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Zhang T, Han Y, Peng Y, Deng Z, Shi W, Xu X, Wu Y, Dong X. The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms. mSystems 2025:e0157124. [PMID: 40396743 DOI: 10.1128/msystems.01571-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Accepted: 04/23/2025] [Indexed: 05/22/2025] Open
Abstract
Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research. IMPORTANCE In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.
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Affiliation(s)
- Tianxueyu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, Shanghai, China
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, Zhejiang, China
- Ocean Research Center of Zhoushan, Zhejiang University, Zhoushan, Zhejiang, China
| | - Wenqing Shi
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University College of Ocean and Earth Science, Xiamen, Fujian, China
- RU Marine Symbioses, RD3 Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Xuewei Xu
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Yuehong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, Shanghai, China
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
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Chamley A, Baley C, Matabos M, Vannier P, Sarradin PM, Freyermouth F, Davies P. Polymer material biodegradation in the deep sea. A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 957:177637. [PMID: 39579889 DOI: 10.1016/j.scitotenv.2024.177637] [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: 07/31/2024] [Revised: 11/15/2024] [Accepted: 11/17/2024] [Indexed: 11/25/2024]
Abstract
The phenomenon of marine plastic pollution is now well-established, with documented impacts on marine biodiversity and biogeochemical cycles. In order to mitigate this environmental impact, a significant amount of research has been conducted in recent years with the objective of developing biodegradable alternatives to conventional polymers and their composites in marine environments. The findings of this research significantly enhanced our understanding of biodegradation mechanisms and identified promising candidates. However, the majority of these studies have been conducted in coastal marine environments, which represent a minor component of the marine ecosystem. Recent models on the transport of plastic debris in the oceans indicate that deep-sea environments are likely to be the ultimate sink for a significant proportion of plastics entering the oceans. The aim of this review is to provide an overview of the processes of biodegradation of polymers in these deep-sea environments. The diversity and specific characteristics of these environments with respect to degradation mechanisms are discussed. While the majority of deep-sea conditions are not conducive to biodegradation, studies on organic falls (wood and whale carcasses) and a few investigations into materials previously shown to be biodegradable in coastal marine environments demonstrate mechanisms that are similar to those observed in shallow waters. Nevertheless, further research is necessary to reach definitive conclusions. It is essential to extend these studies to a broader range of deep-sea environments. Additionally, new methodologies that integrate microbiology and polymer science are required to accurately assess the process of assimilation of these materials in these environments.
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Affiliation(s)
- Alexandre Chamley
- Université Bretagne-Sud, IRDL, CNRS UMR 6027, BP 92116, Lorient Cedex 56321, France; Thales DMS, Brest, France; Ifremer RDT, Research and Technology Development Unit, Plouzané 29280, France.
| | - Christophe Baley
- Université Bretagne-Sud, IRDL, CNRS UMR 6027, BP 92116, Lorient Cedex 56321, France
| | - Marjolaine Matabos
- University Brest, CNRS, Ifremer, UMR 6197 Biologie Et Ecologie Des Ecosystèmes Marins Profonds, Plouzané 29280, France
| | - Pauline Vannier
- Laboratoire MAPIEM, E.A.4323, Université de Toulon, CS 60584, 83041 Cedex 9 Toulon, France
| | - Pierre Marie Sarradin
- University Brest, CNRS, Ifremer, UMR 6197 Biologie Et Ecologie Des Ecosystèmes Marins Profonds, Plouzané 29280, France
| | | | - Peter Davies
- Ifremer RDT, Research and Technology Development Unit, Plouzané 29280, France
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Rethinavelu G, Dharshini RS, Manickam R, Balakrishnan A, Ramya M, Maddela NR, Prasad R. Unveiling the microbial diversity of biofilms on titanium surfaces in full-scale water-cooling plants using metagenomics approach. Folia Microbiol (Praha) 2024; 69:1331-1341. [PMID: 38771555 DOI: 10.1007/s12223-024-01170-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024]
Abstract
Microbial colonization on the titanium condenser material (TCM) used in the cooling system leads to biofouling and corrosion and influences the water supply. The primary investigation of the titanium condenser was infrequently studied on characterizing biofilm-forming bacterial communities. Different treatment methods like electropotential charge, ultrasonication, and copper coating of titanium condenser material may influence the microbial population over the surface of the titanium condensers. The present study aimed to catalog the primary colonizers and the effect of different treatment methods on the microbial community. CFU (1.7 × 109 CFU/mL) and ATP count (< 5000 × 10-7 relative luminescence units) showed a minimal microbial population in copper-coated surface biofilm as compared with the other treatments. Live and dead cell result also showed consistency with colony count. The biofilm sample on the copper-coated surface showed an increased dead cell count and decreased live cells. In the metagenomic approach, the microbiome coverage was 10.06 Mb in samples derived from copper-coated TCM than in other treated samples (electropotential charge-17.94 Mb; ultrasonication-20.01 Mb), including control (10.18 Mb). Firmicutes preponderate the communities in the biofilm samples, and Proteobacteria stand next in the population in all the treated condenser materials. At the genus level, Lactobacillaceae and Azospirillaceae dominated the biofilm community. The metagenome data suggested that the attached community is different from those biofilm samples based on the environment that influences the bacterial community. The outcome of the present study depicts that copper coating was effective against biofouling and corrosion resistance of titanium condenser material for designing long-term durability.
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Affiliation(s)
- Gayathri Rethinavelu
- Molecular Genetics Laboratory, Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu, Tamil Nadu, India
| | - Rajathirajan Siva Dharshini
- Molecular Genetics Laboratory, Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu, Tamil Nadu, India
- Microbiology Team, CavinKare Research Center, 12 Poonamallee Road, Ekkattuthangal, Chennai, 600032, India
| | - Ranjani Manickam
- SRM-DBT Platform for Advanced Life Science Technologies, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu, Tamil Nadu, India
| | - Anandkumar Balakrishnan
- Corrosion Science and Technology Division, Metallurgy and Materials Group, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu, India
| | - Mohandass Ramya
- Molecular Genetics Laboratory, Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu, Tamil Nadu, India.
| | - Naga Raju Maddela
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Salud, Universidad Técnica de Manabí, Portoviejo, Manabí, Ecuador
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, 845401, Bihar, India.
