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Zhang D, Chu B, Yang Q, Zhang X, Fang Y, Liu G, Liang L, Guo Y, Yin Y, Cai Y, Jiang G. Degradation of organic mercury in high salt environments by a marine aerobic bacterium Alteromonas macleodii KD01. BIORESOURCE TECHNOLOGY 2024; 402:130831. [PMID: 38734262 DOI: 10.1016/j.biortech.2024.130831] [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: 01/04/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024]
Abstract
Mercury (Hg), particularly organic mercury, poses a global concern due to its pronounced toxicity and bioaccumulation. Bioremediation of organic mercury in high-salt wastewater faces challenges due to the growth limitations imposed by elevated Cl- and Na+ concentrations on microorganisms. In this study, an isolated marine bacterium Alteromonas macleodii KD01 was demonstrated to degrade methylmercury (MeHg) efficiently in seawater and then was applied to degrade organic mercury (MeHg, ethylmercury, and thimerosal) in simulated high-salt wastewater. Results showed that A. macleodii KD01 can rapidly degrade organic mercury (within 20 min) even at high concentrations (>10 ng/mL), volatilizing a portion of Hg from the wastewater. Further analysis revealed an increased transcription of organomercury lyase (merB) with rising organic mercury concentrations during the exposure process, suggesting the involvement of mer operon (merA and merB). These findings highlight A. macleodii KD01 as a promising candidate for addressing organic mercury pollution in high-salt wastewater.
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Affiliation(s)
- Dingxi Zhang
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bowei Chu
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Yang
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Zhang
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingying Fang
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangliang Liu
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Lina Liang
- Beijing Zhongke PUYAN Science and Technology Co., Ltd, Beijing 100096, China
| | - Yingying Guo
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Yongguang Yin
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Yong Cai
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Chai YJ, Syauqi TA, Sudesh K, Ee TL, Ban CC, Kar Mun AC, Anne Strain EM, Merican F, Rahim MA, Md Salleh K, Yin CS. Effects of poly(3-hydroxybutyrate) [P(3HB)] coating on the bacterial communities of artificial structures. PLoS One 2024; 19:e0300929. [PMID: 38635673 PMCID: PMC11025745 DOI: 10.1371/journal.pone.0300929] [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: 09/21/2023] [Accepted: 03/06/2024] [Indexed: 04/20/2024] Open
Abstract
The expanding urbanization of coastal areas has led to increased ocean sprawl, which has had both physical and chemical adverse effects on marine and coastal ecosystems. To maintain the health and functionality of these ecosystems, it is imperative to develop effective solutions. One such solution involves the use of biodegradable polymers as bioactive coatings to enhance the bioreceptivity of marine and coastal infrastructures. Our study aimed to explore two main objectives: (1) investigate PHA-degrading bacteria on polymer-coated surfaces and in surrounding seawater, and (2) comparing biofilm colonization between surfaces with and without the polymer coating. We applied poly(3-hydroxybutyrate) [P(3HB)) coatings on concrete surfaces at concentrations of 1% and 6% w/v, with varying numbers of coating cycles (1, 3, and 6). Our findings revealed that the addition of P(3HB) indeed promoted accelerated biofilm growth on the coated surfaces, resulting in an occupied area approximately 50% to 100% larger than that observed in the negative control. This indicates a remarkable enhancement, with the biofilm expanding at a rate roughly 1.5 to 2 times faster than the untreated surfaces. We observed noteworthy distinctions in biofilm growth patterns based on varying concentration and number of coating cycles. Interestingly, treatments with low concentration and high coating cycles exhibited comparable biofilm enhancements to those with high concentrations and low coating cycles. Further investigation into the bacterial communities responsible for the degradation of P(3HB) coatings identified mostly common and widespread strains but found no relation between the concentration and coating cycles. Nevertheless, this microbial degradation process was found to be highly efficient, manifesting noticeable effects within a single month. While these initial findings are promising, it's essential to conduct tests under natural conditions to validate the applicability of this approach. Nonetheless, our study represents a novel and bio-based ecological engineering strategy for enhancing the bioreceptivity of marine and coastal structures.
