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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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2
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Ali Y, Simachew A, Gessesse A. Diversity of Culturable Alkaliphilic Nitrogen-Fixing Bacteria from a Soda Lake in the East African Rift Valley. Microorganisms 2022; 10:microorganisms10091760. [PMID: 36144362 PMCID: PMC9501543 DOI: 10.3390/microorganisms10091760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/23/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Lake Chitu is a highly productive soda lake found in the East African Rift Valley, where Arthrospira fusiformis (Spirulina platensis) is the main primary producer. High biomass accumulation requires an adequate supply of nitrogen. However, Lake Chitu is a closed system without any external nutrient input. A recent study has also demonstrated the presence of a diverse group of denitrifying bacteria, indicating a possible loss of nitrate released from the oxidation of organic matter. The aim of this study was to isolate culturable nitrogen-fixing alkaliphiles and evaluate their potential contribution in the nitrogen economy of the soda lake. A total of 118 alkaliphiles belonging to nine different operational taxonomic units (OTUs) were isolated using a nitrogen-free medium. Nineteen isolates were tested for the presence of the nifH gene, and 11 were positive. The ability to fix nitrogen was tested by co-culturing with a non-nitrogen-fixing alkaliphile, Alkalibacterium sp. 3.5*R1. When inoculated alone, Alkalibacterium sp. 3.5*R1 failed to grow on a nitrogen-free medium, but grew very well when co-cultured with the nitrogen-fixing alkaliphile NF10m6 isolated in this study, indicating the availability of nitrogen. These results show that nitrogen fixation by alkaliphiles may have an important contribution as a source of nitrogen in soda lakes.
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Affiliation(s)
- Yordanos Ali
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- Industrial Biotechnology Research Directorate, Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye 10071, Botswana
- Correspondence: ; Tel.: +267-4931871
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3
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Avnaim-Katav S, Holzmann M, Pawlowski J. Carterina labinea sp. nov. – a new alien foraminifer from the southeastern mediterranean shelf. Eur J Protistol 2022; 85:125911. [DOI: 10.1016/j.ejop.2022.125911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
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Bio-Aerosols Negatively Affect Prochlorococcus in Oligotrophic Aerosol-Rich Marine Regions. ATMOSPHERE 2020. [DOI: 10.3390/atmos11050540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The marine cyanobacterium Prochlorococcus is a dominant photoautotroph in many oligotrophic Low-Nutrients-Low-Chlorophyll (LNLC) regions. While the chemical impact of aerosols upon interaction with surface seawater was documented in numerous studies, we show that Prochlorococcus cells are affected also by bio-aerosols (potentially biological agents in the dust/aerosols such as membrane-bound extracellular vesicles, small-size bacteria and/or viruses), resulting in lower surface seawater abundances in the oligotrophic Mediterranean Sea. We conducted experimental amendments of ‘live’ aerosol/dust particles and aerosol filtrates (<0.22-µm) to surface Southeastern Mediterranean seawater or to pure Prochlorococcus cultures (MED4). Results show a significant decline in cell biomass (<90%), while UV-sterilized aerosols elicited a much weaker and non-significant response (~10%). We suggest that the difference is due to a negative effect of bio-aerosols specific to Prochlorococcus. Accordingly, the dominance of Synechococcus over Prochlorococcus throughout the surface Mediterranean Sea (observed mainly in spring when atmospheric aerosol levels are relatively high) and the lack of spatial westward gradient in Prochlorococcus biomass as typically observed for chlorophyll-a or other cyanobacteria may be attributed, at least to some extent, to the impact of bio-aerosol deposition across the basin. Predictions for enhanced desertification and increased dust emissions may intensify the transport and potential impact of bio-aerosols in LNLC marine systems.
