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Zhang L, Okabe S. Ecological niche differentiation among anammox bacteria. WATER RESEARCH 2020; 171:115468. [PMID: 31926373 DOI: 10.1016/j.watres.2020.115468] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/03/2019] [Accepted: 01/02/2020] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria can directly convert ammonium and nitrite to nitrogen gas anaerobically and were responsible for a substantial part of the fixed nitrogen loss and re-oxidation of nitrite to nitrate in freshwater and marine ecosystems. Although a wide variety of studies have been undertaken to investigate the abundance and biodiversity of anammox bacteria so far, ecological niche differentiation of anammox bacteria is still not fully understood. To assess their growth behavior and consequent population dynamics at a given environment, the Monod model is often used. Here, we summarize the Monod kinetic parameters such as the maximum specific growth rate (μmax) and the half-saturation constant for nitrite (KNO2-) and ammonium (KNH4+) of five known candidatus genera of anammox bacteria. We also discuss potential pivotal environmental factors and metabolic flexibility that influence the community compositions of anammox bacteria. Particularly biodiversity of the genus "Scalindua" might have been largely underestimated. Several anammox bacteria have been successfully enriched from various source of biomass. We reevaluate their enrichment methods and culture medium compositions to gain a clue of niche differentiation of anammox bacteria. Furthermore, we formulate the current issues that must be addressed. Overall this review re-emphasizes the importance of enrichment cultures (preferably pure cultures), physiological characterization and direct microbial competition studies using enrichment cultures in laboratories.
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Affiliation(s)
- Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Sapporo, Hokkaido, 060-8628, Japan.
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52
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Fernandes GL, Shenoy BD, Damare SR. Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing. Front Microbiol 2020; 10:3153. [PMID: 32038585 PMCID: PMC6985565 DOI: 10.3389/fmicb.2019.03153] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/30/2019] [Indexed: 11/13/2022] Open
Abstract
The Indian Ocean harbors oxygen minimum zones (OMZs) in the Arabian Sea and Bay of Bengal, with dissolved oxygen < 20 μM, located at the mid-depths of the water column. Till date, high-throughput sequence-data on depth-wise distribution of prokaryotic communities have rarely been reported from these OMZs. The present study aimed to characterize the prokaryotic diversity inhabiting Arabian Sea Time Series (ASTS) and India's Idea 2 (II2) in the Arabian Sea, and Bay of Bengal Time Series (BoBTS) in the Bay of Bengal OMZs based on amplicon sequencing of 16S rRNA gene regions, along six sampled depths in the water column. High prokaryotic richness was observed in the Arabian Sea and Bay of Bengal samples. Operational taxonomic units (OTUs) in the range of 1249-3298 were identified, wherein, less prokaryotic diversity was observed at surface and within oxygen minimum depths. At phylum level, most OTUs were affiliated to Bacteroidetes, Chloroflexi, Cyanobacteria, Marinimicrobia, Planctomycetes, and Proteobacteria. Prokaryotic community differed between ASTS, II2 and BoBTS locations along varying physicochemical conditions. Predictive functional profiling of the bacterial communities suggested the involvement of abundant microbes in nitrogen and sulfur metabolism pathways. Bacterial isolates belonging to genera from the clades, δ-Proteobacteria and γ-Proteobacteria, described previously for their participation in biogeochemical cycling of N-and-S in the OMZs were reported from deoxygenated waters of both the basins. Bacteria involved in anammox such as Candidatus Scalindua were found to be relatively high at ASTS and II2 locations in the Arabian Sea. Further studies are required to ascertain the role of abundant bacteria along the dynamic oceanographic processes in the OMZs.
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Affiliation(s)
- Genevieve L Fernandes
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India.,Department of Microbiology, Goa University, Taleigao, India
| | | | - Samir R Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, India
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53
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2019; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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55
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Happel EM, Markussen T, Teikari JE, Huchaiah V, Alneberg J, Andersson AF, Sivonen K, Middelboe M, Kisand V, Riemann L. Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites. FEMS Microbiol Ecol 2019; 95:5545591. [PMID: 31397876 DOI: 10.1093/femsec/fiz123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022] Open
Abstract
Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.
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Affiliation(s)
- Elisabeth M Happel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Trine Markussen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jonna E Teikari
- University of Helsinki, Department of Microbiology, Helsinki, Finland
| | - Vimala Huchaiah
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Johannes Alneberg
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Kaarina Sivonen
- University of Helsinki, Department of Microbiology, Helsinki, Finland
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Veljo Kisand
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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56
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Yang QS, Dong JD, Ahmad M, Ling J, Zhou WG, Tan YH, Zhang YZ, Shen DD, Zhang YY. Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs. BMC Microbiol 2019; 19:188. [PMID: 31416417 PMCID: PMC6694519 DOI: 10.1186/s12866-019-1565-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea. RESULTS The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high. CONCLUSIONS The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.
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Affiliation(s)
- Qing-Song Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-De Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Wei-Guo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye-Hui Tan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yuan-Zhou Zhang
- State Oceanic Administration Sansha Marine Environmental Monitoring Center Station, Haikou, 570311, China
| | - Dan-Dan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, 18119, Warnemünde, Germany.
| | - Yan-Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
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57
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Direct Detection of Heterotrophic Diazotrophs Associated with Planktonic Aggregates. Sci Rep 2019; 9:9288. [PMID: 31243322 PMCID: PMC6594930 DOI: 10.1038/s41598-019-45505-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/24/2019] [Indexed: 12/03/2022] Open
Abstract
N2 fixation by planktonic heterotrophic diazotrophs is more wide spread than previously thought, including environments considered “unfavorable” for diazotrophy. These environments include a substantial fraction of the aquatic biosphere such as eutrophic estuaries with high ambient nitrogen concentrations and oxidized aphotic water. Different studies suggested that heterotrophic diazotrophs associated with aggregates may promote N2 fixation in such environments. However, this association was never validated directly and relies mainly on indirect relationships and different statistical approaches. Here, we identified, for the first time, a direct link between active heterotrophic diazotrophs and aggregates that comprise polysaccharides. Our new staining method combines fluorescent tagging of active diazotrophs by nitrogenase-immunolabeling, polysaccharides staining by Alcian blue or concanavalin-A, and total bacteria via nucleic-acid staining. Concomitant to N2 fixation rates and bacterial activity, this new method provided specific localization of heterotrophic diazotrophs on artificial and natural aggregates. We postulate that the insights gained by this new visualization approach will have a broad significance for future research on the aquatic nitrogen cycle, including environments in which diazotrophy has traditionally been overlooked.
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Albright MBN, Timalsina B, Martiny JBH, Dunbar J. Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea. MICROBIAL ECOLOGY 2019; 77:597-606. [PMID: 30105504 DOI: 10.1007/s00248-018-1239-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.
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Affiliation(s)
- Michaeline B N Albright
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, P.O. Box 1663, Los Alamos, NM, 87545, USA.
| | - Bibek Timalsina
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, P.O. Box 1663, Los Alamos, NM, 87545, USA
- Department of Biochemistry, Mississippi State University, Starkville, MS, USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, P.O. Box 1663, Los Alamos, NM, 87545, USA.
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Enhanced Nitrogen Fixation in a glgX-Deficient Strain of Cyanothece sp. Strain ATCC 51142, a Unicellular Nitrogen-Fixing Cyanobacterium. Appl Environ Microbiol 2019; 85:AEM.02887-18. [PMID: 30709817 DOI: 10.1128/aem.02887-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 01/15/2023] Open
Abstract
Cyanobacteria are oxygenic photosynthetic prokaryotes with important roles in the global carbon and nitrogen cycles. Unicellular nitrogen-fixing cyanobacteria are known to be ubiquitous, contributing to the nitrogen budget in diverse ecosystems. In the unicellular cyanobacterium Cyanothece sp. strain ATCC 51142, carbon assimilation and carbohydrate storage are crucial processes that occur as part of a robust diurnal cycle of photosynthesis and nitrogen fixation. During the light period, cells accumulate fixed carbon in glycogen granules to use as stored energy to power nitrogen fixation in the dark. These processes have not been thoroughly investigated, due to the lack of a genetic modification system in this organism. In bacterial glycogen metabolism, the glgX gene encodes a debranching enzyme that functions in storage polysaccharide catabolism. To probe the consequences of modifying the cycle of glycogen accumulation and subsequent mobilization, we engineered a strain of Cyanothece 51142 in which the glgX gene was genetically disrupted. We found that the ΔglgX strain exhibited a higher growth rate than the wild-type strain and displayed a higher rate of nitrogen fixation. Glycogen accumulated to higher levels at the end of the light period in the ΔglgX strain, compared to the wild-type strain. These data suggest that the larger glycogen pool maintained by the ΔglgX mutant is able to fuel greater growth and nitrogen fixation ability.IMPORTANCE Cyanobacteria are oxygenic photosynthetic bacteria that are found in a wide variety of ecological environments, where they are important contributors to global carbon and nitrogen cycles. Genetic manipulation systems have been developed in a number of cyanobacterial strains, allowing both the interruption of endogenous genes and the introduction of new genes and entire pathways. However, unicellular diazotrophic cyanobacteria have been generally recalcitrant to genetic transformation. These cyanobacteria are becoming important model systems to study diurnally regulated processes. Strains of the Cyanothece genus have been characterized as displaying robust growth and high rates of nitrogen fixation. The significance of our study is in the establishment of a genetic modification system in a unicellular diazotrophic cyanobacterium, the demonstration of the interruption of the glgX gene in Cyanothece sp. strain ATCC 51142, and the characterization of the increased nitrogen-fixing ability of this strain.
