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Pérez Gallego R, Bale NJ, Sinninghe Damste JS, Villanueva L. Developing a genetic approach to target cyanobacterial producers of heterocyte glycolipids in the environment. Front Microbiol 2023; 14:1257040. [PMID: 37840743 PMCID: PMC10569477 DOI: 10.3389/fmicb.2023.1257040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
Heterocytous cyanobacteria are important players in the carbon and nitrogen cycle. They can fix dinitrogen by using heterocytes, specialized cells containing the oxygen-sensitive nitrogenase enzyme surrounded by a thick polysaccharide and glycolipid layer which prevents oxygen diffusion and nitrogenase inactivation. Heterocyte glycolipids can be used to detect the presence of heterocytous cyanobacteria in present-day and past environments, providing insight into the functioning of the studied ecosystems. However, due to their good preservation throughout time, heterocyte glycolipids are not ideal to detect and study living communities, instead methods based on DNA are preferred. Currently cyanobacteria can be detected using untargeted genomic approaches such as metagenomics, or they can be specifically targeted by, for example, the use of primers that preferentially amplify their 16S rRNA gene or their nifH gene in the case of nitrogen fixing cyanobacteria. However, since not all cyanobacterial nitrogen fixers are heterocytous, there is currently no fast gene-based method to specifically detect and distinguish heterocytous cyanobacteria. Here, we developed a PCR-based method to specifically detect heterocytous cyanobacteria by designing primers targeting the gene (hglT) encoding the enzyme responsible for the last step in the biosynthesis of heterocyte glycolipid (i.e., a glycosyltransferase). We designed several primer sets using the publicly available sequences of 23 heterocytous cyanobacteria, after testing them on DNA extracts of 21 heterocyte-forming and 7 non-heterocyte forming freshwater cyanobacteria. The best primer set was chosen and successfully used to confirm the presence of heterocytous cyanobacteria in a marine environmental sample.
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Affiliation(s)
- Ruth Pérez Gallego
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damste
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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Colette M, Guentas L, Patrona LD, Ansquer D, Callac N. Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds. ENVIRONMENTAL MICROBIOME 2023; 18:58. [PMID: 37438848 DOI: 10.1186/s40793-023-00512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species (Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata) on active sediment microbial communities and their implications on organic matter degradation. RESULTS Drying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture. CONCLUSION The efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.
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Affiliation(s)
- Marie Colette
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia.
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia.
| | - Linda Guentas
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia
| | - Luc Della Patrona
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Dominique Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Nolwenn Callac
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
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3
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Trebuch LM, Schoofs K, Vaessen SMF, Neu TR, Janssen M, Wijffels RH, Vet LEM, Fernandes TV. N 2 -fixation can sustain wastewater treatment performance of photogranules under nitrogen-limiting conditions. Biotechnol Bioeng 2023; 120:1303-1315. [PMID: 36779371 DOI: 10.1002/bit.28349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/23/2022] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Wastewater characteristics can vary significantly, and in some municipal wastewaters the N:P ratio is as low as 5 resulting in nitrogen-limiting conditions. In this study, the microbial community, function, and morphology of photogranules under nitrogen-replete (N+) and limiting (N-) conditions was assessed in sequencing batch reactors. Photogranules under N- condition were nitrogen deprived 2/3 of a batch cycle duration. Surprisingly, this nitrogen limitation had no adverse effect on biomass productivity. Moreover, phosphorus and chemical oxygen demand removal were similar to their removal under N+ conditions. Although performance was similar, the difference in granule morphology was obvious. While N+ photogranules were dense and structurally confined, N- photogranules showed loose structures with occasional voids. Microbial community analysis revealed high abundance of cyanobacteria capable of N2 -fixation. These were higher at N- (38%) than N+ (29%) treatments, showing that photogranules could adjust and maintain treatment performance and high biomass productivity by means of N2 -fixation.
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Affiliation(s)
- Lukas M Trebuch
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - Kobe Schoofs
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - Stijn M F Vaessen
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - Thomas R Neu
- Microbiology of Interfaces, Department River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Marcel Janssen
- Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Louise E M Vet
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Tânia V Fernandes
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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4
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Aubé J, Senin P, Bonin P, Pringault O, Jeziorski C, Bouchez O, Klopp C, Guyoneaud R, Goñi-Urriza M. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. MICROBIAL ECOLOGY 2020; 80:286-295. [PMID: 32076743 DOI: 10.1007/s00248-020-01493-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.