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Phytoplankton and Bacterial Response to Desert Dust Deposition in the Coastal Waters of the Southeastern Mediterranean Sea: A Four-Year In Situ Survey. ATMOSPHERE 2018. [DOI: 10.3390/atmos9080305] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Atmospheric dust/aerosol deposition is an important source of external nutrients for the surface of the ocean. This study shows high-resolution observational data gathered in situ over a period of four years on bacterial and phytoplankton abundance and activity during typical background atmospheric conditions and during intense dust storm events in the low-nutrient, low-chlorophyll (LNLC) coastal waters of the southeastern Mediterranean Sea (SEMS). Chlorophyll a (an estimate for phytoplankton biomass) and bacterial abundance show moderate changes in response to dust deposition/events (−10% and +20%, respectively), while primary production, bacterial production, and N2 fixation rates were all significantly and positively affected by deposition (+25 to +40%; p < 0.05). The rapid changes in bacterial and/or phytoplankton rate parameters suggest that the released micro-/macronutrients from atmospheric deposition are tunneled directly in metabolic processes and, to a lesser extent, for biomass accumulation. The predicted expansion of LNLC areas in oceans in the future, and the projected increase in dust emission due to desertification, may affect the production of marine microbial communities in the surface of the ocean, yet only moderately affect their biomass or standing stock. Such alterations may impact carbon sequestration to the deep ocean.
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Moisander PH, Benavides M, Bonnet S, Berman-Frank I, White AE, Riemann L. Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments. Front Microbiol 2017; 8:1736. [PMID: 28943875 PMCID: PMC5596534 DOI: 10.3389/fmicb.2017.01736] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/25/2017] [Indexed: 11/22/2022] Open
Abstract
Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N2) fixation. Other potentially N2-fixing bacteria and archaea have also been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N2 fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N2 fixation NCNF in the ocean. Rates attributed to NCNF have generally been near the detection limit thus far (<1 nmol N L−1 d−1). Yet, if considering the large volume of the dark ocean, even low rates of NCNF could make a significant contribution to the new nitrogen input to the ocean. The synthesis here shows that nifH transcription data for NCDs have been reported in only a few studies where N2 fixation rates were detected in the absence of diazotrophic cyanobacteria. In addition, high apparent diversity and regional variability in the NCDs complicate investigations of these communities. Future studies should focus on further investigating impacts of environmental drivers including oxygen, dissolved organic matter, and dissolved inorganic nitrogen on NCNF. Describing the ecology of NCDs and accurately measuring NCNF rates, are critical for a future evaluation of the contribution of NCNF to the marine nitrogen budget.
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Affiliation(s)
- Pia H Moisander
- Department of Biology, University of Massachusetts DartmouthNorth Dartmouth, MA, United States
| | - Mar Benavides
- Marine Biology Section, Department of Biology, University of CopenhagenHelsingør, Denmark
| | - Sophie Bonnet
- Centre National de la Recherche Scientifique, IRD, Aix-Marseille Université, Université de ToulonMarseille, France
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat Gan, Israel
| | - Angelicque E White
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State UniversityCorvallis, OR, United States
| | - Lasse Riemann
- Marine Biology Section, Department of Biology, University of CopenhagenHelsingør, Denmark
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7
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Sewage outburst triggers Trichodesmium bloom and enhance N 2 fixation rates. Sci Rep 2017; 7:4367. [PMID: 28663560 PMCID: PMC5491490 DOI: 10.1038/s41598-017-04622-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/25/2017] [Indexed: 11/09/2022] Open
Abstract
The southeastern Mediterranean Sea (SEMS) is a warm and sunlit marine environment with low ambient N concentration, thus considered ideal for diazotrophy by autotrophic diazotrophs such as Trichodesmium. Despite the favorable conditions, N2 fixation rates are often low and Trichodesmium has hardly been spotted in the SEMS. This study reports on the occurrence of a Trichodesmium bloom in the SEMS which was ascribed to T. erythraeum according to DNA fingerprinting of the nifH gene. We found that this bloom (1407 ± 983 cells L−1) was triggered by an intense outburst of raw sewage that supplied high concentrations of N, P and dissolved organic carbon (DOC), which resulted in low N:P (~12:1) and exceptionally high C:P (~1340:1) ratios. We surmise that these conditions provided favorable conditions for Trichodesmium bloom to form via mixotrophic metabolism. As a result, a fourfold increase in N2 fixation was recorded, which contributed ~70% to new primary production and spur a sharp increase in phytoplankton activity and biomass. The conclusions of this study point on a new paradigm for bloom-forming T. erythraeum which is tightly linked to anthropogenic sources and prompt microbial productivity in oligotrophic marine environments such as the SEMS.