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60
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Annual nitrification dynamics in a seasonally ice-covered lake. PLoS One 2019; 14:e0213748. [PMID: 30893339 PMCID: PMC6426244 DOI: 10.1371/journal.pone.0213748] [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: 10/23/2018] [Accepted: 02/27/2019] [Indexed: 11/25/2022] Open
Abstract
We investigated the variability in ammonia oxidation (AO) rates and the presence of ammonia-oxidizing archaea and bacteria (AOB and AOA) over an annual cycle in the water column of a small, seasonnally ice covered, temperate shield lake. AO, the first step of nitrification, was measured in situ using 15N-labelled ammonium (NH4+) at 1% and 10% of photosynthetic active radiation during day and at the same depths during night. AO was active across seasons and light levels, ranging from undetectable to 333 nmol L-1 d-1 with peak activity in winter under ice cover. NH4+ concentration was the single most important positive predictor of AO rates. High NH4+ concentrations and reduced chlorophyll a concentrations under ice, which favoured AO, were coherent with high nitrate concentrations and super saturation in nitrous oxide. When targeting the ammonia monooxygenase (amoA) gene in samples from the photic zone, we found AOA to be omnipresent throughout the year while AOB were observed predominantly during winter. Our results demonstrate that AO is an ongoing process in sunlit surface waters of temperate lakes and at all seasons with pronounced nitrification activity observed during winter under ice. The combination of high NH4+ concentrations due to fall overturn, reduced light availability that limited phytoplankton competition, and the presence of AOB together with AOA apparently favoured these elevated rates under ice. We suggest that lake ice could be a control point for nitrification in oligotrophic temperate shield lakes, characterized as a moment and place that exerts disproportionate influence on the biogeochemical behaviour of ecosystems.
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61
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Evaluation of the Nitrous Oxide Emission Reduction Potential of an Aerobic Bioreactor Packed with Carbon Fibres for Swine Wastewater Treatment. ENERGIES 2019. [DOI: 10.3390/en12061013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas that is emitted from wastewater treatment plants. To reduce emissions of N2O from swine wastewater treatment plants, we constructed an experimental aerobic bioreactor packed with carbon fibres (ca. 1 m3 bioreactor) as an alternative to conventional activated sludge treatment. The N2O emission factor for the aerobic bioreactor packed with carbon fibres (CF) was 0.002 g N2O-N/g TN-load and the value for the typical activated sludge (AS) reactor was 0.013 g N2O-N/g TN-load. The CF treatment method achieved more than 80% reduction of N2O emissions, compared with the AS treatment method. The experimental introduction of a CF carrier into an actual wastewater treatment plant also resulted in a large reduction in N2O generation. Specifically, the N2O emission factors decreased from 0.040 to 0.005 g N2O-N/g TN-load following application of the carrier. This shows that it is possible to reduce N2O generation by more than 80% by using a CF carrier during the operation of an actual wastewater treatment plant. Some bacteria from the phylum Chloroflexi, which are capable of reducing N2O emissions, were detected at a higher frequency in the biofilm on the CF carrier than in the biofilm formed on the AS reactor.
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62
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Richert I, Yager PL, Dinasquet J, Logares R, Riemann L, Wendeberg A, Bertilsson S, Scofield DG. Summer comes to the Southern Ocean: how phytoplankton shape bacterioplankton communities far into the deep dark sea. Ecosphere 2019. [DOI: 10.1002/ecs2.2641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Inga Richert
- Department of Ecology and Genetics: Limnology Uppsala University Uppsala Sweden
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Patricia L. Yager
- Department of Marine Science University of Georgia Athens Georgia USA
| | - Julie Dinasquet
- Department of Biology University of Copenhagen Helsingør Denmark
- Scripps Institution of Oceanography UCSD San Diego California USA
| | | | - Lasse Riemann
- Department of Biology University of Copenhagen Helsingør Denmark
| | - Annelie Wendeberg
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Stefan Bertilsson
- Department of Ecology and Genetics: Limnology Uppsala University Uppsala Sweden
- Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Douglas G. Scofield
- Department of Ecology and Genetics: Evolutionary Biology Uppsala University Uppsala Sweden
- Uppsala Multidisciplinary Center for Advanced Computational Science Uppsala University Uppsala Sweden
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63
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Efficient recycling of nutrients in modern and past hypersaline environments. Sci Rep 2019; 9:3718. [PMID: 30842491 PMCID: PMC6403304 DOI: 10.1038/s41598-019-40174-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/11/2019] [Indexed: 11/09/2022] Open
Abstract
The biogeochemistry of hypersaline environments is strongly influenced by changes in biological processes and physicochemical parameters. Although massive evaporation events have occurred repeatedly throughout Earth history, their biogeochemical cycles and global impact remain poorly understood. Here, we provide the first nitrogen isotopic data for nutrients and chloropigments from modern shallow hypersaline environments (solar salterns, Trapani, Italy) and apply the obtained insights to δ15N signatures of the Messinian salinity crisis (MSC) in the late Miocene. Concentrations and δ15N of chlorophyll a, bacteriochlorophyll a, nitrate, and ammonium in benthic microbial mats indicate that inhibition of nitrification suppresses denitrification and anammox, resulting in efficient ammonium recycling within the mats and high primary productivity. We also suggest that the release of 15N-depleted NH3(gas) with increasing salinity enriches ammonium 15N in surface brine (≈34.0‰). Such elevated δ15N is also recorded in geoporphyrins isolated from sediments of the MSC peak (≈20‰), reflecting ammonium supply sufficient for sustaining phototrophic primary production. We propose that efficient nutrient supply combined with frequent bottom-water anoxia and capping of organic-rich sediments by evaporites of the Mediterranean MSC could have contributed to atmospheric CO2 reduction during the late Miocene.
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64
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Calderoli PA, Espínola FJ, Dionisi HM, Gil MN, Jansson JK, Lozada M. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. PLoS One 2018; 13:e0207606. [PMID: 30496195 PMCID: PMC6264515 DOI: 10.1371/journal.pone.0207606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.
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Affiliation(s)
- Priscila A Calderoli
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Fernando J Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Mónica N Gil
- Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina.,Laboratorio de Química General y Análisis de Elementos, CCT CONICET CENPAT, Puerto Madryn, Chubut Province, Argentina
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
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65
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Bolay P, Muro-Pastor MI, Florencio FJ, Klähn S. The Distinctive Regulation of Cyanobacterial Glutamine Synthetase. Life (Basel) 2018; 8:E52. [PMID: 30373240 PMCID: PMC6316151 DOI: 10.3390/life8040052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/23/2018] [Accepted: 10/25/2018] [Indexed: 12/02/2022] Open
Abstract
Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes. These include the interaction with small proteins, the so-called inactivating factors (IFs) that inhibit GS linearly with their abundance. In addition to this protein interaction-based regulation of GS activity, cyanobacteria use alternative elements to control the synthesis of GS and IFs at the transcriptional level. Moreover, cyanobacteria evolved unique RNA-based regulatory mechanisms such as glutamine riboswitches to tightly tune IF abundance. In this review, we aim to outline the current knowledge on the distinctive features of the cyanobacterial GS encompassing the overall control of its activity, sensing the nitrogen status, transcriptional and post-transcriptional regulation, as well as strain-specific differences.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
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66
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Morando M, Capone DG. Direct Utilization of Organic Nitrogen by Phytoplankton and Its Role in Nitrogen Cycling Within the Southern California Bight. Front Microbiol 2018; 9:2118. [PMID: 30271389 PMCID: PMC6146108 DOI: 10.3389/fmicb.2018.02118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/20/2018] [Indexed: 01/21/2023] Open
Abstract
The new production model attempts to quantify the amount of organic material exported from surface waters based on the form of nitrogen (N) being utilized. Dissolved organic N (DON) is rarely assessed during such investigations and even less is understood about the organisms involved in these different transformations within the complex N cycle. Stable isotope probing (SIP) and uptake activity measurements were combined to investigate the dynamics of new and regenerated production during the spring within the Southern California Bight (SCB). We examined the uptake and assimilation of several nitrogenous substrates at several depths to quantify these processes and identify the active communities across all three domains of life that are driving each transformation. Several reoccurring members closely related to the eukaryotic diatom Chaetoceros, dominated assimilation of NO3 - and urea through the water column, and contributed greatly to the overall production. Prokaryotic growth was predominantly carried out through NH4 + assimilation with transitions from Flavobacteria to Rhodobacteraceae and Marine Group II Euryarchaeota to Marine Group I Thaumarchaeota with increasing depth for bacterial and archaeal clades, respectively. Only urea uptake and SIP activity correlated with each other, likely demonstrating that cellular transport and incorporation of urea were coupled. SIP was therefore able to identify the organisms primarily responsible for urea cycling at each depth during this investigation. The role of diatoms within high nutrient areas are well defined but their part in DON cycling in highly stratified regimes is less well understood. Here we demonstrate their ability to efficiently scavenge urea in situ, allowing certain diatoms to outcompete the rest of the community. This diversion of DON away from the trophically inefficient microbial loop directly back into the larger, particle forming populations would alter the current view of microbial food webs. This proposed "phytoplankton shunt" of organic material could potentially enhance the biological pump by mitigating losses due to trophic transfers while increasing DON flux due to ballasting. Our results provide unique biogeochemical and ecological insight into the dynamics and diversity of N cycling and the organisms involved within the surface waters of the SCB.