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Affiliation(s)
- Yee Jean Chai
- Centre for Global Sustainability Studies, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Taufiq Ahmad Syauqi
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Tan Leng Ee
- School of Housing, Building and Planning, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Cheah Chee Ban
- School of Housing, Building and Planning, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Amanda Chong Kar Mun
- Centre for Global Sustainability Studies, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Elisabeth Marijke Anne Strain
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
- Centre for Marine Socioecology, University of Tasmania, Hobart, Australia
| | - Faradina Merican
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | | | | | - Chee Su Yin
- Centre for Global Sustainability Studies, Universiti Sains Malaysia, Minden, Penang, Malaysia
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Pereira-Garcia C, Sanz-Sáez I, Sánchez P, Coutinho FH, Bravo AG, Sánchez O, Acinas SG. Genomic and transcriptomic characterization of methylmercury detoxification in a deep ocean Alteromonas mediterranea ISS312. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123725. [PMID: 38467369 DOI: 10.1016/j.envpol.2024.123725] [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: 10/03/2023] [Revised: 01/12/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
Methylmercury (MeHg) is one of the most worrisome pollutants in marine systems. MeHg detoxification is mediated by merB and merA genes, responsible for the demethylation of MeHg and the reduction of inorganic mercury, respectively. Little is known about the biological capacity to detoxify this compound in marine environments, and even less the bacterial transcriptional changes during MeHg detoxification. This study provides the genomic and transcriptomic characterization of the deep ocean bacteria Alteromonas mediterranea ISS312 with capacity for MeHg degradation. Its genome sequence revealed four mer operons containing three merA gene and two merB gene copies, that could be horizontally transferred among distant related genomes by mobile genetic elements. The transcriptomic profiling in the presence of 5 μM MeHg showed that merA and merB genes are within the most expressed genes, although not all mer genes were equally transcribed. Besides, we aimed to identify functional orthologous genes that displayed expression profiles highly similar or identical to those genes within the mer operons, which could indicate they are under the same regulatory controls. We found contrasting expression profiles for each mer operon that were positively correlated with a wide array of functions mostly related to amino acid metabolism, but also to flagellar assembly or two component systems. Also, this study highlights that all merAB genes of the four operons were globally distributed across oceans layers with higher transcriptional activity in the mesopelagic deeper waters. Our study provides new insights about the transcriptional patterns related to the capacity of marine bacteria to detoxify MeHg, with important implications for the understanding of this process in marine ecosystems.
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Affiliation(s)
- Carla Pereira-Garcia
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Catalunya, Spain.
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain; Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Felipe H Coutinho
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Andrea G Bravo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Catalunya, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain.
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McNichol SM, Sanchez-Quete F, Loeb SK, Teske AP, Shah Walter SR, Mahmoudi N. Dynamics of carbon substrate competition among heterotrophic microorganisms. THE ISME JOURNAL 2024; 18:wrae018. [PMID: 38366177 PMCID: PMC10942773 DOI: 10.1093/ismejo/wrae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/06/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Growing evidence suggests that interactions among heterotrophic microorganisms influence the efficiency and rate of organic matter turnover. These interactions are dynamic and shaped by the composition and availability of resources in their surrounding environment. Heterotrophic microorganisms inhabiting marine environments often encounter fluctuations in the quality and quantity of carbon inputs, ranging from simple sugars to large, complex compounds. Here, we experimentally tested how the chemical complexity of carbon substrates affects competition and growth dynamics between two heterotrophic marine isolates. We tracked cell density using species-specific polymerase chain reaction (PCR) assays and measured rates of microbial CO2 production along with associated isotopic signatures (13C and 14C) to quantify the impact of these interactions on organic matter remineralization. The observed cell densities revealed substrate-driven interactions: one species exhibited a competitive advantage and quickly outgrew the other when incubated with a labile compound whereas both species seemed to coexist harmoniously in the presence of more complex organic matter. Rates of CO2 respiration revealed that coincubation of these isolates enhanced organic matter turnover, sometimes by nearly 2-fold, compared to their incubation as mono-cultures. Isotopic signatures of respired CO2 indicated that coincubation resulted in a greater remineralization of macromolecular organic matter. These results demonstrate that simple substrates promote competition whereas high substrate complexity reduces competitiveness and promotes the partitioning of degradative activities into distinct niches, facilitating coordinated utilization of the carbon pool. Taken together, this study yields new insight into how the quality of organic matter plays a pivotal role in determining microbial interactions within marine environments.