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Frank IE, Turk-Kubo KA, Zehr JP. Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:905-916. [PMID: 27557869 DOI: 10.1111/1758-2229.12455] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 08/16/2016] [Indexed: 05/22/2023]
Abstract
The nifH gene is a widely used molecular proxy for studying nitrogen fixation. Phylogenetic classification of nifH gene sequences is an essential step in diazotroph community analysis that requires a fast automated solution due to increasing size of environmental sequence libraries and increasing yield of nifH sequences from high-throughput technologies. A novel approach to rapidly classify nifH amino acid sequences into well-defined phylogenetic clusters that provides a common platform for comparative analysis across studies is presented. Phylogenetic group membership can be accurately predicted with decision tree-type statistical models that identify and utilize signature residues in the amino acid sequences. Our classification models were trained and evaluated with a publicly available and manually curated nifH gene database containing cluster annotations. Model-independent sequence sets from diverse ecosystems were used for further assessment of the models' prediction accuracy. The utility of this novel sequence binning approach was demonstrated in a comparative study where joint treatment of diazotroph assemblages from a wide range of habitats identified habitat-specific and widely-distributed diazotrophs and revealed a marine - terrestrial distinction in community composition. Our rapid and automated phylogenetic cluster assignment circumvents extensive phylogenetic analysis of nifH sequences; hence, it saves substantial time and resources in nitrogen fixation studies.
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Affiliation(s)
- Ildiko E Frank
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
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9
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Rahav E, Giannetto MJ, Bar-Zeev E. Contribution of mono and polysaccharides to heterotrophic N2 fixation at the eastern Mediterranean coastline. Sci Rep 2016; 6:27858. [PMID: 27306501 PMCID: PMC4910064 DOI: 10.1038/srep27858] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/26/2016] [Indexed: 11/15/2022] Open
Abstract
N2 fixation should be a critical process in the nitrogen-poor surface water of the eastern Mediterranean Sea. Despite favorable conditions, diazotroph abundance and N2 fixation rates remains low for reasons yet explained. The main goal of this study was to investigate the limiting nutrients for diazotrophy in this oligotrophic environment. Hence, we conducted dedicated bottle-microcosms with eastern Mediterranean Sea water that were supplemented with mono and polysaccharides as well as inorganic nitrogen and phosphorous. Our results indicate that the diazotrophic community expressing nifH was primarily represented by heterotrophic Proteobacteria. N2 fixation and heterotrophic bacterial activity increased up-to tenfold following two days of dark incubations, once seawater was supplemented with organic carbon substrate in the form of glucose (monosaccharides) or gum-xanthan (polysaccharide surrogate). Furthermore, our results point that carbon-rich polysaccharides, such as transparent exopolymer particles, enhance heterotrophic N2 fixation, by forming microenvironments of intense metabolic activity, high carbon: nitrogen ratio, and possibly low O2 levels. The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions.