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Affiliation(s)
- Michael Morando
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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67
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Haywood BJ, White JR, Cook RL. Investigation of an early season river flood pulse: Carbon cycling in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 635:867-877. [PMID: 29710609 PMCID: PMC5988978 DOI: 10.1016/j.scitotenv.2018.03.379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 06/01/2023]
Abstract
The January 2016 Bonnet Carré Spillway (BCS) opening resulted in a large-scale Mississippi River (MR) flood discharge that qualitatively and quantitatively impacted the dissolved organic matter (DOM) cycling in the Lake Pontchartrain Estuary (LPE) located in Louisiana, USA. This early season flood event was a result of the delay of snow formation caused by warmer than normal watershed temperatures. During the diversion period and the subsequent weeks, the LPE water temperature remained lower than pre-flood water temperatures, suppressing carbon cycling. Following that period, the water temperature increased, leading to an increase in the rate of abiotic and biological carbon processing (i.e., mineralization, degradation, and consumption). There were multiple and abnormally high discharges into LPE from the northern tributaries, totaling 43% of the MR flood discharge. As a secondary DOM source, the northern tributaries discharge was qualitatively and quantitatively different from the discharge originating from the river or estuarine sources. The dominant DOM source was determined using satellite images in conjunction with UV-Vis, fluorescence EEMs, and PARAFAC indicators. Overall, the three sources (MR, northern tributaries, and LPE) characteristics were identified by UV-Vis, fluorescence EEMs, and PARAFAC parameters, namely: i) spectral slope (S275), serving as an indicator of lignin-like compounds' molecular weights, with a trend of MR > northern tributaries > LPE; ii) biological index (BIX), indicating freshness of DOM, with a trend of LPE > MR > northern tributaries; and iii) Fluorophore T intensity, serving as an indicator of the amount of terrestrial-like sourced DOM, with a trend of northern tributaries > LPE > MR. It was possible to identify DOM sources and monitor DOM transformation in the water column, increasing our understanding of DOM, carbon, and nitrogen ecological processing.
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Affiliation(s)
- Benjamin J Haywood
- Department of Chemistry, Louisiana State University, Baton Rouge, United States
| | - John R White
- Department of Oceanography & Coastal Sciences, Louisiana State University, Baton Rouge, United States
| | - Robert L Cook
- Department of Chemistry, Louisiana State University, Baton Rouge, United States.
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68
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Lane PA. Ecosystems as Chimeras: A thought experiment in Rosennean Complexity. ECOLOGICAL COMPLEXITY 2018. [DOI: 10.1016/j.ecocom.2018.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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69
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Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ. Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. ISME JOURNAL 2018; 12:2706-2722. [PMID: 29991764 DOI: 10.1038/s41396-018-0223-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.
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Affiliation(s)
- Sangita Ganesh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.,Radiant Genomics, Emeryville, 94608, CA, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Laura A Bristow
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Nigel Blackwood
- Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Montserrat Aldunate
- Graduate Program in Oceanography, Department of Oceanography, Faculty of Natural Sciences and Oceanography, University of Concepción, Casilla 160-C, Concepción, Chile.,Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | - Annie Bourbonnais
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Mark A Altabet
- School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | | | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.
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70
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Inorganic carbon and nitrogen assimilation in cellular compartments of a benthic kleptoplastic foraminifer. Sci Rep 2018; 8:10140. [PMID: 29973634 PMCID: PMC6031614 DOI: 10.1038/s41598-018-28455-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 11/08/2022] Open
Abstract
Haynesina germanica, an ubiquitous benthic foraminifer in intertidal mudflats, has the remarkable ability to isolate, sequester, and use chloroplasts from microalgae. The photosynthetic functionality of these kleptoplasts has been demonstrated by measuring photosystem II quantum efficiency and O2 production rates, but the precise role of the kleptoplasts in foraminiferal metabolism is poorly understood. Thus, the mechanism and dynamics of C and N assimilation and translocation from the kleptoplasts to the foraminiferal host requires study. The objective of this study was to investigate, using correlated TEM and NanoSIMS imaging, the assimilation of inorganic C and N (here ammonium, NH4+) in individuals of a kleptoplastic benthic foraminiferal species. H. germanica specimens were incubated for 20 h in artificial seawater enriched with H13CO3- and 15NH4+ during a light/dark cycle. All specimens (n = 12) incorporated 13C into their endoplasm stored primarily in the form of lipid droplets. A control incubation in darkness resulted in no 13C-uptake, strongly suggesting that photosynthesis is the process dominating inorganic C assimilation. Ammonium assimilation was observed both with and without light, with diffuse 15N-enrichment throughout the cytoplasm and distinct 15N-hotspots in fibrillar vesicles, electron-opaque bodies, tubulin paracrystals, bacterial associates, and, rarely and at moderate levels, in kleptoplasts. The latter observation might indicate that the kleptoplasts are involved in N assimilation. However, the higher N assimilation observed in the foraminiferal endoplasm incubated without light suggests that another cytoplasmic pathway is dominant, at least in darkness. This study clearly shows the advantage provided by the kleptoplasts as an additional source of carbon and provides observations of ammonium uptake by the foraminiferal cell.
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71
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Cho S, Kim J, Kim S, Lee SS. Nitrogen and phosphorus treatment of marine wastewater by a laboratory-scale sequencing batch reactor with eco-friendly marine high-efficiency sediment. ENVIRONMENTAL TECHNOLOGY 2018; 39:1721-1732. [PMID: 28590161 DOI: 10.1080/09593330.2017.1337234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED We screened and identified a NH3-N-removing bacterial strain, Bacillus sp. KGN1, and a [Formula: see text] removing strain, Vibrio sp. KGP1, from 960 indigenous marine isolates from seawater and marine sediment from Tongyeong, South Korea. We developed eco-friendly high-efficiency marine sludge (eco-HEMS), and inoculated these marine bacterial strains into the marine sediment. A laboratory-scale sequencing batch reactor (SBR) system using the eco-HEMS for marine wastewater from land-based fish farms improved the treatment performance as indicated by 88.2% removal efficiency (RE) of total nitrogen (initial: 5.6 mg/L) and 90.6% RE of total phosphorus (initial: 1.2 mg/L) under the optimal operation conditions (food and microorganism (F/M) ratio, 0.35 g SCODCr/g mixed liquor volatile suspended solids (MLVSS)·d; dissolved oxygen (DO) 1.0 ± 0.2 mg/L; hydraulic retention time (HRT), 6.6 h; solids retention time (SRT), 12 d). The following kinetic parameters were obtained: cell yield (Y), 0.29 g MLVSS/g SCODCr; specific growth rate (µ), 0.06 d-1; specific nitrification rate (SNR), 0.49 mg NH3-N/g MLVSS·h; specific denitrification rate (SDNR), 0.005 mg [Formula: see text]/g MLVSS·h; specific phosphorus uptake rate (SPUR), 0.12 mg [Formula: see text]/g MLVSS·h. The nitrogen- and phosphorus-removing bacterial strains comprised 18.4% of distribution rate in the microbial community of eco-HEMS under the optimal operation conditions. Therefore, eco-HEMS effectively removed nitrogen and phosphorus from highly saline marine wastewater from land-based fish farms with improving SNR, SDNR, and SPUR values in more diverse microbial communities. ABBREVIATIONS DO: dissolved oxygen; Eco-HEMS: eco-friendly high efficiency marine sludge; F/M: food and microorganism ratio; HRT: hydraulic retention time; ML(V)SS: mixed liquor (volatile) suspended solids; NCBI: National Center for Biotechnology Information; ND: not determined; qPCR: quantitative real-time polymerase chain reaction; RE: removal efficiency; SBR: sequencing batch reactor; SD: standard deviation; SDNR: specific denitrification rate; SNR: specific nitrification rate; SPUR: specific phosphate uptake rate; SRT: solids retention time; T-N: total nitrogen; T-P: total phosphorus; (V)SS: (volatile) suspended solids; w.w.: wet weight.