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Affiliation(s)
- Johanne Aubé
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, IFREMER, CNRS, Université de Bretagne Occidentale, Plouzané, France
| | - Pavel Senin
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Patricia Bonin
- Mediterranean Institute of Oceanography (MIO), Aix Marseille University, Université de Toulon, CNRS/INSU/IRD, UM 110, Marseille, France
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Rémy Guyoneaud
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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5
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Reinold M, Wong HL, MacLeod FI, Meltzer J, Thompson A, Burns BP. The Vulnerability of Microbial Ecosystems in A Changing Climate: Potential Impact in Shark Bay. Life (Basel) 2019; 9:life9030071. [PMID: 31480795 PMCID: PMC6789446 DOI: 10.3390/life9030071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/22/2019] [Accepted: 08/28/2019] [Indexed: 12/26/2022] Open
Abstract
The potential impact of climate change on eukaryotes, including humans, has been relatively well described. In contrast, the contribution and susceptibility of microorganisms to a changing climate have, until recently, received relatively less attention. In this review, the importance of microorganisms in the climate change discourse is highlighted. Microorganisms are responsible for approximately half of all primary production on earth, support all forms of macroscopic life whether directly or indirectly, and often persist in “extreme” environments where most other life are excluded. In short, microorganisms are the life support system of the biosphere and therefore must be included in decision making regarding climate change. Any effects climate change will have on microorganisms will inevitably impact higher eukaryotes and the activity of microbial communities in turn can contribute to or alleviate the severity of the changing climate. It is of vital importance that unique, fragile, microbial ecosystems are a focus of research efforts so that their resilience to extreme weather events and climate change are thoroughly understood and that conservation efforts can be implemented as a response. One such ecosystem under threat are the evolutionarily significant microbial mats and stromatolites, such as those present in Shark Bay, Western Australia. Climate change models have suggested the duration and severity of extreme weather events in this region will increase, along with rising temperatures, sea levels, and ocean acidification. These changes could upset the delicate balance that fosters the development of microbial mats and stromatolites in Shark Bay. Thus, the challenges facing Shark Bay microbial communities will be presented here as a specific case study.
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Affiliation(s)
- Max Reinold
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Julia Meltzer
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - April Thompson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia.
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6
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Hörnlein C, Confurius-Guns V, Stal LJ, Bolhuis H. Daily rhythmicity in coastal microbial mats. NPJ Biofilms Microbiomes 2018; 4:11. [PMID: 29796291 PMCID: PMC5953948 DOI: 10.1038/s41522-018-0054-5] [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: 11/09/2017] [Revised: 03/26/2018] [Accepted: 04/17/2018] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria are major primary producers in coastal microbial mats and provide biochemical energy, organic carbon, and bound nitrogen to the mat community through oxygenic photosynthesis and dinitrogen fixation. In order to anticipate the specific requirements to optimize their metabolism and growth during a day-and-night cycle, Cyanobacteria possess a unique molecular timing mechanism known as the circadian clock that is well-studied under laboratory conditions but little is known about its function in a natural complex community. Here, we investigated daily rhythmicity of gene expression in a coastal microbial mat community sampled at 6 time points during a 24-h period. In order to identify diel expressed genes, meta-transcriptome data was fitted to periodic functions. Out of 24,035 conserved gene transcript clusters, approximately 7% revealed a significant rhythmic expression pattern. These rhythmic genes were assigned to phototrophic micro-eukaryotes, Cyanobacteria but also to Proteobacteria and Bacteroidetes. Analysis of MG-RAST annotated genes and mRNA recruitment analysis of two cyanobacterial and three proteobacterial microbial mat members confirmed that homologs of the cyanobacterial circadian clock genes were also found in other bacterial members of the microbial mat community. These results suggest that various microbial mat members other than Cyanobacteria have their own molecular clock, which can be entrained by a cocktail of Zeitgebers such as light, temperature or metabolites from neighboring species. Hence, microbial mats can be compared to a complex organism consisting of multiple sub-systems that have to be entrained in a cooperative way such that the corpus functions optimally.
