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Marietou A, Schmidt JS, Rasmussen MR, Scoma A, Rysgaard S, Vergeynst L. The effect of hydrostatic pressure on the activity and community composition of hydrocarbon-degrading bacteria in Arctic seawater. Appl Environ Microbiol 2023; 89:e0098723. [PMID: 37943057 PMCID: PMC10686064 DOI: 10.1128/aem.00987-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Increased ship traffic in the Arctic region raises the risk of oil spills. With an average sea depth of 1,000 m, there is a growing concern over the potential release of oil sinking in the form of marine oil snow into deep Arctic waters. At increasing depth, the oil-degrading community is exposed to increasing hydrostatic pressure, which can reduce microbial activity. However, microbes thriving in polar regions may adapt to low temperature by modulation of membrane fluidity, which is also a well-known adaptation to high hydrostatic pressure. At mild hydrostatic pressures up to 8-12 MPa, we did not observe an altered microbial activity or community composition, whereas comparable studies using deep-sea or sub-Arctic microbial communities with in situ temperatures of 4-5°C showed pressure-induced effects at 10-15 MPa. Our results suggest that the psychrophilic nature of the underwater microbial communities in the Arctic may be featured by specific traits that enhance their fitness at increasing hydrostatic pressure.
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Affiliation(s)
- Angeliki Marietou
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | | | - Martin R. Rasmussen
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Alberto Scoma
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Søren Rysgaard
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Leendert Vergeynst
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
- Centre for Water Technology (WATEC), Aarhus University, Aarhus, Denmark
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Gorrasi S, Franzetti A, Brandt A, Minzlaff U, Pasqualetti M, Fenice M. Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench. ENVIRONMENTAL MICROBIOME 2023; 18:67. [PMID: 37533108 PMCID: PMC10398949 DOI: 10.1186/s40793-023-00522-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment. RESULTS As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench. CONCLUSIONS This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.
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Affiliation(s)
- Susanna Gorrasi
- Laboratory of Microbiology, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Andrea Franzetti
- Laboratory of Microbiology, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum, 60325, Frankfurt am Main, Germany
- Institute of Ecology, Diversity and Evolution, Goethe University, 60438, Frankfurt am Main, Germany
| | - Ulrike Minzlaff
- Institute of Ecology, Diversity and Evolution, Goethe University, 60438, Frankfurt am Main, Germany
| | - Marcella Pasqualetti
- Laboratory of Ecology of Marine Fungi - CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Massimiliano Fenice
- Laboratory of Microbiology, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
- Laboratory of Applied Marine Microbiology - CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
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Scheffer G, Gieg LM. The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface. Microorganisms 2023; 11:1629. [PMID: 37512802 PMCID: PMC10384521 DOI: 10.3390/microorganisms11071629] [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: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed.
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Affiliation(s)
- Gabrielle Scheffer
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.
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Affiliation(s)
- Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Barbara Bayer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
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Barbato M, Palma E, Marzocchi U, Cruz Viggi C, Rossetti S, Aulenta F, Scoma A. Snorkels enhance alkanes respiration at ambient and increased hydrostatic pressure (10 MPa) by either supporting the TCA cycle or limiting alternative routes for acetyl-CoA metabolism. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115244. [PMID: 35598451 DOI: 10.1016/j.jenvman.2022.115244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
The impact of piezosensitive microorganisms is generally underestimated in the ecology of underwater environments exposed to increasing hydrostatic pressure (HP), including the biodegradation of crude oil components. Yet, no isolated pressure-loving (piezophile) microorganism grows optimally on hydrocarbons, and no isolated piezophile at all has a HP optimum <10 MPa (e.g. 1000 m below sea water level). Piezosensitive heterotrophs are thus largely accountable for oil clean up < 10 MPa, however, they are affected by such a mild HP increase in ways which are not completely clear. In a first study, the application of a bioelectrochemical system (called "oil-spill snorkel") enhanced the alkane oxidation capacity in sediments collected at surface water but tested up to 10 MPa. Here, the fingerprint left on transcript abundance was studied to explore which metabolic routes are 1) supported by snorkels application and 2) negatively impacted by HP increase. Transcript abundance was comparable for beta-oxidation across all treatments (also at a taxonomical level), while the metabolism of acetyl-CoA was highly impacted: at either 0.1 or 10 MPa, snorkels supported acetyl-CoA oxidation within the TCA cycle, while in negative controls using non-conductive rods several alternative routes for acetyl-CoA were stimulated (including those leading to internal carbon reserves e.g. 2,3 butanediol and dihydroxyacetone). In general, increased HP had opposite effects as compared to snorkels, thus indicating that snorkels could enhance hydrocarbons oxidation by alleviating in part the stressing effects imposed by increased HP on the anaerobic, respiratory electron transport chain. 16S rRNA gene analysis of sediments and biofilms on snorkels suggest a crosstalk between oil-degrading, sulfate-reducing microorganisms and sulfur oxidizers. In fact, no sulfur was deposited on snorkels, however, iron, aluminum and phosphorous were found to preferentially deposit on snorkels at 10 MPa. This data indicates that a passive BES such as the oil-spill snorkel can mitigate the stress imposed by increased HP on piezosensitive microorganisms (up to 10 MPa) without being subjected to passivation. An improved setup applying these principles can further support this deep-sea bioremediation strategy.
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Affiliation(s)
- Marta Barbato
- Engineered Microbial Systems (EMS) Lab, Industrial Biotechnology Section, Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus, Denmark; Microbiology Section, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Enza Palma
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Ugo Marzocchi
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark; Center for Water Technology WATEC, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, Italy.
| | - Alberto Scoma
- Engineered Microbial Systems (EMS) Lab, Industrial Biotechnology Section, Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus, Denmark; Microbiology Section, Department of Biology, Aarhus University, Aarhus, Denmark.
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Trouche B, Brandt MI, Belser C, Orejas C, Pesant S, Poulain J, Wincker P, Auguet JC, Arnaud-Haond S, Maignien L. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient. Front Microbiol 2021; 12:702016. [PMID: 34790173 PMCID: PMC8591283 DOI: 10.3389/fmicb.2021.702016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/22/2021] [Indexed: 11/28/2022] Open
Abstract
Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.
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Affiliation(s)
- Blandine Trouche
- Univ Brest, CNRS, IFREMER, Microbiology of Extreme Environments Laboratory (LM2E), Plouzané, France
| | | | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Évry, Université Paris-Saclay, Evry, France
| | - Covadonga Orejas
- Centro Oceanográfico de Baleares, Instituto Español de Oceanografía, Palma de Mallorca, Spain
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Évry, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Évry, Université Paris-Saclay, Evry, France
| | | | | | - Loïs Maignien
- Univ Brest, CNRS, IFREMER, Microbiology of Extreme Environments Laboratory (LM2E), Plouzané, France.,Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United States
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