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Affiliation(s)
- Seonghyeon Cho
- a Department of Biological Engineering , Kyonggi University , Suwon-si , Republic of Korea
| | - Jinsoo Kim
- b Department of Life Science , Kyonggi University , Suwon-si , Republic of Korea
| | - Sungchul Kim
- c Department of Environmental Energy Engineering , Kyonggi University , Suwon-si , Republic of Korea
| | - Sang-Seob Lee
- a Department of Biological Engineering , Kyonggi University , Suwon-si , Republic of Korea
- b Department of Life Science , Kyonggi University , Suwon-si , Republic of Korea
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72
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Zhang Y, Song C, Ji L, Liu Y, Xiao J, Cao X, Zhou Y. Cause and effect of N/P ratio decline with eutrophication aggravation in shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1294-1302. [PMID: 30857093 DOI: 10.1016/j.scitotenv.2018.01.327] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/03/2018] [Accepted: 01/31/2018] [Indexed: 06/09/2023]
Abstract
To explore the relationship and cause and effect between eutrophication and the nitrogen (N)/phosphorus (P) ratio, samples from 38 lakes in Wuhan City, China, with differing degrees of eutrophication, were collected for nutrient levels and extracellular enzyme activities (EEA) in the water column from July 2011 to November 2011. The phosphorus fraction, abundance and potential denitrification rate (PDR) as well as community composition of nirS-type denitrifier in sediments of five typical lakes were further analyzed. A higher trophic level index (TSI) corresponded to a lower N/P ratio, which can be attributed to a loss of N and an increase in P. Specifically, in more eutrophic lakes, the enrichment of total organic carbon and all forms of P in sediments could fuel PDR by shaping community composition and increasing the abundance of nirS-type denitrifier as evidenced by correlation and redundancy analysis, ultimately resulting in a loss of N. Meanwhile, iron-bound phosphorus release induced by anoxia and the hydrolysis of organic P accounted for the observed increase of P in the water column. The lower N/P ratio facilitated the production of leucine aminopeptidase, which was unexpectedly induced by high P but not by low N. Similarly, alkaline phosphatase was induced by high N but not by low P. These findings indicate a mutual coupling and interplay between N and P cycling and confirm our hypothesis that P accumulation accelerates N loss in the process of eutrophication.
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Affiliation(s)
- Yao Zhang
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health and Management, Hubei University of Medicine, Shiyan 442000, PR China
| | - Chunlei Song
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, 7# Donghu South Road, Wuhan 430072, PR China.
| | - Lei Ji
- College of Life Science, Huaibei Normal University, Huaibei 235000, PR China
| | - Yuqian Liu
- Yellow River Water Resources Protection Institution, Zhengzhou 450004, PR China
| | - Jian Xiao
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, 7# Donghu South Road, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100039, PR China
| | - Xiuyun Cao
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, 7# Donghu South Road, Wuhan 430072, PR China.
| | - Yiyong Zhou
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, 7# Donghu South Road, Wuhan 430072, PR China.
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73
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Wu X, Wu L, Liu Y, Zhang P, Li Q, Zhou J, Hess NJ, Hazen TC, Yang W, Chakraborty R. Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession. Front Microbiol 2018; 9:1234. [PMID: 29937762 PMCID: PMC6002664 DOI: 10.3389/fmicb.2018.01234] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.
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Affiliation(s)
- Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Yina Liu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States
| | - Ping Zhang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Qinghao Li
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,National Key Laboratory of Crystal Materials, School of Physics, Shandong University, Jinan, China
| | - Jizhong Zhou
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Nancy J Hess
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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74
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Li YY, Chen XH, Xie ZX, Li DX, Wu PF, Kong LF, Lin L, Kao SJ, Wang DZ. Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean. Front Microbiol 2018; 9:797. [PMID: 29922238 PMCID: PMC5996900 DOI: 10.3389/fmicb.2018.00797] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/10/2018] [Indexed: 11/13/2022] Open
Abstract
Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta-, and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NOX-N was significantly correlated with structure and distribution of N2-fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A (urtA) and ferredoxin-nitrate reductase, while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea metabolism is of vital ecological importance in N-deficient regimes.
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Affiliation(s)
- Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xiao-Huang Chen
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
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75
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Yazdani Foshtomi M, Leliaert F, Derycke S, Willems A, Vincx M, Vanaverbeke J. The effect of bio-irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene. PLoS One 2018; 13:e0192391. [PMID: 29408934 PMCID: PMC5800672 DOI: 10.1371/journal.pone.0192391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 01/23/2018] [Indexed: 11/18/2022] Open
Abstract
The presence of large densities of the piston-pumping polychaete Lanice conchilega can have important consequences for the functioning of marine sediments. It is considered both an allogenic and an autogenic ecosystem engineer, affecting spatial and temporal biogeochemical gradients (oxygen concentrations, oxygen penetration depth and nutrient concentrations) and physical properties (grain size) of marine sediments, which could affect functional properties of sediment-inhabiting microbial communities. Here we investigated whether density-dependent effects of L. conchilega affected horizontal (m-scale) and vertical (cm-scale) patterns in the distribution, diversity and composition of the typical nosZ gene in the active denitrifying organisms. This gene plays a major role in N2O reduction in coastal ecosystems as the last step completing the denitrification pathway. We showed that both vertical and horizontal composition and richness of nosZ gene were indeed significantly affected when large densities of the bio-irrigator were present. This could be directly related to allogenic ecosystem engineering effects on the environment, reflected in increased oxygen penetration depth and oxygen concentrations in the upper cm of the sediment in high densities of L. conchilega. A higher diversity (Shannon diversity and inverse Simpson) of nosZ observed in patches with high L. conchilega densities (3,185-3,440 ind. m-2) at deeper sediment layers could suggest a downward transport of NO3- to deeper layers resulting from bio-irrigation as well. Hence, our results show the effect of L. conchilega bio-irrigation activity on denitrifying organisms in L. conchilega reefs.
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Affiliation(s)
- Maryam Yazdani Foshtomi
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- CeMoFE, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- Botanic Garden Meise, Meise, Belgium
| | - Sofie Derycke
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Institute for Agricultural and Fisheries Research (ILVO), Ostend, Belgium
| | - Anne Willems
- CeMoFE, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Magda Vincx
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
| | - Jan Vanaverbeke
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- Marine Ecology and Management, Operational Directorate Natural Environment (OD Nature), Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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76
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A missing link in the estuarine nitrogen cycle?: Coupled nitrification-denitrification mediated by suspended particulate matter. Sci Rep 2018; 8:2282. [PMID: 29396528 PMCID: PMC5797115 DOI: 10.1038/s41598-018-20688-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/23/2018] [Indexed: 11/17/2022] Open
Abstract
In estuarine and coastal ecosystems, the majority of previous studies have considered coupled nitrification-denitrification (CND) processes to be exclusively sediment based, with little focus on suspended particulate matter (SPM) in the water column. Here, we present evidence of CND processes in the water column of Hangzhou Bay, one of the largest macrotidal embayments in the world. Spearman’s correlation analysis showed that SPM was negatively correlated with nitrate (rho = −0.372, P = 0.018) and marker genes for nitrification and denitrification in the water column were detected by quantitative PCR analysis. The results showed that amoA and nir gene abundances strongly correlated with SPM (all P < 0.01) and the ratio of amoA/nir strongly correlated with nitrate (rho = −0.454, P = 0.003). Furthermore, aggregates consisting of nitrifiers and denitrifiers on SPM were also detected by fluorescence in situ hybridization. Illumina MiSeq sequencing further showed that ammonia oxidizers mainly belonged to the genus Nitrosomonas, while the potential denitrifying genera Bradyrhizobium, Comamonas, Thauera, Stenotrophomonas, Acinetobacter, Anaeromyxobacter, Sulfurimonas, Paenibacillus and Sphingobacterium showed significant correlations with SPM (all P < 0.01). This study suggests that SPM may provide a niche for CND processes to occur, which has largely been missing from our understanding of nitrogen cycling in estuarine waters.
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77
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Electrocatalytic ammonia oxidation over a nickel foam electrode: Role of Ni(OH)2(s)-NiOOH(s) nanocatalysts. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.01.045] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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78
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Pratama AA, van Elsas JD. The 'Neglected' Soil Virome - Potential Role and Impact. Trends Microbiol 2018; 26:649-662. [PMID: 29306554 DOI: 10.1016/j.tim.2017.12.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/10/2017] [Accepted: 12/11/2017] [Indexed: 12/29/2022]
Abstract
Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings. We address the information with respect to the abundance, diversity, ecological significance, and effects of, in particular, bacteriophages on their host's evolutionary trajectories. We also identify the main challenges that soil virology faces and the studies that are required to accompany the current developments in marine settings.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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79
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Zhu W, Wang C, Sun F, Zhao L, Dou W, Mao Z, Wu W. Overall bacterial community composition and abundance of nitrifiers and denitrifiers in a typical macrotidal estuary. MARINE POLLUTION BULLETIN 2018; 126:540-548. [PMID: 28978406 DOI: 10.1016/j.marpolbul.2017.09.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/23/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Coupled nitrogen cycling processes can alleviate the negative effects of eutrophication caused by excessive nitrogen load in estuarine ecosystems. The abundance and diversity of nitrifiers and denitrifiers across different environmental gradients were examined in the sediment of Hangzhou Bay. Quantitative PCR and Pearson's correlation analyses suggested that the bacterial ammonia-oxidizers (AOB) were the dominant phylotypes capable of ammonia oxidation, while the nirS-encoding denitrifiers predominated in the denitrification process. Simultaneously, nitrite and pH were found to be the two major factors influencing amoA and nir gene abundances, and the distribution of bacterial communities. Moreover, the ratio of nirS/AOB amoA gene abundance showed negative correlation with nitrite concentration. Fluorescence in situ hybridization further demonstrated that AOB and acetate-denitrifying cells were closely connected and formed obvious aggregates in the sediment. Together, all these results provided us a preliminary insight for coupled nitrification-denitrification processes in the sediment of Hangzhou Bay.
