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Jia Z, Lipus D, Burckhardt O, Bussert R, Sondermann M, Bartholomäus A, Wagner D, Kallmeyer J. Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO 2 terrestrial subsurface environments. Front Microbiol 2023; 14:1105259. [PMID: 37293225 PMCID: PMC10246774 DOI: 10.3389/fmicb.2023.1105259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/25/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities. Methods To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2. Results and discussion Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.
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Affiliation(s)
- Zeyu Jia
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Oliver Burckhardt
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Robert Bussert
- Applied Geochemistry, Institute of Applied Geosciences, Technische Universität Berlin, Berlin, Germany
| | - Megan Sondermann
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | | | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
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Rodríguez-Romero A, Viguri JR, Calosi P. Acquiring an evolutionary perspective in marine ecotoxicology to tackle emerging concerns in a rapidly changing ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142816. [PMID: 33092841 DOI: 10.1016/j.scitotenv.2020.142816] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Tens of thousands of anthropogenic chemicals and wastes enter the marine environment each year as a consequence of the ever-increasing anthropogenic activities and demographic growth of the human population, which is majorly concentrated along coastal areas. Marine ecotoxicology has had a crucial role in helping shed light on the fate of chemicals in the environment, and improving our understanding of how they can affect natural ecosystems. However, chemical contamination is not occurring in isolation, but rather against a rapidly changing environmental horizon. Most environmental studies have been focusing on short-term within-generation responses of single life stages of single species to single stressors. As a consequence, one-dimensional ecotoxicology cannot enable us to appreciate the degree and magnitude of future impacts of chemicals on marine ecosystems. Current approaches that lack an evolutionary perspective within the context of ongoing and future local and global stressors will likely lead us to under or over estimations of the impacts that chemicals will exert on marine organisms. It is therefore urgent to define whether marine organisms can acclimate, i.e. adjust their phenotypes through transgenerational plasticity, or rapidly adapt, i.e. realign the population phenotypic performances to maximize fitness, to the new chemical environment within a selective horizon defined by global changes. To foster a significant advancement in this research area, we review briefly the history of ecotoxicology, synthesis our current understanding of the fate and impact of contaminants under global changes, and critically discuss the benefits and challenges of integrative approaches toward developing an evolutionary perspective in marine ecotoxicology: particularly through a multigenerational approach. The inclusion of multigenerational studies in Ecological Risk Assessment framework (ERA) would provide significant and more accurately information to help predict the risks of pollution in a rapidly changing ocean.
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Affiliation(s)
- Araceli Rodríguez-Romero
- Departamento de Química Analítica, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Campus Río San Pedro, Puerto Real, 11510 Cádiz, Spain; Departamento de Ecología y Gestión Costera, Instituto de Ciencias Marinas de Andalucía (CSIC), Campus Universitario Río San Pedro, 11519 Puerto Real, Spain.
| | - Javier R Viguri
- Green Engineering & Resources Research Group (GER), Departamento de Química e Ingeniería de Procesos y Recursos, ETSIIT, Universidad de Cantabria, Avda. de los Castros s/n, 39005 Santander, Cantabria, Spain
| | - Piero Calosi
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC G5L 3A1, Canada
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Tangherlini M, Corinaldesi C, Ape F, Greco S, Romeo T, Andaloro F, Danovaro R. Ocean Acidification Induces Changes in Virus-Host Relationships in Mediterranean Benthic Ecosystems. Microorganisms 2021; 9:microorganisms9040769. [PMID: 33917639 PMCID: PMC8067541 DOI: 10.3390/microorganisms9040769] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/31/2021] [Accepted: 04/04/2021] [Indexed: 01/21/2023] Open
Abstract
Acidified marine systems represent "natural laboratories", which provide opportunities to investigate the impacts of ocean acidification on different living components, including microbes. Here, we compared the benthic microbial response in four naturally acidified sites within the Southern Tyrrhenian Sea characterized by different acidification sources (i.e., CO2 emissions at Ischia, mixed gases at Panarea and Basiluzzo and acidified freshwater from karst rocks at Presidiana) and pH values. We investigated prokaryotic abundance, activity and biodiversity, viral abundance and prokaryotic infections, along with the biochemical composition of the sediment organic matter. We found that, despite differences in local environmental dynamics, viral life strategies change in acidified conditions from mainly lytic to temperate lifestyles (e.g., chronic infection), also resulting in a lowered impact on prokaryotic communities, which shift towards (chemo)autotrophic assemblages, with lower organic matter consumption. Taken together, these results suggest that ocean acidification exerts a deep control on microbial benthic assemblages, with important feedbacks on ecosystem functioning.