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Angoshtari R, Scribner KT, Marsh TL. The impact of primary colonizers on the community composition of river biofilm. PLoS One 2023; 18:e0288040. [PMID: 37956125 PMCID: PMC10642824 DOI: 10.1371/journal.pone.0288040] [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: 11/11/2022] [Accepted: 06/19/2023] [Indexed: 11/15/2023] Open
Abstract
As a strategy for minimizing microbial infections in fish hatcheries, we have investigated how putatively probiotic bacterial populations influence biofilm formation. All surfaces that are exposed to the aquatic milieu develop a microbial community through the selective assembly of microbial populations into a surface-adhering biofilm. In the investigations reported herein, we describe laboratory experiments designed to determine how initial colonization of a surface by nonpathogenic isolates from sturgeon eggs influence the subsequent assembly of populations from a pelagic river community, into the existing biofilm. All eight of the tested strains altered the assembly of river biofilm in a strain-specific manner. Previously formed isolate biofilm was challenged with natural river populations and after 24 hours, two strains and two-isolate combinations proved highly resistant to invasion, comprising at least 80% of the biofilm community, four isolates were intermediate in resistance, accounting for at least 45% of the biofilm community and two isolates were reduced to 4% of the biofilm community. Founding biofilms of Serratia sp, and combinations of Brevundimonas sp.-Hydrogenophaga sp. and Brevundimonas sp.-Acidovorax sp. specifically blocked populations of Aeromonas and Flavobacterium, potential fish pathogens, from colonizing the biofilm. In addition, all isolate biofilms were effective at blocking invading populations of Arcobacter. Several strains, notably Deinococcus sp., recruited specific low-abundance river populations into the top 25 most abundant populations within biofilm. The experiments suggest that relatively simple measures can be used to control the assembly of biofilm on the eggs surface and perhaps offer protection from pathogens. In addition, the methodology provides a relatively rapid way to detect potentially strong ecological interactions between bacterial populations in the formation of biofilms.
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Affiliation(s)
- Roshan Angoshtari
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
| | - Kim T. Scribner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America
| | - Terence L. Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
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Qin P, Cui H, Li P, Wang S, Fan S, Lu J, Sun M, Zhang H, Wang S, Su X, Fu H, Hu X, Lin J, Zhang Y, Ding W, Zhang W. Early stage of biofilm assembly on microplastics is structured by substrate size and bacterial motility. IMETA 2023; 2:e121. [PMID: 38867926 PMCID: PMC10989967 DOI: 10.1002/imt2.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 06/14/2024]
Abstract
The taxonomic structure of biofilms on 0.3-mm microplastics differed significantly from that on 3-mm microplastics or glass particles. Compared with the 3-mm microplastics, biofilms on 0.3-mm microplastics were enriched for genes involved in flagellar-based motility and chemotaxis, pointing to a more 'mobile' community. The association between motility and bacterial colonization of 0.3-mm microplastics was observed through laboratory experiments using isolated strains.
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Affiliation(s)
- Peng Qin
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Han Cui
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Panxin Li
- College of Life SciencesYan'an UniversityYan'anChina
| | - Shuaitao Wang
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Shen Fan
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Jie Lu
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Meng Sun
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Heng Zhang
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Shougang Wang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
| | - Xiaoyan Su
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of ChinaQingdaoChina
| | - Hui‐Hui Fu
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of ChinaQingdaoChina
| | - Xiaoli Hu
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
| | - Jinshui Lin
- College of Life SciencesYan'an UniversityYan'anChina
| | - Yu‐Zhong Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of ChinaQingdaoChina
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Wei Ding
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
| | - Weipeng Zhang
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:6491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
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7
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Eskhan A, Johnson D. Microscale characterization of abiotic surfaces and prediction of their biofouling/anti-biofouling potential using the AFM colloidal probe technique. Adv Colloid Interface Sci 2022; 310:102796. [DOI: 10.1016/j.cis.2022.102796] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
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Abstract
Marine biofilms are ubiquitous in the marine environment. These complex microbial communities rapidly respond to environmental changes and encompass hugely diverse microbial structures, functions and metabolisms. Nevertheless, knowledge is limited on the microbial community structures and functions of natural marine biofilms and their influence on global geochemical cycles. Microbial cues, including secondary metabolites and microbial structures, regulate interactions between microorganisms, with their environment and with other benthic organisms, which affects their community succession and metamorphosis. Furthermore, marine biofilms are key mediators of marine biofouling, which greatly affect marine industries. In this Review, we discuss marine biofilm dynamics, including their diversity, abundance and functions. We also highlight knowledge gaps, areas for future research and potential biotechnological applications of marine biofilms.
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Wang X, Jiang X, Yu L. Preparation and evaluation of polyphenol derivatives as potent antifouling agents: addition of a side chain affects the biological activity of polyphenols. BIOFOULING 2022; 38:29-41. [PMID: 34875955 DOI: 10.1080/08927014.2021.2010720] [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: 08/19/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
In this study, eight polyphenol derivatives were prepared to serve as green antifoulants. Polyphenol derivatives, which can hinder the growth of bacteria and algae and decrease the adhesion of some marine organisms, showed good AF activity; in particular, the activities of these derivatives were much higher than those of the corresponding polyphenols. The antibacterial rates of the products (20 μg ml-1) exceeded 88%. Moreover, the anti-algal rates of compounds a3, b1, b2, b3 and b4 (15 μg ml-1) were over 57% at 240 h, but these compounds showed low toxicity, and the 120 h EC50 values were > 6.60 μg ml-1. In addition, there were fewer marine microorganisms on the test panel than on the control. The above results show that some polyphenol derivatives possess relatively high antibacterial, anti-algal, and AF activity; more notably, the addition of chlorine atoms and amide groups can further increase the activity of these derivatives.
