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Banchi E, Corre E, Del Negro P, Celussi M, Malfatti F. Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:126-142. [PMID: 38433960 PMCID: PMC10902248 DOI: 10.1007/s42995-023-00192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00192-z.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Erwan Corre
- FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), Sorbonne Université CNRS, 29680 Roscoff, France
| | - Paola Del Negro
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Francesca Malfatti
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
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Zhang Y, Yang Q, Zhang Y, Ahmad M, Ling J, Tang X, Dong J. Shifts in abundance and network complexity of coral bacteria in response to elevated ammonium stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144631. [PMID: 33434804 DOI: 10.1016/j.scitotenv.2020.144631] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Coral bacteria are highly dynamic and acutely affected by host health and environmental conditions. However, there is limited knowledge of how the dynamics of coral-associated bacterial communities and interactions among bacterial members change in response to dissolved inorganic nutrient stressors. Here, we used high-throughput sequencing of the 16S rRNA gene to examine dynamic changes in coral-associated bacterial communities under elevated ammonium stress. Short-term exposure to high levels of ammonium does not significantly harm coral holobiont. Physiological parameters such as carbohydrate, chlorophyll a, and lipid content of coral holobiont were not affected. After three weeks of elevated ammonium stress, however, the coral-associated bacterial community changed significantly. The abundance of certain bacterial populations increased significantly, with enrichment of pathogenic and opportunistic bacteria and a decrease in defensive and core bacteria. Keystone bacterial species in the co-occurrence network changed considerably. Under elevated ammonium stress, the abundance of keystone species associated with corals was lower and the complexity of keystone bacterial relationships decreased significantly. Our results indicate that bacteria respond to elevated ammonium stress through changes in abundance and co-occurrence among bacterial members. This precedes visual symptoms of changes in coral physiological conditions and could be used as an early warning indicator of elevated ammonium stress in coastal coral reef management.
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Affiliation(s)
- Yanying Zhang
- Ocean School, Yantai University, Yantai 264005, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou 510301, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiaoyu Tang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sanya National Marine Ecosystem Research Station and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China.
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Sun H, Zhang Y, Tan S, Zheng Y, Zhou S, Ma QY, Yang GP, Todd JD, Zhang XH. DMSP-Producing Bacteria Are More Abundant in the Surface Microlayer than Subsurface Seawater of the East China Sea. MICROBIAL ECOLOGY 2020; 80:350-365. [PMID: 32335713 DOI: 10.1007/s00248-020-01507-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
Microbial production and catabolism of dimethylsulfoniopropionate (DMSP), generating the climatically active gases dimethyl sulfide (DMS) and methanethiol (MeSH), have key roles in global carbon and sulfur cycling, chemotaxis, and atmospheric chemistry. Microorganisms in the sea surface microlayer (SML), the interface between seawater and atmosphere, likely play an important role in the generation of DMS and MeSH and their exchange to the atmosphere, but little is known about these SML microorganisms. Here, we investigated the differences between bacterial community structure and the distribution and transcription profiles of the key bacterial DMSP synthesis (dsyB and mmtN) and catabolic (dmdA and dddP) genes in East China Sea SML and subsurface seawater (SSW) samples. Per equivalent volume, bacteria were far more abundant (~ 7.5-fold) in SML than SSW, as were those genera predicted to produce DMSP. Indeed, dsyB (~ 7-fold) and mmtN (~ 4-fold), robust reporters for bacterial DMSP production, were also far more abundant in SML than SSW. In addition, the SML had higher dsyB transcripts (~ 3-fold) than SSW samples, which may contribute to the significantly higher DMSP level observed in SML compared with SSW. Furthermore, the abundance of bacteria with dmdA and their transcription were higher in SML than SSW samples. Bacteria with dddP and transcripts were also prominent, but less than dmdA and presented at similar levels in both layers. These data indicate that the SML might be an important hotspot for bacterial DMSP production as well as generating the climatically active gases DMS and MeSH, a portion of which are likely transferred to the atmosphere.
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Affiliation(s)
- Hao Sun
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yunhui Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Siyin Tan
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yanfen Zheng
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shun Zhou
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Qian-Yao Ma
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266100, China
| | - Gui-Peng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266100, China
- Institute of Marine Chemistry, Ocean University of China, Qingdao, 266100, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China.