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Affiliation(s)
- E. Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, 8030, Israel
| | - M. J. Giannetto
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520, USA
| | - E. Bar-Zeev
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Midreshet Ben-Gurion, Israel
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10
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Newell SE, Pritchard KR, Foster SQ, Fulweiler RW. Molecular evidence for sediment nitrogen fixation in a temperate New England estuary. PeerJ 2016; 4:e1615. [PMID: 26977375 PMCID: PMC4788212 DOI: 10.7717/peerj.1615] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/01/2016] [Indexed: 11/22/2022] Open
Abstract
Primary production in coastal waters is generally nitrogen (N) limited with
denitrification outpacing nitrogen fixation (N2-fixation). However, recent work
suggests that we have potentially underestimated the importance of heterotrophic sediment
N2-fixation in marine ecosystems. We used clone libraries to examine
transcript diversity of nifH (a gene associated with
N2-fixation) in sediments at three sites in a temperate New England estuary
(Waquoit Bay, Massachusetts, USA) and compared our results to net sediment N2
fluxes previously measured at these sites. We observed nifH expression at
all sites, including a site heavily impacted by anthropogenic N. At this N impacted site,
we also observed mean net sediment N2-fixation, linking the geochemical rate
measurement with nifH expression. This same site also had the lowest
diversity (non-parametric Shannon = 2.75). At the two other sites, we also detected
nifH transcripts, however, the mean N2 flux indicated net
denitrification. These results suggest that N2-fixation and denitrification
co-occur in these sediments. Of the unique sequences in this study, 67% were most closely
related to uncultured bacteria from various marine environments, 17% to Cluster III, 15%
to Cluster I, and only 1% to Cluster II. These data add to the growing body of literature
that sediment heterotrophic N2-fixation, even under high inorganic nitrogen
concentrations, may be an important yet overlooked source of N in coastal systems.
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Affiliation(s)
- Silvia E Newell
- Department of Earth and Environment, Boston University, Boston, MA, USA; Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, USA
| | - Kaitlyn R Pritchard
- Department of Marine and Environmental Sciences, Northeastern University , Boston, MA , USA
| | - Sarah Q Foster
- Department of Earth and Environment, Boston University , Boston, MA , USA
| | - Robinson W Fulweiler
- Department of Earth and Environment, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA
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11
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Raveh O, David N, Rilov G, Rahav E. The Temporal Dynamics of Coastal Phytoplankton and Bacterioplankton in the Eastern Mediterranean Sea. PLoS One 2015; 10:e0140690. [PMID: 26474399 PMCID: PMC4608699 DOI: 10.1371/journal.pone.0140690] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/28/2015] [Indexed: 11/18/2022] Open
Abstract
This study considers variability in phytoplankton and heterotrophic bacterial abundances and production rates, in one of the most oligotrophic marine regions in the world–the Levantine Basin. The temporal dynamics of these planktonic groups were studied in the coastal waters of the southeastern Mediterranean Sea approximately every two weeks for a total of two years. Heterotrophic bacteria were abundant mostly during late summer and midwinter, and were positively correlated with bacterial production and with N2 fixation. Based on size fractionating, picophytoplankton was abundant during the summer, whereas nano-microphytoplankton predominated during the winter and early spring, which were also evident in the size-fractionated primary production rates. Autotrophic abundance and production correlated negatively with temperature, but did not correlate with inorganic nutrients. Furthermore, a comparison of our results with results from the open Levantine Basin demonstrates that autotrophic and heterotrophic production, as well as N2 fixation rates, are considerably higher in the coastal habitat than in the open sea, while nutrient levels or cell abundance are not different. These findings have important ecological implications for food web dynamics and for biological carbon sequestration in this understudied region.