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Affiliation(s)
- Samuel M McNichol
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
| | - Fernando Sanchez-Quete
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Stephanie K Loeb
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd, Lewes, DE 19958, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
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Rey-Velasco X, Deulofeu-Capo O, Sanz-Sáez I, Cardelús C, Ferrera I, Gasol JM, Sánchez O. Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability. Microbiol Spectr 2023; 11:e0089023. [PMID: 37747249 PMCID: PMC10580928 DOI: 10.1128/spectrum.00890-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
Isolation of microorganisms is a useful approach to gathering knowledge about their genomic properties, physiology, and ecology, in addition to allowing the characterization of novel taxa. We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site of the northwest Mediterranean to evaluate the impact of grazing, viral mortality, resource competition reduction, and light presence/absence on bacterioplankton growth. Isolates were retrieved using two growth media, and their full 16S rRNA gene was sequenced to assess their identity and calculate their culturability across seasons and experimental conditions. A total of 1,643 isolates were obtained, mainly affiliated to the classes Gammaproteobacteria (44%), Alphaproteobacteria (26%), and Bacteroidia (17%). Isolates pertaining to class Gammaproteobacteria were the most abundant in all experiments, while Bacteroidia were preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole data set, with dramatic increases in the summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top 10 abundant taxa in several experiments and from the whole data set. We also show that top-down and bottom-up controls differentially affect taxa in terms of culturability. Our results indicate that culturing marine bacteria using agar plates can be successful in certain ecological situations. IMPORTANCE Bottom-up and top-down controls greatly influence marine microbial community composition and dynamics, which in turn have effects on their culturability. We isolated a high amount of heterotrophic bacterial strains from experiments where seawater environmental conditions had been manipulated and found that decreasing grazing and viral pressure as well as rising nutrient availability are key factors increasing the success in culturing marine bacteria. Our data hint at factors influencing culturability and underpin bacterial cultures as a powerful way to discover new taxa.
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Affiliation(s)
| | - Ona Deulofeu-Capo
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Sanz-Sáez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Instituto de Diagnóstico Ambiental y Estudios del Agua (IDAEA-CSIC), Barcelona, Catalonia, Spain
| | - Clara Cardelús
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Ferrera
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Sanz-Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME COMMUNICATIONS 2023; 3:92. [PMID: 37660234 PMCID: PMC10475052 DOI: 10.1038/s43705-023-00290-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/04/2023]
Abstract
Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
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Affiliation(s)
- Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering; The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016, Paris, France
- Directors' Research European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Susana Agustí
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
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Gattoni G, de la Haba RR, Martín J, Reyes F, Sánchez-Porro C, Feola A, Zuchegna C, Guerrero-Flores S, Varcamonti M, Ricca E, Selem-Mojica N, Ventosa A, Corral P. Genomic study and lipidomic bioassay of Leeuwenhoekiella parthenopeia: A novel rare biosphere marine bacterium that inhibits tumor cell viability. Front Microbiol 2023; 13:1090197. [PMID: 36687661 PMCID: PMC9859067 DOI: 10.3389/fmicb.2022.1090197] [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: 11/05/2022] [Accepted: 12/09/2022] [Indexed: 01/09/2023] Open
Abstract