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Ziesche L, Wolter L, Wang H, Brinkhoff T, Pohlner M, Engelen B, Wagner-Döbler I, Schulz S. An Unprecedented Medium-Chain Diunsaturated N-acylhomoserine Lactone from Marine Roseobacter Group Bacteria. Mar Drugs 2018; 17:md17010020. [PMID: 30602652 PMCID: PMC6356624 DOI: 10.3390/md17010020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 01/29/2023] Open
Abstract
N-acylhomoserine lactones (AHLs), bacterial signaling compounds involved in quorum-sensing, are a structurally diverse group of compounds. We describe here the identification, synthesis, occurrence and biological activity of a new AHL, N-((2E,5Z)-2,5-dodecadienoyl)homoserine lactone (11) and its isomer N-((3E,5Z)-3,5-dodecadienoyl)homoserine lactone (13), occurring in several Roseobacter group bacteria (Rhodobacteraceae). The analysis of 26 strains revealed the presence of 11 and 13 in six of them originating from the surface of the macroalgae Fucus spiralis or sediments from the North Sea. In addition, 18 other AHLs were detected in 12 strains. Compound identification was performed by GC/MS. Mass spectral analysis revealed a diunsaturated C12 homoserine lactone as structural element of the new AHL. Synthesis of three likely candidate compounds, 11, 13 and N-((2E,4E)-2,4-dodecadienoyl)homoserine lactone (5), revealed the former to be the natural AHLs. Bioactivity test with quorum-sensing reporter strains showed high activity of all three compounds. Therefore, the configuration and stereochemistry of the double bonds in the acyl chain seemed to be unimportant for the activity, although the chains have largely different shapes, solely the chain length determining activity. In combination with previous results with other Roseobacter group bacteria, we could show that there is wide variance between AHL composition within the strains. Furthermore, no association of certain AHLs with different habitats like macroalgal surfaces or sediment could be detected.
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Affiliation(s)
- Lisa Ziesche
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
| | - Laura Wolter
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany.
| | - Hui Wang
- Helmholtz Centre for Infection Research, Department of Medical Microbiology, Group Microbial Communication, Inhoffenstr. 7, 38124 Braunschweig, Germany.
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany.
| | - Marion Pohlner
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany.
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany.
| | - Irene Wagner-Döbler
- Helmholtz Centre for Infection Research, Department of Medical Microbiology, Group Microbial Communication, Inhoffenstr. 7, 38124 Braunschweig, Germany.
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
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Pujalte MJ, Lucena T, Rodrigo-Torres L, Arahal DR. Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov. Front Microbiol 2018; 8:2645. [PMID: 29375512 PMCID: PMC5770400 DOI: 10.3389/fmicb.2017.02645] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/19/2017] [Indexed: 11/13/2022] Open
Abstract
A taxogenomic study was conducted to describe two new Thalassobius species and to analyze the internal consistency of the genus Thalassobius along with Shimia and Thalassococcus. Strains CECT 5113T, CECT 5114, CECT 5118T, and CECT 5120 were isolated from coastal Mediterranean seawater, Spain. Cells were Gram-negative, non- motile coccobacilli, aerobic chemoorganotrophs, with an optimum temperature of 26°C and salinity of 3.5-5%. Major cellular fatty acids of strains CECT 5113T and CECT 5114 were C18 : 1 ω7c/ω6c and C10 : 0 3OH, G+C content was 54.4-54.5 mol% and were able to utilize propionate, L-threonine, L- arginine, and L-aspartate as carbon sources. They exhibited 98.3% 16S rRNA gene sequence similarity, 75.0-75.1 ANIb and 19.5-20.9 digital DDH to type strain of their closest species, Thalassobius maritimus. Based on these data, strains CECT 5113T and CECT 5114 are recognized as a new species, for which the name Thalassobius activus is proposed, with strain CECT 5113T (=LMG 29900T) as type strain. Strains CECT 5118T and CECT 5120 were found to constitute another new species, with major cellular fatty acids C18 : 1 ω7c/ω6c and C18 : 1 ω7c 11-methyl and a G+C content of 59.8 mol%; they were not able to utilize propionate, L-threonine, L- arginine or L-aspartate. Their closest species was Thalassobius mediterraneus, with values of 99.6% 16S rRNA gene sequence similarity, 79.1% ANIb and 23.2% digital DDH compared to the type strain, CECT 5383T. The name Thalassobius autumnalis is proposed for this second new species, with strain CECT 5118T (=LMG 29904T) as type strain. To better determine the phylogenetic relationship of the two new species, we submitted 12 genomes representing species of Thalassobius, Shimia, and Thalassoccocus, to a phylogenomic analysis based on 54 single protein-encoding genes (BCG54). The resulting phylogenomic tree did not agree with the current genera classification, as Thalassobius was divided in three clades, Thalassobius sensu stricto (T. mediterraneus, T. autumnalis sp. nov., and T. gelatinovorus), Thalassobius aestuarii plus the three Shimia spp (S. marina, S. haliotis, and Shimia sp. SK013) and finally, Thalasobius maritimus plus T. activus sp. nov. Thalassococcus halodurans remained apart from the two genera. Phenotypic inferences from explored genomes are presented.
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Affiliation(s)
- María J Pujalte
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
| | - Teresa Lucena
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain
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