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Affiliation(s)
- Ofrat Raveh
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Niv David
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Gil Rilov
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Eyal Rahav
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
- * E-mail:
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12
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Techtmann SM, Fortney JL, Ayers KA, Joyner DC, Linley TD, Pfiffner SM, Hazen TC. The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth. PLoS One 2015; 10:e0120605. [PMID: 25807542 PMCID: PMC4373936 DOI: 10.1371/journal.pone.0120605] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/24/2015] [Indexed: 11/26/2022] Open
Abstract
The waters of the Eastern Mediterranean are characterized by unique physical and chemical properties within separate water masses occupying different depths. Distinct water masses are present throughout the oceans, which drive thermohaline circulation. These water masses may contain specific microbial assemblages. The goal of this study was to examine the effect of physical and geological phenomena on the microbial community of the Eastern Mediterranean water column. Chemical measurements were combined with phospholipid fatty acid (PLFA) analysis and high-throughput 16S rRNA sequencing to characterize the microbial community in the water column at five sites. We demonstrate that the chemistry and microbial community of the water column were stratified into three distinct water masses. The salinity and nutrient concentrations vary between these water masses. Nutrient concentrations increased with depth, and salinity was highest in the intermediate water mass. Our PLFA analysis indicated different lipid classes were abundant in each water mass, suggesting that distinct groups of microbes inhabit these water masses. 16S rRNA gene sequencing confirmed the presence of distinct microbial communities in each water mass. Taxa involved in autotrophic nitrogen cycling were enriched in the intermediate water mass suggesting that microbes in this water mass may be important to the nitrogen cycle of the Eastern Mediterranean. The Eastern Mediterranean also contains numerous active hydrocarbon seeps. We sampled above the North Alex Mud Volcano, in order to test the effect of these geological features on the microbial community in the adjacent water column. The community in the waters overlaying the mud volcano was distinct from other communities collected at similar depths and was enriched in known hydrocarbon degrading taxa. Our results demonstrate that physical phenomena such stratification as well as geological phenomena such as mud volcanoes strongly affect microbial community structure in the Eastern Mediterranean water column.
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Affiliation(s)
- Stephen M. Techtmann
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Julian L. Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kati A. Ayers
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Dominique C. Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas D. Linley
- Ocean Lab, University of Aberdeen, Newburgh, Aberdeenshire, United Kingdom
| | - Susan M. Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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13
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Lang-Yona N, Lehahn Y, Herut B, Burshtein N, Rudich Y. Marine aerosol as a possible source for endotoxins in coastal areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 499:311-8. [PMID: 25201818 DOI: 10.1016/j.scitotenv.2014.08.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/12/2014] [Accepted: 08/19/2014] [Indexed: 04/15/2023]
Abstract
Marine aerosols, that are very common in the highly populated coastal cities and communities, may contain biological constituents. Some of this biological fraction of marine aerosols, such as cyanobacteria and plankton debris, may influence human health by inflammation and allergic reactions when inhaled. In this study we identify and compare sources for endotoxins sampled on filters in an on-shore and more-inland site. Filter analysis included endotoxin content, total bacteria, gram-negative bacteria and cyanobacteria genome concentrations as well as ion content in order to identify possible sources for the endotoxins. Satellite images of chlorophyll-a levels and back trajectory analysis were used to further study the cyanobacteria blooms in the sea, close to the trajectory of the sampled air. The highest endotoxin concentrations found in the shoreline site were during winter (3.23±0.17 EU/m(3)), together with the highest cyanobacteria genome (1065.5 genome/m(3)). The elevated endotoxin concentrations were significantly correlated with cyanobacterial levels scaled to the presence of marine aerosol (r=0.90), as well as to chlorophyll-a (r=0.96). Filters sampled further inland showed lower and non-significant correlation between endotoxin and cyanobacteria (r=0.70, P value=0.19), suggesting decrease in marine-originated endotoxin, with possible contributions from other sources of gram-negative non-cyanobacteria. We conclude that marine cyanobacteria may be a dominant contributor to elevated endotoxin levels in coastal areas.
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Affiliation(s)
- Naama Lang-Yona
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Israel
| | - Yoav Lehahn
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Israel
| | - Barak Herut
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Noa Burshtein
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Israel.