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Affiliation(s)
- Christine Hörnlein
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
| | - Veronique Confurius-Guns
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
| | - Lucas J Stal
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands.,2Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
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7
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Pancrace C, Jokela J, Sassoon N, Ganneau C, Desnos-Ollivier M, Wahlsten M, Humisto A, Calteau A, Bay S, Fewer DP, Sivonen K, Gugger M. Rearranged Biosynthetic Gene Cluster and Synthesis of Hassallidin E in Planktothrix serta PCC 8927. ACS Chem Biol 2017; 12:1796-1804. [PMID: 28489343 DOI: 10.1021/acschembio.7b00093] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteria produce a wide range of natural products with antifungal bioactivity. The cyclic glycosylated lipopeptides of the hassallidin family have potent antifungal activity and display a great degree of chemical diversity. Here, we report the discovery of a hassallidin biosynthetic gene cluster from the filamentous cyanobacterium Planktothrix serta PCC 8927. The hassallidin gene cluster showed heavy rearrangement and marks of genomic plasticity. Nucleotide bias, differences in GC content, and phylogenetic incongruence suggested the acquisition of the hassallidin biosynthetic gene cluster in Planktothrix serta PCC 8927 by horizontal gene transfer. Chemical analyses by liquid chromatography and mass spectrometry demonstrated that this strain produced hassallidin E, a new glycosylated hassallidin variant. Hassallidin E was the only structural variant produced by Planktothrix serta PCC 8927 in all tested conditions. Further evaluated on human pathogenic fungi, hassallidin E showed an antifungal bioactivity. Hassallidin production levels correlated with nitrogen availability, in the only nitrogen-fixing Planktothrix described so far. Our results provide insights into the distribution and chemical diversity of cyanobacterial antifungal compounds as well as raise questions on their ecological relevance.
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Affiliation(s)
- Claire Pancrace
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06,
UPEC, UDD, CNRS, INRA, IRD, IEES-Paris, Paris, France
| | - Jouni Jokela
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | | | - Christelle Ganneau
- Institut Pasteur, Unit Chemistry of Biomolecules, Paris, France
- CNRS UMR 3523, Paris, France
| | - Marie Desnos-Ollivier
- Institut Pasteur/CNRS URA3012, National Refence Center
for Invasive Mycoses and Antifungals, Molecular Mycology Unit, Paris, France
| | - Matti Wahlsten
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Anu Humisto
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Alexandra Calteau
- Commissariat à
l’Energie Atomique et aux Energies Alternatives (CEA), Genoscope/CNRS,
UMR 8030, Laboratoire d’Analyse Bioinformatique en Génomique
et Métabolisme, Evry, France
| | - Sylvie Bay
- Institut Pasteur, Unit Chemistry of Biomolecules, Paris, France
- CNRS UMR 3523, Paris, France
| | - David P. Fewer
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Kaarina Sivonen
- Microbiology
and Biotechnology Division, Department of Food and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Muriel Gugger
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
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8
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Guimarães P, Yunes JS, Cretoiu MS, Stal LJ. Growth Characteristics of an Estuarine Heterocystous Cyanobacterium. Front Microbiol 2017; 8:1132. [PMID: 28670308 PMCID: PMC5472669 DOI: 10.3389/fmicb.2017.01132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/02/2017] [Indexed: 11/15/2022] Open
Abstract
A new estuarine filamentous heterocystous cyanobacterium was isolated from intertidal sediment of the Lagoa dos Patos estuary (Brazil). The isolate may represent a new genus related to Cylindrospermopsis. While the latter is planktonic, contains gas vesicles, and is toxic, the newly isolated strain is benthic and does not contain gas vesicles. It is not known whether the new strain is toxic. It grows equally well in freshwater, brackish and full salinity growth media, in the absence of inorganic or organic combined nitrogen, with a growth rate 0.6 d-1. Nitrogenase, the enzyme complex responsible for fixing dinitrogen, was most active during the initial growth phase and its activity was not different between the different salinities tested (freshwater, brackish, and full salinity seawater). Salinity shock also did not affect nitrogenase activity. The frequency of heterocysts was high, coinciding with high nitrogenase activity during the initial growth phase, but decreased subsequently. However, the frequency of heterocysts decreased considerably more at higher salinity, while no change in nitrogenase activity occurred, indicating a higher efficiency of dinitrogen fixation. Akinete frequency was low in the initial growth phase and higher in the late growth phase. Akinete frequency was much lower at high salinity, which might indicate better growth conditions or that akinete differentiation was under the same control as heterocyst differentiation. These trends have hitherto not been reported for heterocystous cyanobacteria but they seem to be well fitted for an estuarine life style.
