeontology, University of Vienna Vienna, Austria
| | - Wolfgang Wanek
- Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Margarete Watzka
- Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | | | - William R Hunter
- School of Biological Sciences, Queen's University Belfast Belfast, UK
| | - Petra Heinz
- Department of Palaeontology, University of Vienna Vienna, Austria
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Kamp A, Høgslund S, Risgaard-Petersen N, Stief P. Nitrate Storage and Dissimilatory Nitrate Reduction by Eukaryotic Microbes. Front Microbiol 2015; 6:1492. [PMID: 26734001 PMCID: PMC4686598 DOI: 10.3389/fmicb.2015.01492] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/10/2015] [Indexed: 11/13/2022] Open
Abstract
The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described. A first compilation of intracellular nitrate inventories in various marine sediments is presented, indicating that intracellular nitrate pools vastly exceed porewater nitrate pools. The relative contribution by foraminifers to total sedimentary denitrification is estimated for different marine settings, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations.
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Affiliation(s)
- Anja Kamp
- AIAS, Aarhus Institute of Advanced Studies Aarhus University Aarhus, Denmark
| | - Signe Høgslund
- Department of Bioscience, Aarhus University Aarhus, Denmark
| | | | - Peter Stief
- Department of Biology, Nordic Center for Earth Evolution, University of Southern Denmark Odense, Denmark
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19
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Stief P, Kamp A, de Beer D. Role of diatoms in the spatial-temporal distribution of intracellular nitrate in intertidal sediment. PLoS One 2013; 8:e73257. [PMID: 24023845 PMCID: PMC3762809 DOI: 10.1371/journal.pone.0073257] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/19/2013] [Indexed: 11/23/2022] Open
Abstract
Intracellular nitrate storage allows microorganisms to survive fluctuating nutrient availability and anoxic conditions in aquatic ecosystems. Here we show that diatoms, ubiquitous and highly abundant microalgae, represent major cellular reservoirs of nitrate in an intertidal flat of the German Wadden Sea and are potentially involved in anaerobic nitrate respiration. Intracellular nitrate (ICNO3) was present year-round in the sediment and was spatially and temporally correlated with fucoxanthin, the marker photopigment of diatoms. Pyrosequencing of SSU rRNA genes of all domains of life confirmed that ICNO3 storage was most likely due to diatoms rather than other known nitrate-storing microorganisms (i.e., large sulfur bacteria and the eukaryotic foraminifers and gromiids). Sedimentary ICNO3 concentrations reached up to 22.3 µmol dm-3 at the sediment surface and decreased with sediment depth to negligible concentrations below 5 cm. Similarly, the ICNO3/fucoxanthin ratio and porewater nitrate (PWNO3) concentrations decreased with sediment depth, suggesting that ICNO3 of diatoms is in equilibrium with PWNO3, but is enriched relative to PWNO3 by 2-3 orders of magnitude. Cell-volume-specific ICNO3 concentrations in a diatom mat covering the sediment surface during spring were estimated at 9.3-46.7 mmol L-1. Retrieval of 18S rRNA gene sequences related to known nitrate-storing and nitrate-ammonifying diatom species suggested that diatoms in dark and anoxic sediment layers might be involved in anaerobic nitrate respiration. Due to the widespread dominance of diatoms in microphytobenthos, the total nitrate pool in coastal marine sediments may generally be at least two times larger than derived from porewater measurements and partially be recycled to ammonium.
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Affiliation(s)
- Peter Stief
- Max Planck Institute for Marine Microbiology, Microsensor Group, Bremen, Germany
- University of Southern Denmark, Institute of Biology, NordCEE, Odense, Denmark
- * E-mail:
| | - Anja Kamp
- Max Planck Institute for Marine Microbiology, Microsensor Group, Bremen, Germany
- Jacobs University Bremen, Molecular Life Science Research Center, Bremen, Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Microsensor Group, Bremen, Germany
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