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Huete-Stauffer TM, Logares R, Ansari MI, Røstad A, Calleja ML, Morán XAG. Increased prokaryotic diversity in the Red Sea deep scattering layer. Environ Microbiome 2023; 18:87. [PMID: 38098078 PMCID: PMC10722844 DOI: 10.1186/s40793-023-00542-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450-600 m. RESULTS Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer. CONCLUSIONS We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200 m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.
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Affiliation(s)
- Tamara Megan Huete-Stauffer
- Red Sea Research Center, Blg 2, Level 2, Office 2217-WS05, BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Mohd Ikram Ansari
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| | - Anders Røstad
- Red Sea Research Center, Blg 2, Level 2, Office 2217-WS05, BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Maria Lluch Calleja
- Marine Ecology and Systematics, Biology Department, University of the Balearic Islands (UIB), Palma, Spain
| | - Xosé Anxelu G Morán
- Red Sea Research Center, Blg 2, Level 2, Office 2217-WS05, BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón (IEO), CSIC, Gijón, Spain
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Pascoal F, Costa R, Assmy P, Duarte P, Magalhães C. Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies. Microb Ecol 2022; 84:59-72. [PMID: 34405249 DOI: 10.1007/s00248-021-01821-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
The Arctic Ocean is facing rapid environmental changes with cascading effects on the entire Arctic marine ecosystem. However, we have a limited understanding of the consequences such changes have on bacteria and archaea (prokaryotes) at the base of the marine food web. In this study, we show how the prokaryotic rare biosphere behaves over a range of highly heterogeneous environmental conditions using 16S rRNA gene reads from amplicon and metagenome sequencing data from seawater samples collected during the Norwegian young sea ICE expedition between late winter and early summer. The prokaryotic rare biosphere was analyzed using different approaches: amplicon sequence variants and operational taxonomic units from the 16S rRNA gene amplicons and operational taxonomic units from the 16S rRNA genes of the metagenomes. We found that prokaryotic rare biosphere communities are specific to certain water masses, and that the majority of the rare taxa identified were always rare and disappeared in at least one sample under changing conditions, suggesting their high sensitivity to environmental heterogeneity. In addition, our methodological comparison revealed a good performance of 16S rRNA gene amplicon sequencing in describing rare biosphere patterns, while the metagenome-derived data were better to capture a significant diversity of so-far uncultivated rare taxa. Our analysis on the dynamics of the rare prokaryotic biosphere, by combining different methodological approaches, improves the description of the types of rarity predicted from Community Assembly theory in the Arctic Ocean.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal.
- Faculty of Sciences, University of Porto, Porto, Portugal.
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | - Pedro Duarte
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- School of Science & Engineering, University of Waikato, Hamilton, New Zealand
- Ocean Frontier Institute, Dalhousie University, Halifax, NS, Canada
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Parera-Valadez Y, Yam-Puc A, López-Aguiar LK, Borges-Argáez R, Figueroa-Saldivar MA, Cáceres-Farfán M, Márquez-Velázquez NA, Prieto-Davó A. Ecological Strategies Behind the Selection of Cultivable Actinomycete Strains from the Yucatan Peninsula for the Discovery of Secondary Metabolites with Antibiotic Activity. Microb Ecol 2019; 77:839-851. [PMID: 30761424 DOI: 10.1007/s00248-019-01329-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
The quest for novel natural products has recently focused on the marine environment as a source for novel microorganisms. Although isolation of marine-derived actinomycete strains is now common, understanding their distribution in the oceans and their adaptation to this environment can be helpful in the selection of isolates for further novel secondary metabolite discovery. This study explores the taxonomic diversity of marine-derived actinomycetes from distinct environments in the coastal areas of the Yucatan Peninsula and their adaptation to the marine environment as a first step towards novel natural product discovery. The use of simple ecological principles, for example, phylogenetic relatedness to previously characterized actinomycetes or seawater requirements for growth, to recognize isolates with adaptations to the ocean in an effort to select for marine-derived actinomycete to be used for further chemical studies. Marine microbial environments are an important source of novel bioactive natural products and, together with methods such as genome mining for detection of strains with biotechnological potential, ecological strategies can bring useful insights in the selection and identification of marine-derived actinomycetes for novel natural product discovery.