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Affiliation(s)
- Xuan Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xiaohui Jiang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
- Open Studio for Marine Corrosion and Protection, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Liangmin Yu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
- Open Studio for Marine Corrosion and Protection, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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Sushmitha TJ, Rajeev M, Sriyutha Murthy P, Ganesh S, Toleti SR, Karutha Pandian S. Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India. PLoS One 2021; 16:e0257961. [PMID: 34570809 PMCID: PMC8476003 DOI: 10.1371/journal.pone.0257961] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023] Open
Abstract
Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz. Proteobacteria decreased over biofilm succession days, while Bacteroidetes increased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz. Alteromonadales and Vibrionales were observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. Phylum Proteobacteria preponderated the biofilm-forming community, while the Bacteroidetes, Cyanobacteria, and Actinobacteria dominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.
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Affiliation(s)
- T. J. Sushmitha
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Meora Rajeev
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - P. Sriyutha Murthy
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - S. Ganesh
- Department of Chemistry, Scott Christian College, Nagercoil, Tamil Nadu, India
| | - Subba Rao Toleti
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
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11
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Rummel CD, Lechtenfeld OJ, Kallies R, Benke A, Herzsprung P, Rynek R, Wagner S, Potthoff A, Jahnke A, Schmitt-Jansen M. Conditioning Film and Early Biofilm Succession on Plastic Surfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11006-11018. [PMID: 34339175 DOI: 10.1021/acs.est.0c07875] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In the context of environmental plastic pollution, it is still under debate if and how the "plastisphere", a plastic-specific microbial community, emerges. In this study, we tested the hypothesis that the first conditioning film of dissolved organic matter (DOM) sorbs selectively to polymer substrates and that microbial attachment is governed in a substrate-dependent manner. We investigated the adsorption of stream water-derived DOM to polyethylene terephthalate (PET), polystyrene (PS), and glass (as control) including UV-weathered surfaces by Fourier-transform ion cyclotron mass spectrometry. Generally, the saturated, high-molecular mass and thus more hydrophobic fraction of the original stream water DOM preferentially adsorbed to the substrates. The UV-weathered polymers adsorbed more polar, hydrophilic OM as compared to the dark controls. The amplicon sequencing data of the initial microbial colonization process revealed a tendency of substrate specificity for biofilm attachment after 24 h and a clear convergence of the communities after 72 h of incubation. Conclusively, the adsorbed OM layer developed depending on the materials' surface properties and increased the water contact angles, indicating higher surface hydrophobicity as compared to pristine surfaces. This study improves our understanding of molecular and biological interactions at the polymer/water interface that are relevant to understand the ecological impact of plastic pollution on a community level.
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Affiliation(s)
- Christoph D Rummel
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - René Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Annegret Benke
- Department of Powder and Suspension Characterization, Fraunhofer Institute for Ceramic Technologies and Systems IKTS, Winterbergstr. 28, 01277 Dresden, Germany
| | - Peter Herzsprung
- Department of Lake Research, Helmholtz Centre for Environmental Research-UFZ, Brückstr. 3a, 39114 Magdeburg, Germany
| | - Robby Rynek
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Stephan Wagner
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Institute for Water and Energy Management (iwe), University of Applied Science, Alfons-Goppel-Platz 1, 95028 Hof, Germany
| | - Annegret Potthoff
- Department of Powder and Suspension Characterization, Fraunhofer Institute for Ceramic Technologies and Systems IKTS, Winterbergstr. 28, 01277 Dresden, Germany
| | - Annika Jahnke
- Department Ecological Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52047 Aachen, Germany
| | - Mechthild Schmitt-Jansen
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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12
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Wright RJ, Bosch R, Langille MGI, Gibson MI, Christie-Oleza JA. A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere. MICROBIOME 2021; 9:141. [PMID: 34154652 PMCID: PMC8215760 DOI: 10.1186/s40168-021-01054-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere. RESULTS We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. CONCLUSIONS Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Rafael Bosch
- University of the Balearic Islands, Palma, Spain
- IMEDEA (CSIC-UIB), Esporles, Spain
| | - Morgan G. I. Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Medical School, University of Warwick, Coventry, UK
| | - Joseph A. Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry, UK
- University of the Balearic Islands, Palma, Spain
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13
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Catão C P E, Pollet T, Garnier C, Barry-Martinet R, Rehel K, Linossier I, Tunin-Ley A, Turquet J, Briand JF. Temperate and tropical coastal waters share relatively similar microbial biofilm communities while free-living or particle-attached communities are distinct. Mol Ecol 2021; 30:2891-2904. [PMID: 33887078 DOI: 10.1111/mec.15929] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/25/2022]
Abstract
Free-living (FL) marine microbial communities differ from those attached to particles (PA). Likewise, biofilms (B) colonizing artificial surfaces, including plastics or ship hulls, hardly resemble their planktonic surroundings. However, few studies have examined the effect of the environment on these lifestyles and on the source of organisms colonizing marine surfaces. Using 16S rRNA gene metabarcoding, we identified specificities of marine prokaryotic community lifestyles (FL, PA or B) sampled in three coastal polluted locations with dissimilar environmental conditions: the North-Western Mediterranean Sea and the Atlantic and Indian Oceans. Biofilms developed over polyvinyl chloride (PVC) were found to be significantly different from FL or PA collected during the immersions. Alpha-diversity increased from FL to PA and to B, illustrating the integrative aspect of the latter, with little proportion of operational taxonomic units shared with the first two. Beta-diversity clustered first the lifestyles and then the sites. FL and PA were more affected by water quality, especially by trace metal contamination, whereas B were as sensitive to trace metals as to nutrients. Although biofilms should be supplied by the planktonic (ultra) rare biosphere, source tracking could only detect small contributions of FL or PA taxa to B communities.