The fraction of low-abundance microbiota in the marine environment is a promising target for discovering new bioactive molecules with pharmaceutical applications. Phenomena in the ocean such as diel vertical migration (DVM) and seasonal dynamic events influence the pattern of diversity of marine bacteria, conditioning the probability of isolation of uncultured bacteria. In this study, we report a new marine bacterium belonging to the rare biosphere, Leeuwenhoekiella parthenopeia sp. nov. Mr9T, which was isolated employing seasonal and diel sampling approaches. Its complete characterization, ecology, biosynthetic gene profiling of the whole genus Leeuwenhoekiella, and bioactivity of its extract on human cells are reported. The phylogenomic and microbial diversity studies demonstrated that this bacterium is a new and rare species, barely representing 0.0029% of the bacterial community in Mediterranean Sea metagenomes. The biosynthetic profiling of species of the genus Leeuwenhoekiella showed nine functionally related gene cluster families (GCF), none were associated with pathways responsible to produce known compounds or registered patents, therefore revealing its potential to synthesize novel bioactive compounds. In vitro screenings of L. parthenopeia Mr9T showed that the total lipid content (lipidome) of the cell membrane reduces the prostatic and brain tumor cell viability with a lower effect on normal cells. The lipidome consisted of sulfobacin A, WB 3559A, WB 3559B, docosenamide, topostin B-567, and unknown compounds. Therefore, the bioactivity could be attributed to any of these individual compounds or due to their synergistic effect. Beyond the rarity and biosynthetic potential of this bacterium, the importance and novelty of this study is the employment of sampling strategies based on ecological factors to reach the hidden microbiota, as well as the use of bacterial membrane constituents as potential novel therapeutics. Our findings open new perspectives on cultivation and the relationship between bacterial biological membrane components and their bioactivity in eukaryotic cells, encouraging similar studies in other members of the rare biosphere.
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Affiliation(s)
- Giuliano Gattoni
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | | | | | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonia Feola
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Candida Zuchegna
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Shaday Guerrero-Flores
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| | - Mario Varcamonti
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Nelly Selem-Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Paulina Corral
- Department of Biology, University of Naples Federico II, Naples, Italy,Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain,*Correspondence: Paulina Corral,
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8
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Gunawan NR, Tessman M, Zhen D, Johnson L, Evans P, Clements SM, Pomeroy RS, Burkart MD, Simkovsky R, Mayfield SP. Biodegradation of renewable polyurethane foams in marine environments occurs through depolymerization by marine microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158761. [PMID: 36154974 DOI: 10.1016/j.scitotenv.2022.158761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/18/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
Accumulation of plastics in the Earth's oceans is causing widespread disruption to marine ecosystems. To help mitigate the environmental burden caused by non-degradable plastics, we have previously developed a commercially relevant polyurethane (PU) foam derived from renewable biological materials that can be depolymerized into its constituent monomers and consumed by microorganisms in soil or compost. Here we demonstrate that these same PU foams can be biodegraded by marine microorganisms in the ocean and by isolated marine microorganisms in an ex situ seawater environment. Using Fourier-transform infrared (FTIR) spectroscopy, we tracked molecular changes imparted by microbial breakdown of the PU polymers; and utilized scanning electron microscopy (SEM) to demonstrate the loss of physical structure associated with colonization of microorganisms on the PU foams. We subsequently enriched, isolated, and identified individual microorganisms, from six marine sites around San Diego, CA, that are capable of depolymerizing, metabolizing, and accumulating biomass using these PU foams as a sole carbon source. Analysis using SEM, FTIR, and gas chromatography-mass spectrometry (GCMS) confirmed that these microorganisms depolymerized the PU into its constitutive diols, diacids, and other PU fragments. SEM and FTIR results from isolated organismal biodegradation experiments exactly matched those from ex situ and ocean biodegradation samples, suggesting that these PU foam would undergo biodegradation in a natural ocean environment by enzymatic depolymerization of the PU foams and eventual uptake of the degradation products into biomass by marine microorganisms, should these foams unintentionally end up in the marine environment, as many plastics do.