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14
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Rubin-Blum M, Antler G, Tsadok R, Shemesh E, Austin JA, Coleman DF, Goodman-Tchernov BN, Ben-Avraham Z, Tchernov D. First evidence for the presence of iron oxidizing zetaproteobacteria at the Levantine continental margins. PLoS One 2014; 9:e91456. [PMID: 24614177 PMCID: PMC3948872 DOI: 10.1371/journal.pone.0091456] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/11/2014] [Indexed: 02/01/2023] Open
Abstract
During the 2010–2011 E/V Nautilus exploration of the Levantine basin’s sediments at the depth of 300–1300 m, densely patched orange-yellow flocculent mats were observed at various locations along the continental margin of Israel. Cores from the mat and the control locations were collected by remotely operated vehicle system (ROV) operated by the E/V Nautilus team. Microscopic observation and phylogenetic analysis of microbial 16S and 23S rRNA gene sequences indicated the presence of zetaproteobacterial stalk forming Mariprofundus spp. – like prokaryotes in the mats. Bacterial tag-encoded FLX amplicon pyrosequencing determined that zetaproteobacterial populations were a dominant fraction of microbial community in the biofilm. We show for the first time that zetaproteobacterial may thrive at the continental margins, regardless of crustal iron supply, indicating significant fluxes of ferrous iron to the sediment-water interface. In light of this discovery, we discuss the potential bioavailability of sediment-water interface iron for organisms in the overlying water column.
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Affiliation(s)
- Maxim Rubin-Blum
- The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- * E-mail:
| | - Gilad Antler
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Rami Tsadok
- The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eli Shemesh
- The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - James A. Austin
- Institute for Geophysics, Jackson School of Geosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Dwight F. Coleman
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, Rhode Island, United States of America
| | | | - Zvi Ben-Avraham
- The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Department of Geophysical, Atmospheric and Planetary Sciences, Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Dan Tchernov
- The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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15
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Turk-Kubo KA, Karamchandani M, Capone DG, Zehr JP. The paradox of marine heterotrophic nitrogen fixation: abundances of heterotrophic diazotrophs do not account for nitrogen fixation rates in the Eastern Tropical South Pacific. Environ Microbiol 2014; 16:3095-114. [PMID: 24286454 DOI: 10.1111/1462-2920.12346] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 11/23/2013] [Indexed: 11/28/2022]
Abstract
Results of recent modelling efforts imply denitrification-influenced waters, such as those in the Eastern Tropical South Pacific (ETSP), may support high rates of biological nitrogen fixation (BNF), yet little is known about the N2 -fixing microbial community in this region. Our characterization of the ETSP diazotrophic community along a gradient from upwelling-influenced to oligotrophic waters did not detect cyanobacterial diazotrophs commonly found in other open ocean regions. Most of the nifH genes amplified by polymerase chain reaction (PCR) from DNA and RNA samples clustered with γ-proteobacterial nifH sequences, although a novel Trichodesmium phylotype was also recovered. Three quantitative PCR assays were developed to target γ-proteobacterial phylotypes, but all were found to be present at low abundances. An analysis of the expected BNF rates based on abundances and plausible cell-specific N2 fixation rates indicates that these γ-proteobacteria are unlikely to be responsible for previously reported BNF rates from corresponding samples. Therefore, the organisms responsible for the measured BNF rates remain poorly understood. Furthermore, there is little direct evidence, at this time, to support the hypothesis that heterotrophic N2 fixation contributes significantly to oceanic BNF rates based on our analysis of heterotrophic cell-specific N2 fixation rates required to explain BNF rates reported in previously published studies.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
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16
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Rahav E, Bar-Zeev E, Ohayon S, Elifantz H, Belkin N, Herut B, Mulholland MR, Berman-Frank I. Dinitrogen fixation in aphotic oxygenated marine environments. Front Microbiol 2013; 4:227. [PMID: 23986748 PMCID: PMC3753716 DOI: 10.3389/fmicb.2013.00227] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 07/26/2013] [Indexed: 11/13/2022] Open
Abstract