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Affiliation(s)
- Elisa Catão C P
- Laboratoire MAPIEM, EA 4323, Université de Toulon, Toulon, France
| | - Thomas Pollet
- Laboratoire MAPIEM, EA 4323, Université de Toulon, Toulon, France.,UMR ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Cédric Garnier
- Mediterranean Institute of Oceanography, CNRS/INSU, IRD, MIO UM 110, Univ Toulon, Aix Marseille Univ, La Garde, France
| | | | - Karine Rehel
- Institut Européen de la Mer, Université de Bretagne-Sud, EA 3884, LBCM, Lorient, France
| | - Isabelle Linossier
- Institut Européen de la Mer, Université de Bretagne-Sud, EA 3884, LBCM, Lorient, France
| | | | - Jean Turquet
- CITEB/c/o CYROI, Sainte Clotilde, La Réunion, France
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14
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Coclet C, Garnier C, D’Onofrio S, Durrieu G, Pasero E, Le Poupon C, Omanović D, Mullot JU, Misson B, Briand JF. Trace Metal Contamination Impacts Predicted Functions More Than Structure of Marine Prokaryotic Biofilm Communities in an Anthropized Coastal Area. Front Microbiol 2021; 12:589948. [PMID: 33679628 PMCID: PMC7933014 DOI: 10.3389/fmicb.2021.589948] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/29/2021] [Indexed: 12/25/2022] Open
Abstract
Trace metal (TM) contamination in marine coastal areas is a worldwide threat for aquatic communities. However, little is known about the influence of a multi-chemical contamination on both marine biofilm communities' structure and functioning. To determine how TM contamination potentially impacted microbial biofilms' structure and their functions, polycarbonate (PC) plates were immerged in both surface and bottom of the seawater column, at five sites, along strong TM contamination gradients, in Toulon Bay. The PC plates were incubated during 4 weeks to enable colonization by biofilm-forming microorganisms on artificial surfaces. Biofilms from the PC plates, as well as surrounding seawaters, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe prokaryotic community diversity, structure and functions, and to determine the relationships between bacterioplankton and biofilm communities. Our results showed that prokaryotic biofilm structure was not significantly affected by the measured environmental variables, while the functional profiles of biofilms were significantly impacted by Cu, Mn, Zn, and salinity. Biofilms from the contaminated sites were dominated by tolerant taxa to contaminants and specialized hydrocarbon-degrading microorganisms. Functions related to major xenobiotics biodegradation and metabolism, such as methane metabolism, degradation of aromatic compounds, and benzoate degradation, as well as functions involved in quorum sensing signaling, extracellular polymeric substances (EPS) matrix, and biofilm formation were significantly over-represented in the contaminated site relative to the uncontaminated one. Taken together, our results suggest that biofilms may be able to survive to strong multi-chemical contamination because of the presence of tolerant taxa in biofilms, as well as the functional responses of biofilm communities. Moreover, biofilm communities exhibited significant variations of structure and functional profiles along the seawater column, potentially explained by the contribution of taxa from surrounding sediments. Finally, we found that both structure and functions were significantly distinct between the biofilm and bacterioplankton, highlighting major differences between the both lifestyles, and the divergence of their responses facing to a multi-chemical contamination.
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Affiliation(s)
- Clément Coclet
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Cédric Garnier
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Sébastien D’Onofrio
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Gaël Durrieu
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Emilie Pasero
- Microbia Environnement Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Christophe Le Poupon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Dario Omanović
- Division for Marine and Environmental Research, Ruðer Bošković Institute, Zagreb, Croatia
| | | | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
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15
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Zhu C, Bass D, Wang Y, Shen Z, Song W, Yi Z. Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters. Front Microbiol 2020; 11:555795. [PMID: 33072015 PMCID: PMC7541896 DOI: 10.3389/fmicb.2020.555795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.
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Affiliation(s)
- Changyu Zhu
- Institute of Evolution and Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao, China.,Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Yutao Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China.,Dongli Planting and Farming Industrial Co., Ltd., Lianzhou, China
| | - Zhuo Shen
- Institute of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Weibo Song
- Institute of Evolution and Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao, China.,Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenzhen Yi
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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16
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Sun X, Chen B, Xia B, Li Q, Zhu L, Zhao X, Gao Y, Qu K. Impact of mariculture-derived microplastics on bacterial biofilm formation and their potential threat to mariculture: A case in situ study on the Sungo Bay, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114336. [PMID: 32443196 DOI: 10.1016/j.envpol.2020.114336] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Microplastics (MPs) pollution in the marine environment has attracted considerable global attention. However, the colonization of microorganisms on mariculture-derived MPs and their effects on mariculture remain poorly understood. In this study, the MPs (fishing nets, foams and floats) and a natural substrate, within size ranges (1-4 mm), were then incubated for 21 days in Sungo Bay (China), and the composition and diversity of bacterial communities attached on all substrates were investigated. Results showed that bacterial communities on MPs mainly originated from their surrounding seawater and sediment, with an average contribution on total MPs adherent population of 47.91% and 37.33%, respectively. Principle coordinate analysis showed that community similarity between MPs and surrounding seawater decreased with exposure time. In addition, lower average bacterial community diversity and higher relative abundances of bacteria from the genera Vibrio, Pseudoalteromonas and Alteromonas on MPs than those in their surrounding seawater and sediments indicated that MPs might enrich potential pathogens and bacteria related with carbohydrate metabolism. They are responsible for the significant differences in KEGG Orthology pathways (infectious disease and carbohydrate metabolism) between MPs and seawater. The KO pathway (Infectious Diseases) associated with MPs was also significantly higher than those with feathers in the nearshore area. MPs might be vectors for enrichment of potentially pathogenic Vibrio, and enhance the ecological risk of MPs to mariculture industry.