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Affiliation(s)
- Yessica Parera-Valadez
- Laboratorio de Ecología Microbiana y Productos Naturales Marinos, Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Alejandro Yam-Puc
- Laboratorio de Ecología Microbiana y Productos Naturales Marinos, Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Lluvia Korynthia López-Aguiar
- Laboratorio de Ecología Microbiana y Productos Naturales Marinos, Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Rocío Borges-Argáez
- CICY - Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico
| | - Mario Alberto Figueroa-Saldivar
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Conjunto E., 04510, Mexico City, Mexico
| | - Mirbella Cáceres-Farfán
- CICY - Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico
| | - Norma Angélica Márquez-Velázquez
- Laboratorio de Ecología Microbiana y Productos Naturales Marinos, Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Alejandra Prieto-Davó
- Laboratorio de Ecología Microbiana y Productos Naturales Marinos, Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico.
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Mandalakis M, Gavriilidou A, Polymenakou PN, Christakis CA, Nomikou P, Medvecký M, Kilias SP, Kentouri M, Kotoulas G, Magoulas A. Microbial strains isolated from CO 2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics. Mar Environ Res 2019; 144:102-110. [PMID: 30654982 DOI: 10.1016/j.marenvres.2019.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/31/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts.
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Affiliation(s)
- Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece.
| | - Asimenia Gavriilidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Paraskevi N Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Christos A Christakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Panepistimioupoli Zographou, 15784, Athens, Greece
| | - Matej Medvecký
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic; Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Stephanos P Kilias
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Panepistimioupoli Zographou, 15784, Athens, Greece
| | - Maroudio Kentouri
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
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Pepi M, Heipieper HJ, Balestra C, Borra M, Biffali E, Casotti R. Toxicity of diatom polyunsaturated aldehydes to marine bacterial isolates reveals their mode of action. Chemosphere 2017; 177:258-265. [PMID: 28314230 DOI: 10.1016/j.chemosphere.2017.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/14/2017] [Accepted: 03/08/2017] [Indexed: 06/06/2023]
Abstract
Diatoms produce and release polyunsaturated aldehydes (PUAs) during senescence in culture and at the end of blooms in nature and these compounds play different ecological roles, as infochemicals, allelochemicals and pheromones In order to elucidate the toxic effects of PUAs, we isolated six bacterial strains from the Mediterranean Sea during a diatom bloom and tested their tolerance to PUA in terms of growth and cell membrane properties. Based upon 16S rRNA sequencing, these bacteria were assigned to the genera Pseudomonas, Sufflavibacter, Halomonas, Vibrio, Idiomarina, and Labrenzia. Growth of these strains was reduced by 50% (EC50) at PUA concentrations ranging from 600 to 1700 μM of 2E,4E/Z-heptadienal (HEPTA), 400-800 μM of 2E, 4E/Z-octadienal (OCTA), and 70-400 μM of 2E, 4E/Z-decadienal (DECA). Two of these strains, Vibrio sp. and Halomonas, sp. were also investigated for membrane fatty acid composition in terms of adaptive modifications of their degree of saturation (ratio between saturated and unsaturated fatty acids) by GC-FID. A direct correlation between hydrophobicity and PUA toxicity was observed, and these bacteria were also found to react to PUAs by increasing the degree of saturation of their membranes fatty acids. Tested PUAs were 4-fold more toxic than the well-investigated n-alkanols, most probably due to their additional chemical aldehyde toxicity to disrupting proteins by the formation of Schiff's bases, and therefore, they act as very toxic and effective poison, probably accumulating in cytoplasmic membranes because of their high hydrophobicity.
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Affiliation(s)
- Milva Pepi
- Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Hermann J Heipieper
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Cecilia Balestra
- Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Marco Borra
- Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Elio Biffali
- Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Napoli, Italy
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Abstract
Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses - not usually considered to be organisms - would merely be part of the environment. Since the late 1980s, however, a growing stream of micrographic, experimental, molecular, and model-based (theoretical) research has been investigating how and why viruses should be understood as ecological actors of the most important sort. Viruses, especially phage, have been revealed as participants in the planet's most crucial food webs, even though viruses technically consume nothing (they do not metabolize by themselves). Even more impressively, viruses have been identified as regulators of planetary biogeochemistry, in which they control cycles such as carbon, nitrogen and phosphorus - cycles on which all life depends. Although much biogeochemical research black-boxes the entities filling functional roles, it is useful to focus a little more closely to understand how viruses can be held responsible for the global processes of life. This paper will give a brief overview of the history of virus ecology and tease out the implications of large-scale ecological modelling with viruses. This analysis suggests that viruses should be conceptualized as ecological actors that are at least comparable and possibly equal to organismal actors. Ecological agency can therefore be distinguished from standard interpretations of biological agency.
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