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Celussi M, Manna V, Banchi E, Fonti V, Bazzaro M, Flander-Putrle V, Klun K, Kralj M, Orel N, Tinta T. Annual recurrence of prokaryotic climax communities in shallow waters of the North Mediterranean. Environ Microbiol 2024; 26:e16595. [PMID: 38418391 DOI: 10.1111/1462-2920.16595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024]
Abstract
In temperate coastal environments, wide fluctuations of biotic and abiotic factors drive microbiome dynamics. To link recurrent ecological patterns with planktonic microbial communities, we analysed a monthly-sampled 3-year time series of 16S rRNA amplicon sequencing data, alongside environmental variables, collected at two stations in the northern Adriatic Sea. Time series multivariate analyses allowed us to identify three stable, mature communities (climaxes), whose recurrence was mainly driven by changes in photoperiod and temperature. Mixotrophs (e.g., Ca. Nitrosopumilus, SUP05 clade, and Marine Group II) thrived under oligotrophic, low-light conditions, whereas copiotrophs (e.g., NS4 and NS5 clades) bloomed at higher temperatures and substrate availability. The early spring climax was characterised by a more diverse set of amplicon sequence variants, including copiotrophs associated with phytoplankton-derived organic matter degradation, and photo-auto/heterotrophic organisms (e.g., Synechococcus sp., Roseobacter clade), whose rhythmicity was linked to photoperiod lengthening. Through the identification of recurrent climax assemblages, we begin to delineate a typology of ecosystem based on microbiome composition and functionality, allowing for the intercomparison of microbial assemblages among different biomes, a still underachieved goal in the omics era.
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Affiliation(s)
- Mauro Celussi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Elisa Banchi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Matteo Bazzaro
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | | | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Martina Kralj
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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Banchi E, Manna V, Fonti V, Fabbro C, Celussi M. Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67466-67482. [PMID: 36056283 PMCID: PMC9492620 DOI: 10.1007/s11356-022-22752-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Cinzia Fabbro
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
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Dang H. Grand Challenges in Microbe-Driven Marine Carbon Cycling Research. Front Microbiol 2020; 11:1039. [PMID: 32655507 PMCID: PMC7324536 DOI: 10.3389/fmicb.2020.01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/27/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Frontiers Science Center for Ocean Carbon Sink and Climate Change, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Manna V, Malfatti F, Banchi E, Cerino F, De Pascale F, Franzo A, Schiavon R, Vezzi A, Del Negro P, Celussi M. Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters. Front Microbiol 2020; 11:1242. [PMID: 32582131 PMCID: PMC7296054 DOI: 10.3389/fmicb.2020.01242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/14/2020] [Indexed: 12/31/2022] Open
Abstract
Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L-1) and intense (10 μg of Chlorophyll a L-1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes' abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.
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Affiliation(s)
- Vincenzo Manna
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
- Department of Life Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Francesca Malfatti
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Elisa Banchi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Federica Cerino
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Fabio De Pascale
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Annalisa Franzo
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Riccardo Schiavon
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Alessandro Vezzi
- Department of Biology, Università degli Studi di Padova, Padua, Italy
| | - Paola Del Negro
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
| | - Mauro Celussi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale – OGS, Trieste, Italy
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Quero GM, Celussi M, Relitti F, Kovačević V, Del Negro P, Luna GM. Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait). MICROBIAL ECOLOGY 2020; 79:823-839. [PMID: 31728602 DOI: 10.1007/s00248-019-01451-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.
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Affiliation(s)
- Grazia Marina Quero
- Stazione Zoologica Anton Dohrn, Integrative Marine Ecology Department, Napoli, Italy
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Consiglio Nazionale delle Ricerche, Ancona, Italy
| | - Mauro Celussi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy.
| | - Federica Relitti
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Vedrana Kovačević
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Paola Del Negro
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Gian Marco Luna
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Consiglio Nazionale delle Ricerche, Ancona, Italy
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La Cono V, Ruggeri G, Azzaro M, Crisafi F, Decembrini F, Denaro R, La Spada G, Maimone G, Monticelli LS, Smedile F, Giuliano L, Yakimov MM. Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO 2-Fixing Bathypelagic Prokaryotic Consortia. Front Microbiol 2018; 9:3. [PMID: 29403458 PMCID: PMC5780414 DOI: 10.3389/fmicb.2018.00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/03/2018] [Indexed: 11/16/2022] Open
Abstract
Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m-3 d-1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m-2 d-1. This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.
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Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gioachino Ruggeri
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Maurizio Azzaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesca Crisafi
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Franco Decembrini
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Renata Denaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gina La Spada
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Giovanna Maimone
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Luis S. Monticelli
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Laura Giuliano
- Mediterranean Science Commission (CIESM), Monaco, Monaco
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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