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Affiliation(s)
- Xuemei Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Bijuan Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Bin Xia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Qiufen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Lin Zhu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xinguo Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Yaping Gao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Keming Qu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
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17
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Song J, Jongmans-Hochschulz E, Mauder N, Imirzalioglu C, Wichels A, Gerdts G. The Travelling Particles: Investigating microplastics as possible transport vectors for multidrug resistant E. coli in the Weser estuary (Germany). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137603. [PMID: 32143053 DOI: 10.1016/j.scitotenv.2020.137603] [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: 01/14/2020] [Revised: 02/07/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
The prevalence of multidrug-resistant Gram-negative bacteria in aquatic environments has been a long withstanding health concern, namely extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Given increasing reports on microplastic (MP) pollution in these environments, it has become crucial to better understand the role of MP particles as transport vectors for such multidrug-resistant bacteria. In this study, an incubation experiment was designed where particles of both synthetic and natural material (HDPE, tyre wear, and wood) were sequentially incubated at multiple sites along a salinity gradient from the Lower Weser estuary (Germany) to the offshore island Helgoland (German Bight, North Sea). Following each incubation period, particle biofilms and water samples were assessed for ESBL-producing E. coli, first by the enrichment and detection of E. coli using Fluorocult® LMX Broth followed by cultivation on CHROMAgar™ ESBL media to select for ESBL-producers. Results showed that general E. coli populations were present on the surfaces of wood particles across all sites but none were found to produce ESBLs. Additionally, neither HDPE nor tyre wear particles were found to harbour any E. coli. Conversely, ESBL-producing E. coli were present in surrounding waters from all sites, 64% of which conferred resistances against up to 3 other antibiotic groups, additional to the beta-lactam resistances intrinsic to ESBL-producers. This study provides a first look into the potential of MP to harbour and transport multidrug-resistant E. coli across different environments and the approach serves as an important precursor to further studies on other potentially harmful MP-colonizing species.
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Affiliation(s)
- Jessica Song
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany; Faculty of Engineering, Computing, and Science, Swinburne University of Technology, Sarawak Campus, 93350 Kuching, Sarawak, Malaysia.
| | - Elanor Jongmans-Hochschulz
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany
| | - Norman Mauder
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Antje Wichels
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany
| | - Gunnar Gerdts
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, 27498 Helgoland, Germany
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18
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Li L, Ma ZS. Species Sorting and Neutral Theory Analyses Reveal Archaeal and Bacterial Communities Are Assembled Differently in Hot Springs. Front Bioeng Biotechnol 2020; 8:464. [PMID: 32548097 PMCID: PMC7271673 DOI: 10.3389/fbioe.2020.00464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/21/2020] [Indexed: 12/03/2022] Open
Abstract
Although the recognition of archaea as one of the three kingdoms in the tree of life has been nearly a half-century long, the comparative investigations on their ecological adaptations with bacteria have been limited. The mechanisms of their community assembly and diversity maintenance in hot springs have not been addressed. The mechanistic study is critical not only for understanding the hot-spring microbiome structure and dynamics, but also for shedding light on their evolutionary adaptations. We applied the neutral theory model and species sorting paradigm of metacommunity theory to investigate how hot-spring microbial communities were assembled, how their diversities were maintained, and how the temperature and pH influence these mechanisms. Through rigorous statistical tests based on the neutral theory and species sorting paradigm, we found (i) According to the neutral theory, archaeal and bacterial communities are assembled differently, with stochastic neutral force playing a more significant role in archaeal communities than in bacterial communities (neutrality-rate = 52.9 vs. 15.8%, p-value < 0.05). (ii) Temperature and pH account for rather limited (<10%) variations in hot-spring microbiomes based on the species sorting paradigm. The pH has more significant influences than temperature on archaeal communities, and both pH and temperature have similarly low influences on bacterial community structure. (iii) We postulate that the differences between archaea and bacteria are likely due to the longer evolutionary history and better adaptation of archaea to host spring environments.
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Affiliation(s)
- Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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19
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Microbial Colonization in Marine Environments: Overview of Current Knowledge and Emerging Research Topics. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8020078] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microbial biofilms are biological structures composed of surface-attached microbial communities embedded in an extracellular polymeric matrix. In aquatic environments, the microbial colonization of submerged surfaces is a complex process involving several factors, related to both environmental conditions and to the physical-chemical nature of the substrates. Several studies have addressed this issue; however, more research is still needed on microbial biofilms in marine ecosystems. After a brief report on environmental drivers of biofilm formation, this study reviews current knowledge of microbial community attached to artificial substrates, as obtained by experiments performed on several material types deployed in temperate and extreme polar marine ecosystems. Depending on the substrate, different microbial communities were found, sometimes highlighting the occurrence of species-specificity. Future research challenges and concluding remarks are also considered. Emphasis is given to future perspectives in biofilm studies and their potential applications, related to biofouling prevention (such as cell-to-cell communication by quorum sensing or improved knowledge of drivers/signals affecting biological settlement) as well as to the potential use of microbial biofilms as sentinels of environmental changes and new candidates for bioremediation purposes.
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20
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Rajeev M, Sushmitha TJ, Toleti SR, Pandian SK. Culture dependent and independent analysis and appraisal of early stage biofilm-forming bacterial community composition in the Southern coastal seawater of India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:308-320. [PMID: 30798240 DOI: 10.1016/j.scitotenv.2019.02.171] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/21/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
Microbial aggregation on artificial surfaces is a fundamental phenomenon in aquatic systems that lead to biofouling, corrosion and influence the buoyancy of plastic materials. Despite the maritime activities and with nearshore large industrial sector, Laccadive Sea in the Indian Ocean has rarely been investigated for characterizing early biofilm-forming bacterial community. The present investigation was aimed to catalogue the primary colonizers on artificial surfaces and their comparison with planktonic community in southern coastal seawater of India. Surface seawater samples and biofilm assembled on three artificial surfaces over a period of 72 h of immersion in the intake area of a nuclear power plant at Kudankulam, India were collected. The structure of surface assemblages and plankton were unveiled by employing culture dependent, DGGE and NGS methods. In static condition, a collection of aerobic heterotrophic bacteria was screened in vitro for their ability to form potent biofilm. Proteobacteria preponderated the communities both in seawater and natural biofilm and Gammaproteobacteria accounted for >85% in the latter. Vibrionaceae, Alteromonadaceae and Pseudoalteromonadaceae dominated the biofilm community and constituted for 41, 25 and 8%, respectively. In contrast to other studies that showed Rhodobacteraceae family of Alphaproteobacteria as predominant component, we found Vibrionaceae of Gammaproteobacteria as dominant group in early stage of biofilm formation. Both DGGE and NGS data indicated that the attached community is noticeably distinct from those suspended in water column and form the basis for the proposed hypothesis of species sorting theory, that is, the local environmental conditions influence bacterial community assembly. Collectively, the data are testament for species sorting process that occur during initial assembly of bacterial community in marine environment and shed light on the structure of marine bacterial biofilm development. The outcome of the present study is of immense importance for designing long-term, efficient and appropriate strategies to control the biofouling phenomenon.