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Affiliation(s)
- Michael Tangherlini
- Fano Marine Centre, Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Viale Adriatico 1-N, 61032 Fano, Italy
- Correspondence: (M.T.); (C.C.)
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Correspondence: (M.T.); (C.C.)
| | - Francesca Ape
- Institute of Anthropic Impacts and Sustainability in Marine Environment-National Research Council (IAS-CNR), Lungomare Cristoforo Colombo n. 4521 (ex Complesso Roosevelt), Località Addaura, 90149 Palermo, Italy;
| | - Silvestro Greco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Via Po 25c, 00198 Rome, Italy;
| | - Teresa Romeo
- Sicily Marine Centre, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Via dei Mille 46, 98057 Milazzo, Italy or (T.R.); (F.A.)
- National Institute for Environmental Protection and Research, ISPRA Via dei Mille 46, 98057 Milazzo, Italy
| | - Franco Andaloro
- Sicily Marine Centre, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Via dei Mille 46, 98057 Milazzo, Italy or (T.R.); (F.A.)
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
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Cheng JH, Wang Y, Zhang XY, Sun ML, Zhang X, Song XY, Zhang YZ, Zhang Y, Chen XL. Characterization and Diversity Analysis of the Extracellular Proteases of Thermophilic Anoxybacillus caldiproteolyticus 1A02591 From Deep-Sea Hydrothermal Vent Sediment. Front Microbiol 2021; 12:643508. [PMID: 33796092 PMCID: PMC8007923 DOI: 10.3389/fmicb.2021.643508] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/24/2021] [Indexed: 11/13/2022] Open
Abstract
Protease-producing bacteria play key roles in the degradation of marine organic nitrogen. Although some deep-sea bacteria are found to produce proteases, there has been no report on protease-secreting Anoxybacillus from marine hydrothermal vent regions. Here, we analyzed the diversity and functions of the proteases, especially the extracellular proteases, of Anoxybacillus caldiproteolyticus 1A02591, a protease-secreting strain isolated from a deep-sea hydrothermal vent sediment of the East Pacific Ocean. Strain 1A02591 is a thermophilic bacterium with a strong protease-secreting ability, which displayed the maximum growth rate (0.139 h–1) and extracellular protease production (307.99 U/mL) at 55°C. Strain 1A02591 contains 75 putative proteases, including 65 intracellular proteases and 10 extracellular proteases according to signal peptide prediction. When strain 1A02591 was cultured with casein, 12 proteases were identified in the secretome, in which metalloproteases (6/12) and serine proteases (4/12) accounted for the majority, and a thermolysin-like protease of the M4 family was the most abundant, suggesting that strain 1A02591 mainly secreted a thermophilic metalloprotease. Correspondingly, the secreted proteases of strain 1A02591 showed the highest activity at the temperature as high as 70°C, and was inhibited 70% by metalloprotease inhibitor o-phenanthroline and 50% by serine protease inhibitor phenylmethylsulfonyl fluoride. The secreted proteases could degrade different proteins, suggesting the role of strain 1A02591 in organic nitrogen degradation in deep-sea hydrothermal ecosystem. These results provide the first insight into the proteases of an Anoxybacillus strain from deep-sea hydrothermal ecosystem, which is helpful in understanding the function of Anoxybacillus in the marine biogeochemical cycle.
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Affiliation(s)
- Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yu Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Mei-Ling Sun
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Lin YS, Lin HT, Wang BS, Huang WJ, Lin LH, Tsai AY. Intense but variable autotrophic activity in a rapidly flushed shallow-water hydrothermal plume (Kueishantao Islet, Taiwan). GEOBIOLOGY 2021; 19:87-101. [PMID: 33043601 DOI: 10.1111/gbi.12418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/11/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
Shallow-water hydrothermal plumes concomitantly host both photosynthetic and chemoautotrophic organisms in a single biotope. Yet, rate measurements to quantify the contributions of different autotrophic activity types are scarce. Herein, we measured the light and dark dissolved inorganic carbon (DIC) uptake rates in the plume water of the Kueishantao hydrothermal field using the 13 C-labeling approach. Seventy percent of the plume-water samples had chemoautotrophy as the dominant mode of carbon fixation, with the dark DIC uptake rates (up to 18.6 mg C/m3 /h) within the range of the primary production in productive inner-shelf waters. When considered alongside the geochemical and microbiological observations, the rate data reveal the distribution of different trophic activities in the hydrothermal plume. The autotrophic activity at the initial phase of plume dispersal is low. This is explained by the short response time the chemoautotrophs have to the stimulation from vent-fluid discharge, and the harmful effects of hydrothermal substances on phytoplankton. As plume dispersal and mixing continue, chemoautotrophic activities begin to rise and peak in waters that have low-to-moderate Si(OH)4 content. Toward the plume margin, chemoautotrophy declines to background levels, whereas photosynthesis by phytoplankton regains importance. Our results also provide preliminary indication to the loci of enhanced heterotrophy in the plume. Results of artificial mixing experiments suggest that previously formed plume water is the primary source of microbial inoculum for new plume water. This self-inoculation mechanism, in combination with the intense DIC uptake, helps to sustain a distinct planktonic autotrophic community in this rapidly flushed hydrothermal plume.
