1
|
Bhowmick T, Sarkar A, Islam KH, Karmakar S, Mukherjee J, Das R. Molecular insights into cobalt homeostasis in estuarine microphytobenthos: A meta-transcriptomics and biogeochemical approach. JOURNAL OF HAZARDOUS MATERIALS 2025; 490:137716. [PMID: 40024116 DOI: 10.1016/j.jhazmat.2025.137716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 01/09/2025] [Accepted: 02/21/2025] [Indexed: 03/04/2025]
Abstract
Meta-transcriptomics data supported by biofilm physico-chemical parameters unravelled the molecular and biochemical processes utilized by multicomponent intertidal biofilms to endure cobalt toxicity. Findings indicated activation of influx (BtuB, ABC-type transporters) and efflux pumps (RND, CZC) to maintain metal ion homeostasis. Enhanced specific activity of antioxidant enzymes namely catalases and peroxidases (KatG, SodA) mitigated oxidative damage. Heightened synthesis of capsular polysaccharide components, specifically uronic acid and carbohydrate via PEP-CTERM sorting system, wzy pathway and glycosyltransferases protected biofilms against cobalt exposure. Despite chlorophyll biosynthesis genes being upregulated, metal toxicity impeded chlorophyll replenishment. Principal pathways associated with iron acquisition (AfuA), energy metabolism (AtpG), general metabolic activities (FruK, NifD, coABC) and central dogma regulation (DPS, AsrR, RRM) were activated to combat cobalt toxicity. This investigation offered novel insights into the regulatory network employed by intertidal microphytobenthic communities for maintaining cobalt homeostasis and underlined the basis for their application as biomarkers for estuarine cobalt pollution.
Collapse
Affiliation(s)
- Tanaya Bhowmick
- School of Environmental Studies, Jadavpur University, Kolkata 700032, India
| | - Arnab Sarkar
- Department of Pharmaceutical Technology. Jadavpur University, Kolkata 700032, India
| | - Kazi Hamidul Islam
- School of Environmental Studies, Jadavpur University, Kolkata 700032, India
| | - Sanmoy Karmakar
- Department of Pharmaceutical Technology. Jadavpur University, Kolkata 700032, India
| | - Joydeep Mukherjee
- School of Environmental Studies, Jadavpur University, Kolkata 700032, India.
| | - Reshmi Das
- School of Environmental Studies, Jadavpur University, Kolkata 700032, India; Earth Observatory of Singapore, Nanyang Technological University, 639798, Singapore.
| |
Collapse
|
2
|
Yang M, Qi Y, Gao P, Li L, Guo J, Zhao Y, Liu J, Chen Z, Yu L. Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress. Commun Biol 2025; 8:766. [PMID: 40389724 PMCID: PMC12089287 DOI: 10.1038/s42003-025-08196-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 05/07/2025] [Indexed: 05/21/2025] Open
Abstract
Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.
Collapse
Affiliation(s)
- Min Yang
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Ying Qi
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Penghua Gao
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Lifang Li
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Jianwei Guo
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Yongteng Zhao
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Jiani Liu
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Zebin Chen
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Lei Yu
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China.