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Affiliation(s)
- Meora Rajeev
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India
| | - T J Sushmitha
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India
| | - Subba Rao Toleti
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam 603 102, Tamil Nadu, India
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21
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Ding W, Zhang W, Alikunhi NM, Batang Z, Pei B, Wang R, Chen L, Al-Suwailem A, Qian PY. Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms. MICROBIAL ECOLOGY 2019; 77:406-416. [PMID: 30612183 DOI: 10.1007/s00248-018-01313-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/20/2018] [Indexed: 05/10/2023]
Abstract
Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.
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Affiliation(s)
- Wei Ding
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Weipeng Zhang
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Zenon Batang
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Bite Pei
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruojun Wang
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Lianguo Chen
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China.
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22
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Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nat Commun 2019; 10:517. [PMID: 30705275 PMCID: PMC6355793 DOI: 10.1038/s41467-019-08463-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/21/2018] [Indexed: 01/28/2023] Open
Abstract
Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and the Tara Oceans metagenomes to study the diversity of biofilm-forming marine microorganisms. We identify more than 7,300 biofilm-forming ‘species’ that are undetected in seawater analyses, increasing the known microbial diversity in the oceans by more than 20%, and provide evidence for differentiation across oceanic niches. Generation of a gene distribution profile reveals a functional core across the biofilms, comprised of genes from a variety of microbial phyla that may play roles in stress responses and microbe-microbe interactions. Analysis of 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and CRISPR-Cas systems. Our data highlight the previously underestimated ocean microbial diversity, and allow mining novel microbial lineages and gene resources. Previous surveys of global ocean microbial diversity have focused on planktonic microbes. Here, Zhang et al. use metagenomics to study biofilm-forming marine microbes, increasing the known microbial diversity in the oceans by more than 20% and revealing new biosynthetic gene clusters and CRISPR-Cas systems.
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Development and Characterization of Mechanically Durable Silicone-Polythiourethane Composites Modified with Tetrapodal Shaped ZnO Particles for the Potential Application as Fouling-Release Coating in the Marine Sector. MATERIALS 2018; 11:ma11122413. [PMID: 30501063 PMCID: PMC6316896 DOI: 10.3390/ma11122413] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/25/2018] [Indexed: 11/24/2022]
Abstract
Ecological considerations strongly necessitate the development of environmentally friendly antifouling paints. A promising alternative to biocide containing antifouling paints are fouling-release coatings, which are non-toxic and designed to prevent permanent attachment of marine organisms to the surface, due to their low surface energy. However, these coatings suffer from insufficient mechanical properties, which make them unsuitable for mechanically stressed surfaces e.g., on ship hulls. To overcome those obstacles, polydimethylsiloxane (PDMS)-polythiourethane (PTU) composites modified with tetrapodal shaped micro-nano ZnO particles (t-ZnO) were produced and characterized by evaluating the surface energy, mechanical properties, and fouling-release performance. Among all variations, PTU/1 wt.% PDMS composites with 1 wt.% t-ZnO particles possess superior properties for applications as fouling-release coatings for maritime purposes.
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Ogonowski M, Motiei A, Ininbergs K, Hell E, Gerdes Z, Udekwu KI, Bacsik Z, Gorokhova E. Evidence for selective bacterial community structuring on microplastics. Environ Microbiol 2018; 20:2796-2808. [DOI: 10.1111/1462-2920.14120] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Martin Ogonowski
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
- Aquabiota Water Research AB; Stockholm SE-115 50 Sweden
| | - Asa Motiei
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
| | - Karolina Ininbergs
- Department of Molecular Biosciences; The Wenner-Gren Institute, Stockholm University; Stockholm SE-106 91 Sweden
| | - Eva Hell
- Department of Molecular Biosciences; The Wenner-Gren Institute, Stockholm University; Stockholm SE-106 91 Sweden
| | - Zandra Gerdes
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
| | - Klas I. Udekwu
- Department of Molecular Biosciences; The Wenner-Gren Institute, Stockholm University; Stockholm SE-106 91 Sweden
| | - Zoltan Bacsik
- Department of Materials and Environmental Chemistry; Stockholm University; Stockholm SE-106 91 Sweden
| | - Elena Gorokhova
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
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Ding W, Ma C, Zhang W, Chiang H, Tam C, Xu Y, Zhang G, Qian PY. Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses. BIOFOULING 2018; 34:111-122. [PMID: 29334812 DOI: 10.1080/08927014.2017.1409891] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 11/20/2017] [Indexed: 06/07/2023]
Abstract
Butenolide is an environmentally friendly antifouling natural product, but its efficiency and mechanism in preventing biofilm formation have not been examined. Furthermore, controlling the release of butenolide from paints into seawater is technically challenging. A coating was developed by mixing butenolide with a biodegradable polymer, poly (ε-caprolactone)-based polyurethane, and a one-month in situ anti-biofilm test was conducted in a subtidal area. The constant release of butenolide from the surface suggested that its release was well controlled. Direct observation and confocal microscope investigation indicated that the coating was effective against both biofilm formation and attachment of large fouling organisms. Metatranscriptomic analysis of biofilm samples implied that the coating selectively inhibited the adhesion of microbes from a variety of phyla and targeted particular functional pathways including energy metabolism, drug transport and toxin release. These integrated analyses demonstrated the potential application of this butenolide/polymer coating as an anti-biofilm material.