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Affiliation(s)
- Weijing Zhu
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Cheng Wang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Faqian Sun
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Liancheng Zhao
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, 36 Baochu North Road, Hangzhou 310012, China
| | - Wenjie Dou
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, 36 Baochu North Road, Hangzhou 310012, China
| | - Zhihua Mao
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, 36 Baochu North Road, Hangzhou 310012, China
| | - Weixiang Wu
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
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80
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Binod Kumar S, Trivedi H, Baraiya NR, Haldar S. An improved device with an affinity membrane to collect depth specific contamination free water for environmental assessment. Analyst 2018; 143:662-669. [DOI: 10.1039/c7an01528c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The prime requirement for marine water studies is a competent sampling device that can collect water samples perfectly without any contamination to avoid false analysis.
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Affiliation(s)
- Sweta Binod Kumar
- Analytical and Environmental Science Division & CIF
- CSIR-CSMCRI
- Bhavnagar-364002
- India
- Academy of Scientific and Innovative Research
| | - Hardik Trivedi
- Analytical and Environmental Science Division & CIF
- CSIR-CSMCRI
- Bhavnagar-364002
- India
| | | | - Soumya Haldar
- Analytical and Environmental Science Division & CIF
- CSIR-CSMCRI
- Bhavnagar-364002
- India
- Academy of Scientific and Innovative Research
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81
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Dolch LJ, Lupette J, Tourcier G, Bedhomme M, Collin S, Magneschi L, Conte M, Seddiki K, Richard C, Corre E, Fourage L, Laeuffer F, Richards R, Reith M, Rébeillé F, Jouhet J, McGinn P, Maréchal E. Nitric Oxide Mediates Nitrite-Sensing and Acclimation and Triggers a Remodeling of Lipids. PLANT PHYSIOLOGY 2017; 175:1407-1423. [PMID: 28924015 PMCID: PMC5664477 DOI: 10.1104/pp.17.01042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/13/2017] [Indexed: 05/20/2023]
Abstract
Nitric oxide (NO) is an intermediate of the nitrogen cycle, an industrial pollutant, and a marker of climate change. NO also acts as a gaseous transmitter in a variety of biological processes. The impact of environmental NO needs to be addressed. In diatoms, a dominant phylum in phytoplankton, NO was reported to mediate programmed cell death in response to diatom-derived polyunsaturated aldehydes. Here, using the Phaeodactylum Pt1 strain, 2E,4E-decadienal supplied in the micromolar concentration range led to a nonspecific cell toxicity. We reexamined NO biosynthesis and response in Phaeodactylum NO inhibits cell growth and triggers triacylglycerol (TAG) accumulation. Feeding experiments indicate that NO is not produced from Arg but via conversion of nitrite by the nitrate reductase. Genome-wide transcriptional analysis shows that NO up-regulates the expression of the plastid nitrite reductase and genes involved in the subsequent incorporation of ammonium into amino acids, via both Gln synthesis and Orn-urea pathway. The phosphoenolpyruvate dehydrogenase complex is also up-regulated, leading to the production of acetyl-CoA, which can feed TAG accumulation upon exposure to NO. Transcriptional reprogramming leading to higher TAG content is balanced with a decrease of monogalactosyldiacylglycerol (MGDG) in the plastid via posttranslational inhibition of MGDG synthase enzymatic activity by NO. Intracellular and transient NO emission acts therefore at the basis of a nitrite-sensing and acclimating system, whereas a long exposure to NO can additionally induce a redirection of carbon to neutral lipids and a stress response.
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Affiliation(s)
- Lina-Juana Dolch
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Josselin Lupette
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Guillaume Tourcier
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Mariette Bedhomme
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
- Total Refining Chemicals, Tour Michelet, 24 Cours Michelet - La Défense 10, 92069 Paris La Défense Cedex, France
| | - Séverine Collin
- Total Refining Chemicals, Tour Michelet, 24 Cours Michelet - La Défense 10, 92069 Paris La Défense Cedex, France
| | - Leonardo Magneschi
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Melissa Conte
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Khawla Seddiki
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Christelle Richard
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Erwan Corre
- Station Biologique de Roscoff, CNRS - Université Pierre et Marie Curie, Analyses and Bioinformatics for Marine Science, 29680 Roscoff, France
| | - Laurent Fourage
- Total Refining Chemicals, Tour Michelet, 24 Cours Michelet - La Défense 10, 92069 Paris La Défense Cedex, France
| | - Frédéric Laeuffer
- Total Refining Chemicals, Tour Michelet, 24 Cours Michelet - La Défense 10, 92069 Paris La Défense Cedex, France
| | - Robert Richards
- National Research Council of Canada, Aquatic and Crop Resource Development, 1411 Oxford Street, Halifax, Nova Scotia B3H3Z1, Canada
| | - Michael Reith
- National Research Council of Canada, Aquatic and Crop Resource Development, 1411 Oxford Street, Halifax, Nova Scotia B3H3Z1, Canada
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
| | - Patrick McGinn
- National Research Council of Canada, Aquatic and Crop Resource Development, 1411 Oxford Street, Halifax, Nova Scotia B3H3Z1, Canada
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixte de recherche 5168 CNRS - CEA - INRA - Université Grenoble Alpes, Institut de Biosciences Biotechnologies de Grenoble, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France
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82
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Dittami SM, Heesch S, Olsen JL, Collén J. Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae. JOURNAL OF PHYCOLOGY 2017; 53:731-745. [PMID: 28509401 DOI: 10.1111/jpy.12547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 04/19/2017] [Indexed: 05/03/2023]
Abstract
Marine-freshwater and freshwater-marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here, we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized freshwater on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times. Next, we review the early evolutionary events leading to the colonization of current habitats. It is commonly assumed that the conquest of land proceeded in a sequence from marine to freshwater habitats. However, recent evidence suggests that early photosynthetic eukaryotes may have arisen in subaerial or freshwater environments and only later colonized marine environments as hypersaline oceans were diluted to the contemporary level. Although this hypothesis remains speculative, it is important to keep these alternative scenarios in mind when interpreting the current habitat distribution of plants and algae. Finally, we discuss the roles of structural and functional adaptations of the cell wall, reactive oxygen species scavengers, osmoregulation, and reproduction. These are central for acclimatization to freshwater or to marine environments. We observe that successful transitions appear to have occurred more frequently in morphologically simple forms and conclude that, in addition to physiological studies of euryhaline species, comparative studies of closely related species fully adapted to one or the other environment are necessary to better understand the adaptive processes.
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Affiliation(s)
- Simon M Dittami
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
| | - Svenja Heesch
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Jonas Collén
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
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83
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Bhattacharya A, Biswas P, Kar P, Roychoudhury P, Basu S, Ganguly S, Ghosh S, Panda K, Pal R, Dasgupta AK. Nitric oxide sensing by chlorophyll a. Anal Chim Acta 2017; 985:101-113. [PMID: 28864180 DOI: 10.1016/j.aca.2017.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/19/2017] [Accepted: 07/07/2017] [Indexed: 12/16/2022]
Abstract
Nitric oxide (NO) acts as a signalling molecule that has direct and indirect regulatory roles in various functional processes in biology, though in plant kingdom its role is relatively unexplored. One reason for this is the fact that sensing of NO is always challenging. There are very few probes that can classify the different NO species. The present paper proposes a simple but straightforward way for sensing different NO species using chlorophyll, the source of inspiration being hemoglobin that serves as NO sink in mammalian systems. The proposed method is able to classify NO from DETA-NONOate or (Z)-1-[N-(2-aminoethyl)-N-(2-ammonioethyl) amino] diazen-1-ium-1,2-diolate, nitrite, nitrate and S-nitrosothiol or SNO. This discrimination is carried out by chlorophyll a (chl a) at nano molar (nM) order of sensitivity and at 293 K-310 K. Molecular docking reveals the differential binding effects of NO and SNO with chlorophyll, the predicted binding affinity matching with the experimental observation. Additional experiments with a diverse range of cyanobacteria reveal that apart from the spectroscopic approach the proposed sensing module can be used in microscopic inspection of NO species. Binding of NO is sensitive to temperature and static magnetic field. This provides additional support for the involvement of the porphyrin ring structures to the NO sensing process. This also, broadens the scope of the sensing methods as hinted in the text.
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Affiliation(s)
- Abhishek Bhattacharya
- Department of Biochemistry, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Pranjal Biswas
- Department of Biochemistry, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Puranjoy Kar
- Department of Biochemistry, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Piya Roychoudhury
- Department of Botany, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Sankar Basu
- Department of Biochemistry, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Souradipta Ganguly
- Department of Biotechnology and Guha Centre for Genetic Engineering & Biotechnology, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Sanjay Ghosh
- Department of Biochemistry, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Koustubh Panda
- Department of Biotechnology and Guha Centre for Genetic Engineering & Biotechnology, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Ruma Pal
- Department of Botany, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India
| | - Anjan Kr Dasgupta
- Department of Biochemistry, University of Calcutta 35, Ballygunge Circular Road, Kolkata 700019, India.