| |
Collapse
|
3
|
Ma TF, Yu XY, Xing CY, Fu HM, Duan HY, Chen YP. Impacts of sulfamethoxazole on heterotrophic nitrification-aerobic denitrification bacteria and its response strategies: Insights from physiology to proteomics. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 379:124890. [PMID: 40056593 DOI: 10.1016/j.jenvman.2025.124890] [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: 12/16/2024] [Revised: 02/04/2025] [Accepted: 03/04/2025] [Indexed: 03/10/2025]
Abstract
The effects of sulfonamide antibiotics on heterotrophic nitrification-aerobic denitrification (HN-AD) and the response mechanisms of HN-AD bacteria are not fully understood. This study investigated the physiological changes and proteomic responses of the HN-AD bacteria Pseudomonas stutzeri (P. stutzeri) under varying concentrations of sulfamethoxazole (SMX). Results indicated that SMX inhibited the growth and HN-AD performance of P. stutzeri in a concentration-dependent manner. SMX exposure led to decreased motility, reduced electron transfer system activity, and diminished activities of key denitrifying enzymes, accompanied by increased levels of intracellular reactive oxygen species and compromised cell membrane integrity. Additionally, the production of extracellular polymeric substances and self-aggregation ability of P. stutzeri initially increased and then decreased with rising SMX concentrations. Proteomic analysis revealed that SMX primarily suppressed pathways involved in bacterial chemotaxis, ABC transporters, two-component systems, fatty acid metabolism, and nitrogen metabolism. In response, P. stutzeri upregulated pathways associated with starch and sucrose metabolism, carotenoid biosynthesis, styrene degradation, O-antigen nucleotide sugar biosynthesis, and the pentose phosphate pathway. These findings provide insights into the effects of sulfonamide antibiotics on HN-AD bacteria and their response mechanisms, offering references for the application of HN-AD processes in treating antibiotic-containing wastewater.
Collapse
Affiliation(s)
- Teng-Fei Ma
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Xiao-Yao Yu
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Chong-Yang Xing
- School of Environment and Resource, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Hui-Min Fu
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Hao-Yang Duan
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
| |
Collapse
|
4
|
Jean N, James A, Balliau T, Martino C, Ghersy J, Savar V, Laabir M, Caruana AMN. Warming and polymetallic stress induce proteomic and physiological shifts in the neurotoxic Alexandrium pacificum as possible response to global changes. MARINE POLLUTION BULLETIN 2024; 209:117221. [PMID: 39522120 DOI: 10.1016/j.marpolbul.2024.117221] [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: 07/25/2024] [Revised: 10/18/2024] [Accepted: 10/27/2024] [Indexed: 11/16/2024]
Abstract
Harmful Algal Blooms involving the dinoflagellate Alexandrium pacificum continue to increase in ecosystems suffering the climate warming and anthropogenic pressure. Changes in the total proteome and physiological traits of the Mediterranean A. pacificum SG C10-3 strain were measured in response to increasing temperature (24 °C, 27 °C, 30 °C) and trace metal contamination (Cu2+, Pb2+, Zn2+, Cd2+). Warming reduced the cell densities and maximal growth rate (μmax), but the strain persisted at 30 °C with more large cells. The polymetallic stress increased cell sizes, reduced cell growth at 24 °C-27 °C and it increased this at 30 °C. Toxin profiles showed a predominance of GTX4 (32-38 %), then C2 (11-34 %) or GTX6 (18-24 %) among the total Paralytic Shellfish Toxins, however these were modified under warming, showing increased contents in GTX1 (among the most toxic), GTX5, C1 and NeoSTX, while dc-NeoSTX and STX (among the most toxic) only appeared at 30 °C. Under polymetallic contamination, warming also increased contents in GTX5 and NeoSTX. In contrast, polymetallic stress, or warming had harmful effects on C2 contents. Proteins were more quantitatively produced by A. pacificum SG C10-3 under warming in accordance with the high levels of up-regulated proteins found in the total proteome in this condition. Polymetallic stress, only or combined with warming, led to low proteomic modifications (1 % or 4 %), whereas warming induced strong 52 % modified proteomic response, mainly based on up-regulated proteins involved in photosynthesis (light harvesting complex protein), carbohydrate metabolism (arylsulfatase) and translation (ribosomal proteins), and with the lesser down-regulated proteins principally associated with the lipid metabolism (type I polyketide synthase). Our results show that warming triggers a strong up-regulated A. pacificum SG C10-3 proteomic response, which, coupled to modified cell sizes and toxin profiles, could help it to withstand stress conditions. This could presage the success of A. pacificum in anthropized ecosystems submitted to global warming in which this dinoflagellate also might be more toxic.