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Key Words
- ABC transporters, ATP-binding cassette transporters
- Anti-biofilm
- CLSM, confocal laser scanning microscopy
- COGs, Clusters of Orthologous Groups
- DBTDL, dibutyltin dilaurate
- DCOIT, 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one
- FITC, fluorescein isothiocyanate
- HPLC, high performance liquid chromatography
- PCA, principal component analysis
- RTX, repeats-in-toxin
- butenolide
- butenolide, 5-octylfuran-2(5H)-one
- metatranscriptomics
- polymer coating
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Affiliation(s)
- Wei Ding
- a Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Chunfeng Ma
- a Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
- b Faculty of Materials Science and Engineering , South China University of Technology , Guangzhou , PR China
| | - Weipeng Zhang
- a Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Hoyin Chiang
- a Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Chunkit Tam
- a Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Ying Xu
- a Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
- c College of Life Sciences and Oceanography , Shenzhen University , Shenzhen , PR China
| | - Guangzhao Zhang
- b Faculty of Materials Science and Engineering , South China University of Technology , Guangzhou , PR China
| | - Pei-Yuan Qian
- a Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
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26
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Zhang W, Ding W, Yang B, Tian R, Gu S, Luo H, Qian PY. Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool. Front Microbiol 2016; 7:1825. [PMID: 27895636 PMCID: PMC5108811 DOI: 10.3389/fmicb.2016.01825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022] Open
Abstract
The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.
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Affiliation(s)
- Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Wei Ding
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Bo Yang
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Shuo Gu
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Chinese University of Hong Kong Shatin, Hong Kong
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
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Zhang W, Lu L, Lai Q, Zhu B, Li Z, Xu Y, Shao Z, Herrup K, Moore BS, Ross AC, Qian PY. Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria. J Biol Chem 2016; 291:27228-27238. [PMID: 27875306 DOI: 10.1074/jbc.m116.756858] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
The thalassospiramide lipopeptides have great potential for therapeutic applications; however, their structural and functional diversity and biosynthesis are poorly understood. Here, by cultivating 130 Rhodospirillaceae strains sampled from oceans worldwide, we discovered 21 new thalassospiramide analogues and demonstrated their neuroprotective effects. To investigate the diversity of biosynthetic gene cluster (BGC) architectures, we sequenced the draft genomes of 28 Rhodospirillaceae strains. Our family-wide genomic analysis revealed three types of dysfunctional BGCs and four functional BGCs whose architectures correspond to four production patterns. This correlation allowed us to reassess the "diversity-oriented biosynthesis" proposed for the microbial production of thalassospiramides, which involves iteration of several key modules. Preliminary evolutionary investigation suggested that the functional BGCs could have arisen through module/domain loss, whereas the dysfunctional BGCs arose through horizontal gene transfer. Further comparative genomics indicated that thalassospiramide production is likely to be attendant on particular genes/pathways for amino acid metabolism, signaling transduction, and compound efflux. Our findings provide a systematic understanding of thalassospiramide production and new insights into the underlying mechanism.
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Affiliation(s)
- Weipeng Zhang
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Liang Lu
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Qiliang Lai
- the Third Institute of Oceanography, State Oceanic Administration, Xiamen 361000, China
| | - Beika Zhu
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Zhongrui Li
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Ying Xu
- the School of Life Science, Shenzhen University, Shenzhen, Guangdong Province 518060, China
| | - Zongze Shao
- the Third Institute of Oceanography, State Oceanic Administration, Xiamen 361000, China
| | - Karl Herrup
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Bradley S Moore
- the Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92037, and
| | - Avena C Ross
- the Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Pei-Yuan Qian
- From the Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong,
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28
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Zhang W, Sun J, Cao H, Tian R, Cai L, Ding W, Qian PY. Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment. MICROBIOME 2016; 4:49. [PMID: 27600525 PMCID: PMC5012046 DOI: 10.1186/s40168-016-0194-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored. RESULTS We provide here insight into PTMs in a hydrothermal vent microbial community through integration of metagenomics and metaproteomics. In total, 2919 unique proteins and 1306 unique PTMs were identified, whereas the latter included acetylation, deamination, hydroxylation, methylation, nitrosylation, oxidation, and phosphorylation. These modifications were unevenly distributed among microbial taxonomic and functional categories. A connection between modification types and particular functions was demonstrated. Interestingly, PTMs differed among the orthologous proteins derived from different bacterial groups. Furthermore, proteomic mapping to the draft genome of a Nitrospirae bacterium revealed novel modifications for proteins that participate in energy metabolism, signal transduction, and inorganic ion transport. CONCLUSIONS Our results suggest that PTMs are enriched in specific functions, which would be important for microbial adaptation to extreme conditions of the hydrothermal vent. PTMs in deep-sea are highly diverse and divergent, and much broader investigations are needed to obtain a better understanding of their functional roles.
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Affiliation(s)
- Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Huiluo Cao
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Lin Cai
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Wei Ding
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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29
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Hölken I, Hoppe M, Mishra YK, Gorb SN, Adelung R, Baum MJ. Complex shaped ZnO nano- and microstructure based polymer composites: mechanically stable and environmentally friendly coatings for potential antifouling applications. Phys Chem Chem Phys 2016; 18:7114-23. [PMID: 26883913 DOI: 10.1039/c5cp07451g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since the prohibition of tributyltin (TBT)-based antifouling paints in 2008, the development of environmentally compatible and commercially realizable alternatives is a crucial issue. Cost effective fabrication of antifouling paints with desired physical and biocompatible features is simultaneously required and recent developments in the direction of inorganic nanomaterials could play a major role. In the present work, a solvent free polymer/particle-composite coating based on two component polythiourethane (PTU) and tetrapodal shaped ZnO (t-ZnO) nano- and microstructures has been synthesized and studied with respect to mechanical, chemical and biocompatibility properties. Furthermore, antifouling tests have been carried out in artificial seawater tanks. Four different PTU/t-ZnO composites with various t-ZnO filling fractions (0 wt%, 1 wt%, 5 wt%, 10 wt%) were prepared and the corresponding tensile, hardness, and pull-off test results revealed that the composite filled with 5 wt% t-ZnO exhibits the strongest mechanical properties. Surface free energy (SFE) studies using contact angle measurements showed that the SFE value decreases with an increase in t-ZnO filler amounts. The influence of t-ZnO on the polymerization reaction was confirmed by Fourier transform infrared-spectroscopy measurements and thermogravimetric analysis. The immersion tests demonstrated that fouling behavior of the PTU/t-ZnO composite with a 1 wt% t-ZnO filler has been decreased in comparison to pure PTU. The composite with a 5 wt% t-ZnO filler showed almost no biofouling.