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Affiliation(s)
- Pablo Guimarães
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research and Utrecht UniversityDen Burg, Netherlands
- Programa de Pós-Graduação em Oceanografia Física, Química e Geológica, Universidade Federal do Rio Grande – FURGRio Grande, Brazil
| | - João S. Yunes
- Programa de Pós-Graduação em Oceanografia Física, Química e Geológica, Universidade Federal do Rio Grande – FURGRio Grande, Brazil
| | - Mariana Silvia Cretoiu
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research and Utrecht UniversityDen Burg, Netherlands
- Department of Aquatic Microbiology, University of AmsterdamAmsterdam, Netherlands
| | - Lucas J. Stal
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research and Utrecht UniversityDen Burg, Netherlands
- Department of Aquatic Microbiology, University of AmsterdamAmsterdam, Netherlands
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9
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Cardoso DC, Sandionigi A, Cretoiu MS, Casiraghi M, Stal L, Bolhuis H. Comparison of the active and resident community of a coastal microbial mat. Sci Rep 2017; 7:2969. [PMID: 28592823 PMCID: PMC5462767 DOI: 10.1038/s41598-017-03095-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/20/2017] [Indexed: 01/04/2023] Open
Abstract
Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fraction. In addition, we aimed to establish an optimal and feasible sampling protocol that takes potential spatial and temporal heterogeneity into account. The coastal microbial mat investigated here was sampled randomly and at regular time points during one 24-h period. DNA and RNA was extracted and after conversion of the RNA fraction to cDNA, the V1-V3 and the V3-V4 regions of the 16S rRNA gene were targeted for high-throughput amplicon sequencing. We show that the community composition varies little in time and space whereas two amplified 16S regions gave significant different results. The largest differences were found when comparing the "resident community" (DNA) with the "active community" (cDNA/RNA); in the latter, Cyanobacteria dominated for almost 95% while they represented 60% of the resident fraction.
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Affiliation(s)
- Daniela Clara Cardoso
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
| | - Anna Sandionigi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Mariana Silvia Cretoiu
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
- Department of Freshwater and Marine Ecology, IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - Maurizio Casiraghi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Lucas Stal
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
- Department of Freshwater and Marine Ecology, IBED, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands.
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10
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Fan H, Bolhuis H, Stal LJ. Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments. Front Microbiol 2015; 6:738. [PMID: 26257718 PMCID: PMC4508842 DOI: 10.3389/fmicb.2015.00738] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/06/2015] [Indexed: 12/05/2022] Open
Abstract
The fixation of dinitrogen (N2) and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L−1 d−1 and from undetectable to 8.2 nmol N g−1 d−1 in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 μmol m−2 d−1 and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR) data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and oxygen concentration.
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Affiliation(s)
- Haoxin Fan
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands
| | - Lucas J Stal
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands ; Department of Aquatic Microbiology, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
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Cowan DA, Makhalanyane TP, Dennis PG, Hopkins DW. Microbial ecology and biogeochemistry of continental Antarctic soils. Front Microbiol 2014; 5:154. [PMID: 24782842 PMCID: PMC3988359 DOI: 10.3389/fmicb.2014.00154] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/22/2014] [Indexed: 11/13/2022] Open
Abstract
The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.
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Affiliation(s)
- Don A Cowan
- Department of Genetics, Centre for Microbial Ecology and Genetics, University of Pretoria Pretoria, South Africa
| | - Thulani P Makhalanyane
- Department of Genetics, Centre for Microbial Ecology and Genetics, University of Pretoria Pretoria, South Africa
| | - Paul G Dennis
- School of Agriculture and Food Sciences, The University of Queensland Brisbane, QLD, Australia
| | - David W Hopkins
- School of Life Sciences, Heriot-Watt University Edinburgh, UK
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Coastal microbial mat diversity along a natural salinity gradient. PLoS One 2013; 8:e63166. [PMID: 23704895 PMCID: PMC3660559 DOI: 10.1371/journal.pone.0063166] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/29/2013] [Indexed: 11/19/2022] Open
Abstract
The North Sea coast of the Dutch barrier island of Schiermonnikoog is covered by microbial mats that initiate a succession of plant communities that eventually results in the development of a densely vegetated salt marsh. The North Sea beach has a natural elevation running from the low water mark to the dunes resulting in gradients of environmental factors perpendicular to the beach. These gradients are due to the input of seawater at the low water mark and of freshwater from upwelling groundwater at the dunes and rainfall. The result is a natural and dynamic salinity gradient depending on the tide, rainfall and wind. We studied the microbial community composition in thirty three samples taken every ten meters along this natural salinity gradient by using denaturing gradient gel electrophoresis (DGGE) of rRNA gene fragments. We looked at representatives from each Domain of life (Bacteria, Archaea and Eukarya) and with a particular emphasis on Cyanobacteria. Analysis of the DGGE fingerprints together with pigment composition revealed three distinct microbial mat communities, a marine community dominated by diatoms as primary producers, an intermediate brackish community dominated by Cyanobacteria as primary producers and a freshwater community with Cyanobacteria and freshwater green algae.