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Affiliation(s)
- Yu-Shih Lin
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Huei-Ting Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Bo-Shian Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan
- National Academy of Marine Research, Kaohsiung, Taiwan
| | - Wei-Jen Huang
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - An-Yi Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
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Yu T, Chen Y. Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:865-879. [PMID: 30481713 DOI: 10.1016/j.scitotenv.2018.11.301] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 05/24/2023]
Abstract
Before the industrial revolution, the atmospheric CO2 concentration was 180-330 ppm; however, fossil-fuel combustion and forest destruction have led to increased atmospheric CO2 concentration. CO2 capture and storage is regarded as a promising strategy to prevent global warming and ocean acidification and to alleviate elevated atmospheric CO2 concentration, but the leakage of CO2 from storage system can lead to rapid acidification of the surrounding circumstance, which might cause negative influence on environmental microbes. The effects of elevated CO2 on microbes have been reported extensively, but the review regarding CO2 affecting different environmental microorganisms has never been done previously. Also, the mechanisms of CO2 affecting environmental microorganisms are usually contributed to the change of pH values, while the direct influences of CO2 on microorganisms were often neglected. This paper aimed to provide a systematic review of elevated CO2 affecting environmental microbes and its mechanisms. Firstly, the influences of elevated CO2 and potential leakage of CO2 from storage sites on community structures and diversity of different surrounding environmental microbes were assessed and compared. Secondly, the adverse impacts of CO2 on microbial growth, cell morphology and membranes, bacterial spores, and microbial metabolism were introduced. Then, based on biochemical principles and knowledge of microbiology and molecular biology, the fundamental mechanisms of the influences of carbon dioxide on environmental microbes were discussed from the aspects of enzyme activity, electron generation and transfer, and key gene and protein expressions. Finally, key questions relevant to the environmental effect of CO2 that need to be answered in the future were addressed.
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Affiliation(s)
- Tong Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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González-Delgado S, Hernández JC. The Importance of Natural Acidified Systems in the Study of Ocean Acidification: What Have We Learned? ADVANCES IN MARINE BIOLOGY 2018; 80:57-99. [PMID: 30368306 DOI: 10.1016/bs.amb.2018.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Human activity is generating an excess of atmospheric CO2, resulting in what we know as ocean acidification, which produces changes in marine ecosystems. Until recently, most of the research in this area had been done under small-scale, laboratory conditions, using few variables, few species and few life cycle stages. These limitations raise questions about the reproducibility of the environment and about the importance of indirect effects and synergies in the final results of these experiments. One way to address these experimental problems is by conducting studies in situ, in natural areas where expected future pH conditions already occur, such as CO2 vent systems. In the present work, we compile and discuss the latest research carried out in these natural laboratories, with the objective to summarize their advantages and disadvantages for research to improve these investigations so they can better help us understand how the oceans of the future will change.
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Affiliation(s)
- Sara González-Delgado
- Marine Community Ecology and Climate Change, Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias (Biología), Universidad de La Laguna, Tenerife, Canary Islands, Spain
| | - José Carlos Hernández
- Marine Community Ecology and Climate Change, Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias (Biología), Universidad de La Laguna, Tenerife, Canary Islands, Spain.
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Hassenrück C, Fink A, Lichtschlag A, Tegetmeyer HE, de Beer D, Ramette A. Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches. FEMS Microbiol Ecol 2016; 92:fiw027. [PMID: 26887661 PMCID: PMC4828923 DOI: 10.1093/femsec/fiw027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/31/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects.
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Affiliation(s)
- Christiane Hassenrück
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Artur Fink
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Anna Lichtschlag
- National Oceanography Centre, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - Halina E Tegetmeyer
- Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Alban Ramette
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany Institute of Social and Preventive Medicine, Bern University, Finkenhubelweg 11, 3012 Bern, Switzerland
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