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Affiliation(s)
- Iris Hölken
- Functional Nanomaterials, Institute for Materials Science, Faculty of Engineering, University of Kiel, Kaiserstr. 2, D-24143, Kiel, Germany.
| | - Mathias Hoppe
- Functional Nanomaterials, Institute for Materials Science, Faculty of Engineering, University of Kiel, Kaiserstr. 2, D-24143, Kiel, Germany.
| | - Yogendra K Mishra
- Functional Nanomaterials, Institute for Materials Science, Faculty of Engineering, University of Kiel, Kaiserstr. 2, D-24143, Kiel, Germany.
| | - Stanislav N Gorb
- Functional Morphology and Biomechanics, Zoological Institute, Department of Zoology, University of Kiel, Botanischen Garten 1-9, D - 24098 Kiel, Germany
| | - Rainer Adelung
- Functional Nanomaterials, Institute for Materials Science, Faculty of Engineering, University of Kiel, Kaiserstr. 2, D-24143, Kiel, Germany.
| | - Martina J Baum
- Functional Nanomaterials, Institute for Materials Science, Faculty of Engineering, University of Kiel, Kaiserstr. 2, D-24143, Kiel, Germany.
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30
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A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time. Appl Microbiol Biotechnol 2016; 100:6361-6373. [DOI: 10.1007/s00253-016-7604-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 01/06/2023]
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31
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Zhang W, Tian R, Bo Y, Cao H, Cai L, Chen L, Zhou G, Sun J, Zhang X, Al-Suwailem A, Qian PY. Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting. Mol Ecol 2016; 25:1958-71. [DOI: 10.1111/mec.13501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 11/22/2015] [Accepted: 11/24/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Weipeng Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Renmao Tian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Yang Bo
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Huiluo Cao
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Lin Cai
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Lianguo Chen
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Guowei Zhou
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Jin Sun
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
| | - Xixiang Zhang
- King Abdullah University of Science and Technology; Thuwal Saudi Arabia
| | | | - Pei-Yuan Qian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong Hong Kong
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32
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Gulmann LK, Beaulieu SE, Shank TM, Ding K, Seyfried WE, Sievert SM. Bacterial diversity and successional patterns during biofilm formation on freshly exposed basalt surfaces at diffuse-flow deep-sea vents. Front Microbiol 2015; 6:901. [PMID: 26441852 PMCID: PMC4564720 DOI: 10.3389/fmicb.2015.00901] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4-293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50' N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.
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Affiliation(s)
- Lara K Gulmann
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Stace E Beaulieu
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Timothy M Shank
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
| | - Kang Ding
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - William E Seyfried
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA, USA
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33
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Zhang W, Wang Y, Bougouffa S, Tian R, Cao H, Li Y, Cai L, Wong YH, Zhang G, Zhou G, Zhang X, Bajic VB, Al-Suwailem A, Qian PY. Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool. Environ Microbiol 2015; 17:4089-104. [DOI: 10.1111/1462-2920.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Weipeng Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yong Wang
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
| | - Salim Bougouffa
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Renmao Tian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Huiluo Cao
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yongxin Li
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Lin Cai
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yue Him Wong
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Gen Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Guowei Zhou
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Xixiang Zhang
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Abdulaziz Al-Suwailem
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
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34
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Cao H, Zhang W, Wang Y, Qian PY. Microbial community changes along the active seepage site of one cold seep in the Red Sea. Front Microbiol 2015; 6:739. [PMID: 26284035 PMCID: PMC4523032 DOI: 10.3389/fmicb.2015.00739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/06/2015] [Indexed: 01/11/2023] Open
Abstract
The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.
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Affiliation(s)
- Huiluo Cao
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Weipeng Zhang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Yong Wang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong ; Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences Sanya, China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
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35
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Yang B, Zhang W, Tian R, Wang Y, Qian PY. Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea. Antonie van Leeuwenhoek 2015; 108:461-71. [PMID: 26059861 DOI: 10.1007/s10482-015-0499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/01/2015] [Indexed: 11/26/2022]
Abstract
Cold seeps are unique ecosystems that are generally characterized by high salinity and reducing solutions. Seepage fluid, the major water influx of this system, contains hypersaline water, sediment pore water, and other components. The Thuwal cold seeps were recently discovered on the continental margin of the Red Sea. Using 16S rRNA gene pyro-sequencing technology, microbial communities were investigated by comparing samples collected in 2011 and 2013. The results revealed differences in the microbial communities between the two sampling times. In particular, a significantly higher abundance of Marine Group I (MGI) Thaumarchaeota was coupled with lower salinity in 2013. In the brine pool, the dominance of Desulfobacterales in 2011 was supplanted by MGI Thaumarchaeota in 2013, perhaps due to a reduced supply of hydrogen sulfide from the seepage fluid. Collectively, this study revealed a difference in water components in this ecosystem between two sampling times. The results indicated that the seawater in this cold seep displayed a greater number of characteristics of normal seawater in 2013 than in 2011, which might represent the dominant driving force for changes in microbial community structures. This is the first study to provide a temporal comparison of the microbial biodiversity of a cold seep ecosystem in the Red Sea.
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Affiliation(s)
- Bo Yang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong,
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