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84
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Moschonas G, Gowen RJ, Paterson RF, Mitchell E, Stewart BM, McNeill S, Glibert PM, Davidson K. Nitrogen dynamics and phytoplankton community structure: the role of organic nutrients. BIOGEOCHEMISTRY 2017; 134:125-145. [PMID: 32025070 PMCID: PMC6979524 DOI: 10.1007/s10533-017-0351-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 06/07/2017] [Indexed: 06/01/2023]
Abstract
Dissolved organic nitrogen (DON) is recognised as an important N source for phytoplankton. However, its relative importance for phytoplankton nutrition and community composition has not been studied comprehensively. This study, conducted in a typical Scottish fjord, representative of near-pristine coastal environments, evaluates the utilisation of DON and dissolved inorganic nitrogen (DIN) by different microbial size fractions and the relationship of phytoplankton community composition with DON and other parameters. The study demonstrated that DON was important in supporting phytoplankton throughout the yearly production cycle. The higher-than-expected urea uptake rates and large fraction of the spring bloom production supported by DON suggested that organic N not only contributes to regenerated production and to the nutrition of the small phytoplankton fraction, but can also contribute substantially to new production of the larger phytoplankton in coastal waters. Multivariate statistical techniques revealed two phytoplankton assemblages with peaks in abundance at different times of the year: a spring group dominated by Skeletonema spp., Thalassiosira spp., and Pseudo-nitzschia spp. group delicatissima; and a summer/autumn group dominated by Chaetoceros spp., Scrippsiella spp., and Pseudo-nitzschia spp. group seriata. The multivariate pattern in community composition and abundance of these taxa was significantly correlated with the multivariate pattern of DON, urea, dissolved free amino acids, DIN, temperature, salinity, and daylength, with daylength and urea being particularly important, suggesting both physical and chemical controls on community composition.
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Affiliation(s)
- Grigorios Moschonas
- Scottish Association for Marine Science, Argyll, Oban, PA37 1QA Scotland, UK
| | - Richard J. Gowen
- Scottish Association for Marine Science, Argyll, Oban, PA37 1QA Scotland, UK
- Fisheries and Aquatic Ecosystems Branch, Agriculture Food and Environmental Science Division, Agri-Food and Biosciences Institute, Newforge Lane, Belfast, BT9 5PX UK
| | - Ruth F. Paterson
- Scottish Association for Marine Science, Argyll, Oban, PA37 1QA Scotland, UK
| | - Elaine Mitchell
- Scottish Association for Marine Science, Argyll, Oban, PA37 1QA Scotland, UK
| | - Brian M. Stewart
- Fisheries and Aquatic Ecosystems Branch, Agriculture Food and Environmental Science Division, Agri-Food and Biosciences Institute, Newforge Lane, Belfast, BT9 5PX UK
| | - Sharon McNeill
- Scottish Association for Marine Science, Argyll, Oban, PA37 1QA Scotland, UK
| | - Patricia M. Glibert
- Horn Point Laboratory, University of Maryland Center for Environmental Science, PO Box 775, Cambridge, MD 21613 USA
| | - Keith Davidson
- Scottish Association for Marine Science, Argyll, Oban, PA37 1QA Scotland, UK
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85
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Kazamia E, Helliwell KE, Purton S, Smith AG. How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes. Ecol Lett 2017; 19:810-22. [PMID: 27282316 PMCID: PMC5103174 DOI: 10.1111/ele.12615] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/03/2016] [Accepted: 04/07/2016] [Indexed: 01/05/2023]
Abstract
Extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. In particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. Here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co‐cultures are being used to decipher the metabolic and molecular underpinnings of such exchanges. In addition, we explain how metabolic modelling may be used to conduct investigations in reverse, deducing novel molecular exchanges from analysis of large‐scale data sets, which can identify persistently co‐occurring species. Finally, we consider how knowledge of microbial community ecology can be built into evolutionary theories tailored to these species’ unique lifestyles. We propose a novel model for the evolution of metabolic auxotrophy in microorganisms that arises as a result of symbiosis, termed the Foraging‐to‐Farming hypothesis. The model has testable predictions, fits several known examples of mutualism in the aquatic world, and sheds light on how interactions, which cement dependencies within communities of microorganisms, might be initiated.
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Affiliation(s)
- Elena Kazamia
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | | | - Saul Purton
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Alison Gail Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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86
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Siuda W, Chróst RJ, Kalinowska K, Ejsmont-Karabin J, Kiersztyn B. The Role of Planktonic Organisms in Urea Metabolism in Lakes of Temperate Zone - Case Study. POLISH JOURNAL OF ECOLOGY 2016. [DOI: 10.3161/15052249pje2016.64.4.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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87
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Guerrero-Feijóo E, Nieto-Cid M, Sintes E, Dobal-Amador V, Hernando-Morales V, Álvarez M, Balagué V, Varela MM. Optical properties of dissolved organic matter relate to different depth-specific patterns of archaeal and bacterial community structure in the North Atlantic Ocean. FEMS Microbiol Ecol 2016; 93:fiw224. [PMID: 27789536 DOI: 10.1093/femsec/fiw224] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/19/2016] [Accepted: 10/25/2016] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic abundance, activity and community composition were studied in the euphotic, intermediate and deep waters off the Galician coast (NW Iberian margin) in relation to the optical characterization of dissolved organic matter (DOM). Microbial (archaeal and bacterial) community structure was vertically stratified. Among the Archaea, Euryarchaeota, especially Thermoplasmata, was dominant in the intermediate waters and decreased with depth, whereas marine Thaumarchaeota, especially Marine Group I, was the most abundant archaeal phylum in the deeper layers. The bacterial community was dominated by Proteobacteria through the whole water column. However, Cyanobacteria and Bacteroidetes occurrence was considerable in the upper layer and SAR202 was dominant in deep waters. Microbial composition and abundance were not shaped by the quantity of dissolved organic carbon, but instead they revealed a strong connection with the DOM quality. Archaeal communities were mainly related to the fluorescence of DOM (which indicates respiration of labile DOM and generation of refractory subproducts), while bacterial communities were mainly linked to the aromaticity/age of the DOM produced along the water column. Taken together, our results indicate that the microbial community composition is associated with the DOM composition of the water masses, suggesting that distinct microbial taxa have the potential to use and/or produce specific DOM compounds.
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Affiliation(s)
- Elisa Guerrero-Feijóo
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain
| | - Mar Nieto-Cid
- IIM-CSIC, Instituto de Investigacións Mariñas, 36208 Vigo, Spain
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, University of Vienna, A-1090, Vienna, Austria
| | - Vladimir Dobal-Amador
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain.,Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, 36200 Vigo, Spain
| | | | - Marta Álvarez
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain
| | - Vanessa Balagué
- ICM-CSIC, Institut de Ciències del Mar, 08003, Barcelona, Spain
| | - Marta M Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain
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88
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Kim E, Sprung B, Duhamel S, Filardi C, Kyoon Shin M. Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms. Environ Microbiol 2016; 18:4549-4563. [PMID: 27581800 DOI: 10.1111/1462-2920.13523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022]
Abstract
The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso- to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8-V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2741 (V4) and 2606 (V8-V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. About 18.4% (V4) and 13.8% (V8-V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply-branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information.
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Affiliation(s)
- Eunsoo Kim
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Ben Sprung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory, Division of Biology and Paleo Environment, Columbia University, Palisades, NY, 10964, USA
| | - Christopher Filardi
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, 10024, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Nam-Gu, Ulsan, 44610, South Korea
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89
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Powley HR, Dürr HH, Lima AT, Krom MD, Van Cappellen P. Direct Discharges of Domestic Wastewater are a Major Source of Phosphorus and Nitrogen to the Mediterranean Sea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:8722-8730. [PMID: 27409146 DOI: 10.1021/acs.est.6b01742] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Direct discharges of treated and untreated wastewater are important sources of nutrients to coastal marine ecosystems and contribute to their eutrophication. Here, we estimate the spatially distributed annual inputs of phosphorus (P) and nitrogen (N) associated with direct domestic wastewater discharges from coastal cities to the Mediterranean Sea (MS). According to our best estimates, in 2003 these inputs amounted to 0.9 × 10(9) mol P yr(-1) and 15 × 10(9) mol N yr(-1), that is, values on the same order of magnitude as riverine inputs of P and N to the MS. By 2050, in the absence of any mitigation, population growth plus higher per capita protein intake and increased connectivity to the sewer system are projected to increase P inputs to the MS via direct wastewater discharges by 254, 163, and 32% for South, East, and North Mediterranean countries, respectively. Complete conversion to tertiary wastewater treatment would reduce the 2050 inputs to below their 2003 levels, but at an estimated additional cost of over €2 billion yr(-1). Management of coastal eutrophication may be best achieved by targeting tertiary treatment upgrades to the most affected near-shore areas, while simultaneously implementing legislation limiting P in detergents and increasing wastewater reuse across the entire basin.