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Affiliation(s)
| | | | - Daniel Zhen
- Algenesis Inc., 1238 Sea Village Dr., Cardiff, CA, USA
| | | | - Payton Evans
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Samantha M Clements
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert S Pomeroy
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | | | - Stephen P Mayfield
- Department of Molecular Biology, and California Center for Algae Biotechnology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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9
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Kalkan S. Multimodal analysis of south-eastern Black Sea sediment bacterial population diversity. MARINE POLLUTION BULLETIN 2022; 183:114063. [PMID: 36057154 DOI: 10.1016/j.marpolbul.2022.114063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/15/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
This study focused on marine sediments from the Black Sea, mainly due to bacterial diversity-induced public health / biotechnology application value. Sediment samples were gathered from 14 locations at differing depths across Turkish shores on a seasonal basis over 10 months, with bacterial identifications performed through using multimodal analytical platforms. Overall, 26 differing, predominantly Gram-positive (57.5 %) bacterial species were identified for this region, including Bacillaceae (50.0 %) and Pseudomonadaceae (15.0 %). The most dominant classes were identified as Bacilli (52.5 %) and Gammaproteobacteria (40.0 %). Ten isolates (25 %) to the species level and thirty-six isolates (90 %) to the genus level were identified using VITEK® MS and Bruker Microflex® LT/SH, in comparison to 16S rRNA sequencing results. Identified species - particularly, novel reported species - can contribute to the knowledge of microbial life dwelling upon sediments of the south-eastern regions of the Black Sea.
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Affiliation(s)
- Samet Kalkan
- Recep Tayyip Erdogan University, Faculty of Fisheries, Ataturk Street Fener District, 53100 Merkez, Rize, Turkey.
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10
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Sanz-Sáez I, Pereira-García C, Bravo AG, Trujillo L, Pla i Ferriol M, Capilla M, Sánchez P, Rodríguez Martín-Doimeadios RC, Acinas SG, Sánchez O. Prevalence of Heterotrophic Methylmercury Detoxifying Bacteria across Oceanic Regions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3452-3461. [PMID: 35245029 PMCID: PMC8928480 DOI: 10.1021/acs.est.1c05635] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 05/27/2023]
Abstract
Microbial reduction of inorganic divalent mercury (Hg2+) and methylmercury (MeHg) demethylation is performed by the mer operon, specifically by merA and merB genes, respectively, but little is known about the mercury tolerance capacity of marine microorganisms and its prevalence in the ocean. Here, combining culture-dependent analyses with metagenomic and metatranscriptomic data, we show that marine bacteria that encode mer genes are widespread and active in the global ocean. We explored the distribution of these genes in 290 marine heterotrophic bacteria (Alteromonas and Marinobacter spp.) isolated from different oceanographic regions and depths, and assessed their tolerance to diverse concentrations of Hg2+ and MeHg. In particular, the Alteromonas sp. ISS312 strain presented the highest tolerance capacity and a degradation efficiency for MeHg of 98.2% in 24 h. Fragment recruitment analyses of Alteromonas sp. genomes (ISS312 strain and its associated reconstructed metagenome assembled genome MAG-0289) against microbial bathypelagic metagenomes confirm their prevalence in the deep ocean. Moreover, we retrieved 54 merA and 6 merB genes variants related to the Alteromonas sp. ISS312 strain from global metagenomes and metatranscriptomes from Tara Oceans. Our findings highlight the biological reductive MeHg degradation as a relevant pathway of the ocean Hg biogeochemical cycle.
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Affiliation(s)
- Isabel Sanz-Sáez
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Carla Pereira-García
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Andrea G. Bravo
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Laura Trujillo
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Martí Pla i Ferriol
- Departament
de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Miguel Capilla
- Research
Group in Environmental Engineering (GI2AM), Department of Chemical
Engineering, University of Valencia, Av. De la Universitat S/N, 46100 Burjassot, Spain
| | - Pablo Sánchez
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Rosa Carmen Rodríguez Martín-Doimeadios
- Environmental
Sciences Institute (ICAM), Department of Analytical Chemistry and
Food Technology, University of Castilla-La
Mancha, Avda. Carlos
III s/n, 45071 Toledo, Spain
| | - Silvia G. Acinas
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament
de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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11
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Fernández-Juárez V, Jaén-Luchoro D, Brito-Echeverría J, Agawin NSR, Bennasar-Figueras A, Echeveste P. Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration. MICROBIAL ECOLOGY 2022; 83:296-313. [PMID: 33954842 DOI: 10.1007/s00248-021-01766-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12 days (d)) and short-term studies (4 d/96 h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N2-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater.