We measured N2 fixation rates from oceanic zones that have traditionally been ignored as sources of biological N2 fixation; the aphotic, fully oxygenated, nitrate (NO−3)-rich, waters of the oligotrophic Levantine Basin (LB) and the Gulf of Aqaba (GA). N2 fixation rates measured from pelagic aphotic waters to depths up to 720 m, during the mixed and stratified periods, ranged from 0.01 nmol N L−1 d−1 to 0.38 nmol N L−1 d−1. N2 fixation rates correlated significantly with bacterial productivity and heterotrophic diazotrophs were identified from aphotic as well as photic depths. Dissolved free amino acid amendments to whole water from the GA enhanced bacterial productivity by 2–3.5 fold and N2 fixation rates by ~2-fold in samples collected from aphotic depths while in amendments to water from photic depths bacterial productivity increased 2–6 fold while N2 fixation rates increased by a factor of 2 to 4 illustrating that both BP and heterotrophic N2 fixation were carbon limited. Experimental manipulations of aphotic waters from the LB demonstrated a significant positive correlation between transparent exopolymeric particle (TEP) concentrations and N2 fixation rates. This suggests that sinking organic material and high carbon (C): nitrogen (N) micro-environments (such as TEP-based aggregates or marine snow) could support high heterotrophic N2 fixation rates in oxygenated surface waters and in the aphotic zones. Indeed, our calculations show that aphotic N2 fixation accounted for 37 to 75% of the total daily integrated N2 fixation rates at both locations in the Mediterranean and Red Seas with rates equal or greater to those measured from the photic layers. Moreover, our results indicate that that while N2 fixation may be limited in the surface waters, aphotic, pelagic N2 fixation may contribute significantly to new N inputs in other oligotrophic basins, yet it is currently not included in regional or global N budgets.
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Affiliation(s)
- Eyal Rahav
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University Ramat Gan, Israel ; Israel Oceanographic and Limnological Research, National Institute of Oceanography Haifa, Israel
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17
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Drami D, Yacobi YZ, Stambler N, Kress N. Seawater quality and microbial communities at a desalination plant marine outfall. A field study at the Israeli Mediterranean coast. WATER RESEARCH 2011; 45:5449-5462. [PMID: 21889185 DOI: 10.1016/j.watres.2011.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 08/02/2011] [Accepted: 08/05/2011] [Indexed: 05/31/2023]
Abstract
Global desalination quadrupled in the last 15 years and the relative importance of seawater desalination by reverse osmosis (SWRO) increased as well. While the technological aspects of SWRO plants are extensively described, studies on the environmental impact of brine discharge are lacking, in particular in situ marine environmental studies. The Ashqelon SWRO plant (333,000 m(3) d(-1) freshwater) discharges brine and backwash of the pre-treatment filters (containing ferric hydroxide coagulant) at the seashore, next to the cooling waters of a power plant. At the time of this study brine and cooling waters were discharged continuously and the backwash discharge was pulsed, with a frequency dependent on water quality at the intake. The effects of the discharges on water quality and neritic microbial community were identified, quantified and attributed to the different discharges. The mixed brine-cooling waters discharge increased salinity and temperature at the outfall, were positively buoyant, and dispersed at the surface up to 1340 m south of the outfall. Nutrient concentrations were higher at the outfall while phytoplankton densities were lower. Chlorophyll-a and picophytoplankton cell numbers were negatively correlated with salinity, but more significantly with temperature probably as a result of thermal pollution. The discharge of the pulsed backwash increased turbidity, suspended particulate matter and particulate iron and decreased phytoplankton growth efficiency at the outfall, effects that declined with distance from the outfall. The discharges clearly reduced primary production but we could not attribute the effect to a specific component of the discharge. Bacterial production was also affected but differently in the three surveys. The combined and possible synergistic effects of SWRO desalination along the Israeli shoreline should be taken into account when the three existing plants and additional ones are expected to produce 2 Mm(3) d(-1) freshwater by 2020.
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Affiliation(s)
- Dror Drami
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
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18
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Krom MD. Insights on nitrogen balance in the Eastern Mediterranean Sea. Environ Microbiol 2011; 13:851-3. [PMID: 21453438 DOI: 10.1111/j.1462-2920.2010.02404.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael D Krom
- Earth and Biosphere Insititute & water@leeds, School of Earth and Environment, Leeds University, Woodhouse Lane, Leeds LS2 9JT, UK.
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