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Environment-dependent distribution of the sediment nifH-harboring microbiota in the Northern South China Sea. Appl Environ Microbiol 2012; 79:121-32. [PMID: 23064334 DOI: 10.1128/aem.01889-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N(2) fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH(4)(+) concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N(2) fixation and NH(4)(+) production. Several other environmental factors, including sediment pore water PO(4)(3-) concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery.
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Yousuf B, Sanadhya P, Keshri J, Jha B. Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India. BMC Microbiol 2012; 12:150. [PMID: 22834535 PMCID: PMC3438102 DOI: 10.1186/1471-2180-12-150] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 07/06/2012] [Indexed: 11/10/2022] Open
Abstract
Background Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content. Results In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac. Conclusion This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes.
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Affiliation(s)
- Basit Yousuf
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, GB Marg, Bhavnagar, Gujarat, India
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Woebken D, Burow LC, Prufert-Bebout L, Bebout BM, Hoehler TM, Pett-Ridge J, Spormann AM, Weber PK, Singer SW. Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. ISME JOURNAL 2012; 6:1427-39. [PMID: 22237543 DOI: 10.1038/ismej.2011.200] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
N(2) fixation is a key process in photosynthetic microbial mats to support the nitrogen demands associated with primary production. Despite its importance, groups that actively fix N(2) and contribute to the input of organic N in these ecosystems still remain largely unclear. To investigate the active diazotrophic community in microbial mats from the Elkhorn Slough estuary, Monterey Bay, CA, USA, we conducted an extensive combined approach, including biogeochemical, molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. Detailed analysis of dinitrogenase reductase (nifH) transcript clone libraries from mat samples that fixed N(2) at night indicated that cyanobacterial nifH transcripts were abundant and formed a novel monophyletic lineage. Independent NanoSIMS analysis of (15)N(2)-incubated samples revealed significant incorporation of (15)N into small, non-heterocystous cyanobacterial filaments. Mat-derived enrichment cultures yielded a unicyanobacterial culture with similar filaments (named Elkhorn Slough Filamentous Cyanobacterium-1 (ESFC-1)) that contained nifH gene sequences grouping with the novel cyanobacterial lineage identified in the transcript clone libraries, displaying up to 100% amino-acid sequence identity. The 16S rRNA gene sequence recovered from this enrichment allowed for the identification of related sequences from Elkhorn Slough mats and revealed great sequence diversity in this cluster. Furthermore, by combining (15)N(2) tracer experiments, fluorescence in situ hybridization and NanoSIMS, in situ N(2) fixation activity by the novel ESFC-1 group was demonstrated, suggesting that this group may be the most active cyanobacterial diazotroph in the Elkhorn Slough mat. Pyrotag sequences affiliated with ESFC-1 were recovered from mat samples throughout 2009, demonstrating the prevalence of this group. This work illustrates that combining standard and single-cell analyses can link phylogeny and function to identify previously unknown key functional groups in complex ecosystems.
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Affiliation(s)
- Dagmar Woebken
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
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Bolhuis H, Stal LJ. Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. THE ISME JOURNAL 2011; 5:1701-12. [PMID: 21544102 PMCID: PMC3197164 DOI: 10.1038/ismej.2011.52] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 03/14/2011] [Accepted: 03/24/2011] [Indexed: 11/08/2022]
Abstract
Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.
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Affiliation(s)
- Henk Bolhuis
- Department of Marine Microbiology, Centre for Estuarine and Marine Ecology (NIOO-KNAW), Yerseke, The Netherlands.
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