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Affiliation(s)
- Helen R Powley
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Hans H Dürr
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Ana T Lima
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
- Department of Environmental Engineering, Universidade Federal do Espírito Santo , Av. Fernando Ferrari 514, CEP 29075-910 - Vitória, Espírito Santo Brazil
| | - Michael D Krom
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
- School of Earth and Environment, University of Leeds , Leeds LS2 9JT, United Kingdom
- Department of Marine Biology, Haifa University , Mt Carmel, Haifa, Israel
| | - Philippe Van Cappellen
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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90
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Azimuddin KM, Hirai J, Suzuki S, Haider MN, Tachibana A, Watanabe K, Kitamura M, Hashihama F, Takahashi K, Hamasaki K. Possible association of diazotrophs with marine zooplankton in the Pacific Ocean. Microbiologyopen 2016; 5:1016-1026. [PMID: 27353240 PMCID: PMC5221459 DOI: 10.1002/mbo3.385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/03/2016] [Accepted: 05/16/2016] [Indexed: 11/17/2022] Open
Abstract
Dinitrogen fixation, the biological reduction in N2 gas to ammonia contributes to the supply of new nitrogen in the surface ocean. To understand the diversity and abundance of potentially diazotrophic (N2 fixing) microorganisms associated with marine zooplankton, especially copepods, the nifH gene was studied using zooplankton samples collected in the Pacific Ocean. In total, 257 nifH sequences were recovered from 23 nifH‐positive DNA extracts out of 90 copepod samples. The nifH genes derived from cyanobacteria related to Trichodesmium, α‐ and γ‐subdivisions of proteobacteria, and anaerobic euryarchaeota related to Methanosaeta concilii were detected. Our results indicated that Pleuromamma, Pontella, and Euchaeta were the major copepod genera hosting dinitrogen fixers, though we found no species‐specific association between copepods and dinitrogen fixers. Also, the digital PCR provided novel data on the number of copies of the nifH gene in individual copepods, which we report the range from 30 to 1666 copies per copepod. This study is the first systematic study of zooplankton‐associated diazotrophs, covering a large area of the open ocean, which provide a clue to further study of a possible new hotspot of N2 fixation.
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Affiliation(s)
- Kazi Md Azimuddin
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Junya Hirai
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Shotaro Suzuki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Md Nurul Haider
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Aiko Tachibana
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Keigo Watanabe
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Minoru Kitamura
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Fuminori Hashihama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Minato-Ku, Tokyo, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Science, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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91
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Borkman DG, Smayda TJ. Coincident patterns of waste water suspended solids reduction, water transparency increase and chlorophyll decline in Narragansett Bay. MARINE POLLUTION BULLETIN 2016; 107:161-169. [PMID: 27087354 DOI: 10.1016/j.marpolbul.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/22/2016] [Accepted: 04/02/2016] [Indexed: 06/05/2023]
Abstract
Dramatic changes occurred in Narragansett Bay during the 1980s: water clarity increased, while phytoplankton abundance and chlorophyll concentration decreased. We examine how changes in total suspended solids (TSS) loading from wastewater treatment plants may have influenced this decline in phytoplankton chlorophyll. TSS loading, light and phytoplankton observations were compiled and a light- and temperature-dependent Skeletonema-based phytoplankton growth model was applied to evaluate chlorophyll supported by TSS nitrogen during 1983-1995. TSS loading declined 75% from ~0.60×10(6)kgmonth(-1) to ~0.15×10(6)kgmonth(-1) during 1983-1995. Model results indicate that nitrogen reduction related to TSS reduction was minor and explained a small fraction (~15%) of the long-term chlorophyll decline. The decline in NBay TSS loading appears to have increased water clarity and in situ irradiance and contributed to the long-term chlorophyll decline by inducing a physiological response of a ~20% reduction in chlorophyll per cell.
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Affiliation(s)
- David G Borkman
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, 02882, USA.
| | - Theodore J Smayda
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, 02882, USA
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92
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Diner RE, Schwenck SM, McCrow JP, Zheng H, Allen AE. Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms. Front Microbiol 2016; 7:880. [PMID: 27375600 PMCID: PMC4899447 DOI: 10.3389/fmicb.2016.00880] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/25/2016] [Indexed: 12/13/2022] Open
Abstract
Diatoms are a dominant group of eukaryotic phytoplankton that contribute substantially to global primary production and the cycling of important elements such as carbon and nitrogen. Heterotrophic bacteria, including members of the gammaproteobacteria, are commonly associated with diatom populations and may rely on them for organic carbon while potentially competing with them for other essential nutrients. Considering that bacterioplankton drive oceanic release of CO 2 (i.e., bacterial respiration) while diatoms drive ocean carbon sequestration vial the biological pump, the outcome of such competition could influence the direction and magnitude of carbon flux in the upper ocean. Nitrate availability is commonly a determining factor for the growth of diatom populations, particularly in coastal and upwelling regions. Diatoms as well as many bacterial species can utilize nitrate, however the ability of bacteria to compete for nitrate may be hindered by carbon limitation. Here we have developed a genetically tractable model system using the pennate diatom Phaeodactylum tricornutum and the widespread heterotrophic bacteria Alteromonas macleodii to examine carbon-nitrogen dynamics. While subsisting solely on P. tricornutum derived carbon, A. macleodii does not appear to be an effective competitor for nitrate, and may in fact benefit the diatom; particularly in stationary phase. However, allochthonous dissolved organic carbon addition in the form of pyruvate triggers A. macleodii proliferation and nitrate uptake, leading to reduced P. tricornutum growth. Nitrate reductase deficient mutants of A. macleodii (ΔnasA) do not exhibit such explosive growth and associated competitive ability in response to allochthonous carbon when nitrate is the sole nitrogen source, but could survive by utilizing solely P. tricornutum-derived nitrogen. Furthermore, allocthonous carbon addition enables wild-type A. macleodii to rescue nitrate reductase deficient P. tricornutum populations from nitrogen starvation, and RNA-seq transcriptomic evidence supports nitrogen-based interactions between diatoms and bacteria at the molecular level. This study provides key insights into the roles of carbon and nitrogen in phytoplankton-bacteria dynamics and lays the foundation for developing a mechanistic understanding of these interactions using co-culturing and genetic manipulation.
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Affiliation(s)
- Rachel E. Diner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa Jolla, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - Sarah M. Schwenck
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa Jolla, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - John P. McCrow
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - Hong Zheng
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
| | - Andrew E. Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa Jolla, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter InstituteLa Jolla, CA, USA
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93
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An experimentally validated nitrate–ammonium–phytoplankton model including effects of starvation length and ammonium inhibition on nitrate uptake. Ecol Modell 2015. [DOI: 10.1016/j.ecolmodel.2015.08.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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94
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Rogato A, Amato A, Iudicone D, Chiurazzi M, Ferrante MI, d'Alcalà MR. The diatom molecular toolkit to handle nitrogen uptake. Mar Genomics 2015; 24 Pt 1:95-108. [PMID: 26055207 DOI: 10.1016/j.margen.2015.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/26/2015] [Accepted: 05/26/2015] [Indexed: 11/16/2022]
Abstract
Nutrient concentrations in the oceans display significant temporal and spatial variability, which strongly affects growth, distribution and survival of phytoplankton. Nitrogen (N) in particular is often considered a limiting resource for prominent marine microalgae, such as diatoms. Diatoms possess a suite of N-related transporters and enzymes and utilize a variety of inorganic (e.g., nitrate, NO3(-); ammonium, NH4(+)) and organic (e.g., urea; amino acids) N sources for growth. However, the molecular mechanisms allowing diatoms to cope efficiently with N oscillations by controlling uptake capacities and signaling pathways involved in the perception of external and internal clues remain largely unknown. Data reported in the literature suggest that the regulation and the characteristic of the genes, and their products, involved in N metabolism are often diatom-specific, which correlates with the peculiar physiology of these organisms for what N utilization concerns. Our study reveals that diatoms host a larger suite of N transporters than one would expected for a unicellular organism, which may warrant flexible responses to variable conditions, possibly also correlated to the phases of life cycle of the cells. All this makes N transporters a crucial key to reveal the balance between proximate and ultimate factors in diatom life.