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Affiliation(s)
- Víctor Fernández-Juárez
- Marine Ecology and Systematics (MarES), Department of Biology, University of the Balearic Islands, Palma, Spain.
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Jocelyn Brito-Echeverría
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Nona S R Agawin
- Marine Ecology and Systematics (MarES), Department of Biology, University of the Balearic Islands, Palma, Spain
| | | | - Pedro Echeveste
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
- Instituto Milenio de Oceanografía, Concepción, Chile
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12
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Huang Z, Mo S, Yan L, Wei X, Huang Y, Zhang L, Zhang S, Liu J, Xiao Q, Lin H, Guo Y. A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments. Front Microbiol 2021; 12:675048. [PMID: 34194410 PMCID: PMC8236954 DOI: 10.3389/fmicb.2021.675048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 01/19/2023] Open
Abstract
Molecular methods revealed that the majority of microbes in natural environments remains uncultivated. To fully understand the physiological and metabolic characteristics of microbes, however, culturing is still critical for microbial studies. Here, we used bacterial community analysis and four culture media, namely, traditional marine broth 2216 (MB), water extracted matter (WEM), methanol extracted matter (MEM), and starch casein agar (SCA), to investigate the diversity of cultivated bacteria in coastal sediments. A total of 1,036 isolates were obtained in pure culture, and they were classified into five groups, namely, Alphaproteobacteria (52.51%), Gammaproteobacteria (23.26%), Actinobacteria (13.32%), Firmicutes, and Bacteroidetes. Compared to other three media, WEM recovered a high diversity of actinobacteria (42 of 63 genotypes), with Micromonospora and Streptomyces as the most cultivated genera. Amplicon sequencing of the bacterial 16S ribosomal RNA (rRNA) gene V3-V4 fragment revealed eight dominant groups, Alphaproteobacteria (12.81%), Gammaproteobacteria (20.07%), Deltaproteobacteria (12.95%), Chloroflexi (13.09%), Bacteroidetes (8.28%), Actinobacteria (7.34%), Cyanobacteria (6.20%), and Acidobacteria (5.71%). The dominant members affiliated to Actinobacteria belonged to "Candidatus Actinomarinales," "Candidatus Microtrichales," and Nitriliruptorales. The cultivated actinobacteria accounted for a small proportion (<5%) compared to the actinobacterial community, which supported that the majority of actinobacteria are still waiting for cultivation. Our study concluded that WEM could be a useful and simple culture medium that enhanced the recovery of culturable actinobacteria from coastal sediments.
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Affiliation(s)
- Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
- Fujian Province Key Laboratory for the Development of Bioactive Material From Marine Algae, Quanzhou, China
| | - Shiqing Mo
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Lifei Yan
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Xiaomei Wei
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Yuanyuan Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Lizhen Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Shuhui Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Jianzong Liu
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Qingqing Xiao
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Hong Lin
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Yu Guo
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
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13
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Wang L, Shao Z. Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis. Front Microbiol 2021; 12:652766. [PMID: 33815342 PMCID: PMC8014003 DOI: 10.3389/fmicb.2021.652766] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.
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Affiliation(s)
- Liping Wang
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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14
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Semedo M, Lopes E, Baptista MS, Oller-Ruiz A, Gilabert J, Tomasino MP, Magalhães C. Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific. Front Microbiol 2021; 12:624071. [PMID: 33732221 PMCID: PMC7959781 DOI: 10.3389/fmicb.2021.624071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3– concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.
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Affiliation(s)
- Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Eva Lopes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ainhoa Oller-Ruiz
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Javier Gilabert
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
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