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Affiliation(s)
- Alessandra Rogato
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy.
| | - Alberto Amato
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy.
| | - Maurizio Ribera d'Alcalà
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy
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95
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Liu Y, Thornton DCO, Bianchi TS, Arnold WA, Shields MR, Chen J, Yvon-Lewis SA. Dissolved organic matter composition drives the marine production of brominated very short-lived substances. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:3366-3374. [PMID: 25723123 DOI: 10.1021/es505464k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Brominated very short-lived substances (BrVSLS), such as bromoform, are important trace gases for stratospheric ozone chemistry. These naturally derived trace gases are formed via bromoperoxidase-mediated halogenation of dissolved organic matter (DOM) in seawater. Information on DOM type in relation to the observed BrVSLS concentrations in seawater, however, is scarce. We examined the sensitivity of BrVSLS production in relation to the presence of specific DOM moieties. A total of 28 model DOM compounds in artificial seawater were treated with vanadium bromoperoxidase (V-BrPO). Our results show a clear dependence of BrVSLS production on DOM type. In general, molecules that comprise a large fraction of the bulk DOM pool did not noticeably affect BrVSLS production. Only specific cell metabolites and humic acid appeared to significantly enhance BrVSLS production. Amino acids and lignin phenols suppressed enzyme-mediated BrVSLS production and may instead have formed halogenated nonvolatile molecules. Dibromomethane production was not observed in any experiments, suggesting it is not produced by the same pathway as the other BrVSLS. Our results suggest that regional differences in DOM composition may explain the observed BrVSLS concentration variability in the global ocean. Ultimately, BrVSLS production and concentrations are likely affected by DOM composition, reactivity, and cycling in the ocean.
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Affiliation(s)
- Yina Liu
- ‡Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | | | - Thomas S Bianchi
- §Department of Geological Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - William A Arnold
- ∥Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive SE, Minneapolis, Minnesota 55455, United States
| | - Michael R Shields
- §Department of Geological Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Jie Chen
- ⊥South China Sea Marine Engineering and Environment Institution, Guangzhou, Guangdong 510310, China
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96
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Maeda SI, Murakami A, Ito H, Tanaka A, Omata T. Functional Characterization of the FNT Family Nitrite Transporter of Marine Picocyanobacteria. Life (Basel) 2015; 5:432-46. [PMID: 25809962 PMCID: PMC4390861 DOI: 10.3390/life5010432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/29/2015] [Indexed: 11/16/2022] Open
Abstract
Many of the cyanobacterial species found in marine and saline environments have a gene encoding a putative nitrite transporter of the formate/nitrite transporter (FNT) family. The presumed function of the gene (designated nitM) was confirmed by functional expression of the gene from the coastal marine species Synechococcus sp. strain PCC7002 in the nitrite-transport-less mutant (NA4) of the freshwater cyanobacterium Synechococcus elongatus strain PCC7942. The NitM-mediated nitrite uptake showed an apparent Km (NO2-) of about 8 μM and was not inhibited by nitrate, cyanate or formate. Of the nitM orthologs from the three oceanic cyanobacterial species, which are classified as α-cyanobacteria on the basis of the occurrence of Type 1a RuBisCO, the one from Synechococcus sp. strain CC9605 conferred nitrite uptake activity on NA4, but those from Synechococcus sp. strain CC9311 and Prochlorococcus marinus strain MIT9313 did not. A strongly conserved hydrophilic amino acid sequence was found at the C-termini of the deduced NitM sequences from α-cyanobacteria, with a notable exception of the Synechococcus sp. strain CC9605 NitM protein, which entirely lacked the C-terminal amino acids. The C-terminal sequence was not conserved in the NitM proteins from β-cyanobacteria carrying the Type 1b RuBisCO, including the one from Synechococcus sp. strain PCC7002. Expression of the truncated nitM genes from Synechococcus sp. strain CC9311 and Prochlorococcus marinus strain MIT9313, encoding the proteins lacking the conserved C-terminal region, conferred nitrite uptake activity on the NA4 mutant, indicating that the C-terminal region of α-cyanobacterial NitM proteins inhibits the activity of the transporter.
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Affiliation(s)
- Shin-Ichi Maeda
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076 Japan.
| | - Akio Murakami
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076 Japan.
- Research Center for Inland Seas, Kobe University, Awaji, Hyogo 656-2401, Japan.
| | - Hisashi Ito
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076 Japan.
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo 060-0819, Japan.
| | - Ayumi Tanaka
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076 Japan.
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo 060-0819, Japan.
| | - Tatsuo Omata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076 Japan.
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97
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Levipan HA, Molina V, Fernandez C. Nitrospina-like bacteria are the main drivers of nitrite oxidation in the seasonal upwelling area of the Eastern South Pacific (Central Chile ∼36°S). ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:565-573. [PMID: 25756109 DOI: 10.1111/1758-2229.12158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aerobic nitrite oxidation in marine environments plays a key role in the nitrification process. Marine bacteria involved in this nitrate-producing process have however been seldom studied compared with the ammonia-oxidizing community. Here, we report for the first time the community structure of aerobic nitrite-oxidizing bacteria (NOB) in the seasonal upwelling and oxygen-deficient area off Central Chile. Analysis of 16S rRNA by tag pyrosequencing was combined with specific quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR in summer and wintertime. Nitrospina-like bacteria were the only known NOB detected by means of pyrosequencing between 30 and 80 m depth, accounting for up to 5% of total bacteria. This guild was represented by 11 and 7 operational taxonomic units (97% cut-off) in winter and summertime respectively. Nitrospina-like bacteria were phylogenetically related to sequences retrieved from coastal upwelling, oxygen minimum zones and deep-sea environments. This group was also detected by qPCR with abundances that increased with depth throughout the water column. Importantly, Nitrospina from surface layers showed low abundances but high 16S rRNA : rDNA ratios and mainly in summertime. Overall, our results highlight the seasonal variability between the structure and physiological state of this community and suggest a significant role of Nitrospina in the nitrogen cycle of seasonal upwelling areas.
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98
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Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME JOURNAL 2014; 9:563-80. [PMID: 25203836 DOI: 10.1038/ismej.2014.153] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 07/12/2014] [Accepted: 07/15/2014] [Indexed: 02/01/2023]
Abstract
Microbial activities that affect global oceanographic and atmospheric processes happen throughout the water column, yet the long-term ecological dynamics of microbes have been studied largely in the euphotic zone and adjacent seasonally mixed depths. We investigated temporal patterns in the community structure of free-living bacteria, by sampling approximately monthly from 5 m, the deep chlorophyll maximum (∼15-40 m), 150, 500 and 890 m, in San Pedro Channel (maximum depth 900 m, hypoxic below ∼500 m), off the coast of Southern California. Community structure and biodiversity (inverse Simpson index) showed seasonal patterns near the surface and bottom of the water column, but not at intermediate depths. Inverse Simpson's index was highest in the winter in surface waters and in the spring at 890 m, and varied interannually at all depths. Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time. Meanwhile, communities from the surface through 500 m varied interannually. After accounting for seasonality, several environmental parameters co-varied with community structure at the surface and 890 m, but not at the intermediate depths. Abundant and seasonally variable groups included, at 890 m, Nitrospina, Flavobacteria and Marine Group A. Seasonality at 890 m is likely driven by variability in sinking particles, which originate in surface waters, pass transiently through the middle water column and accumulate on the seafloor where they alter the chemical environment. Seasonal subeuphotic groups are likely those whose ecology is strongly influenced by these particles. This surface-to-bottom, decade-long, study identifies seasonality and interannual variability not only of overall community structure, but also of numerous taxonomic groups and near-species level operational taxonomic units.
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99
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Hernández EA, Piquet AMT, Lopez JL, Buma AGJ, Mac Cormack WP. Marine archaeal community structure from Potter Cove, Antarctica: high temporal and spatial dominance of the phylum Thaumarchaeota. Polar Biol 2014. [DOI: 10.1007/s00300-014-1569-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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100
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Kaushik R, Balasubramanian R, Dunstan H. Microbial quality and phylogenetic diversity of fresh rainwater and tropical freshwater reservoir. PLoS One 2014; 9:e100737. [PMID: 24979573 PMCID: PMC4076214 DOI: 10.1371/journal.pone.0100737] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/28/2014] [Indexed: 11/29/2022] Open
Abstract
The impact of rainwater on the microbial quality of a tropical freshwater reservoir through atmospheric wet deposition of microorganisms was studied for the first time. Reservoir water samples were collected at four different sampling points and rainwater samples were collected in the immediate vicinity of the reservoir sites for a period of four months (January to April, 2012) during the Northeast monsoon period. Microbial quality of all fresh rainwater and reservoir water samples was assessed based on the counts for the microbial indicators: Escherichia coli (E. coli), total coliforms, and Enterococci along with total heterotrophic plate counts (HPC). The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. The levels of E. coli were found to be in the range of 0 CFU/100 mL – 75 CFU/100 mL for the rainwater, and were 10–94 CFU/100 mL for the reservoir water. The sampling sites that were influenced by highway traffic emissions showed the maximum counts for all the bacterial indicators assessed. There was no significant increase in the bacterial abundances observed in the reservoir water immediately following rainfall. However, the composite fresh rainwater and reservoir water samples exhibited broad phylogenetic diversity, including sequences representing Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Lentisphaerae and Bacteriodetes. Members of the Betaproteobacteria group were the most dominant in both fresh rainwater and reservoir water, followed by Alphaproteobacteria, Sphingobacteria, Actinobacteria and Gammaproteobacteria.
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Affiliation(s)
- Rajni Kaushik
- Singapore-Delft Water Alliance, National University of Singapore, Singapore, Singapore
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Rajasekhar Balasubramanian
- Singapore-Delft Water Alliance, National University of Singapore, Singapore, Singapore
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
- * E-mail:
| | - Hugh Dunstan
- School of Environmental and Life Sciences, The University of Newcastle, Callahan, NSW, Australia
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