Collapse
Affiliation(s)
- Natacha Jean
- Université de Toulon, Aix Marseille Univ., CNRS, IRD, MIO, Toulon, France.
| | - Amandin James
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), UMR7232, Laboratoire de Biodiversité et Biotechnologie Microbienne (LBBM), UAR3579, Observatoire Océanologique, 66 650 Banyuls-sur-mer, France
| | - Thierry Balliau
- PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91 190 Gif-sur-Yvette, France
| | - Christian Martino
- Université de Toulon, Aix Marseille Univ., CNRS, IRD, MIO, Toulon, France
| | - Jérôme Ghersy
- Université de Toulon, Aix Marseille Univ., CNRS, IRD, MIO, Toulon, France
| | - Véronique Savar
- IFREMER, Phycotoxin Laboratory, rue de l'île d'Yeu, BP 21105, 44 311 Nantes, France
| | - Mohamed Laabir
- Univ Montpellier, UMR Marbec, IRD, Ifremer, CNRS, Montpellier, France
| | - Amandine M N Caruana
- IFREMER, Phycotoxin Laboratory, rue de l'île d'Yeu, BP 21105, 44 311 Nantes, France
| |
Collapse
|
5
|
Wang Z, Wang J, Yu X, Zhang H, Liu J, Cao J, Fang J, Song Z, Zhang L. The metabolic characteristics and environmental adaptations of the intertidal bacterium Palleronia sp. LCG004. Front Microbiol 2024; 15:1469112. [PMID: 39678919 PMCID: PMC11638410 DOI: 10.3389/fmicb.2024.1469112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 11/06/2024] [Indexed: 12/17/2024] Open
Abstract
The intertidal zone, a dynamic interface of marine, atmospheric, and terrestrial ecosystems, exposes microorganisms to rapid shifts in temperature, salinity, and oxidative stress. Strain LCG004, representing a novel Palleronia species, was isolated from the Lu Chao Harbor's intertidal seawater in the Western Pacific Ocean. The genome of the organism reveals its metabolic versatility, enabling the utilization of various organic substrates-ranging from organic acids, amino acids, to sugars, and encompassing complex carbohydrates-as well as adept handling of inorganic nutrients, thereby highlighting its significant role in the cycling of nutrients. The strain is equipped with multiple osmoprotectant transporters, deoxyribodipyrimidine photo-lyase, and a comprehensive antioxidant defense system, featuring with multiple catalases, peroxidases, and superoxide dismutases, enabling it to withstand ever-changing environmental conditions, UV radiation, and oxidative challenges. Notably, LCG004 exhibited enhanced growth and cell aggregation under oligotrophic conditions, promoted by light exposure, underscoring the significant influence of light on its morphological and physiological attributes. This study elucidates strain LCG004's metabolic characteristics and ecological potential, and offers insights into its contributions to biogeochemical cycles and survival strategies in one of nature's most fluctuating environments.
Collapse
Affiliation(s)
- Zekai Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Xi Yu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Hongcai Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Jie Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zengfu Song
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology (Shanghai), Shanghai Ocean University, Shanghai, China
| | - Li Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
6
|
Cui H, Lu J, Ding W, Zhang W. Genomic Features and Antimicrobial Activity of Phaeobacter inhibens Strains from Marine Biofilms. Mar Drugs 2024; 22:492. [PMID: 39590772 PMCID: PMC11595833 DOI: 10.3390/md22110492] [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: 09/16/2024] [Revised: 10/19/2024] [Accepted: 10/29/2024] [Indexed: 11/28/2024] Open
Abstract
Members of the genus Phaeobacter are widely distributed in the marine environment and are known for their ability to produce tropodithietic acid (TDA). Studies investigating the genomic and metabolic features of Phaeobacter strains from marine biofilms are sparse. Here, we analyze the complete genomes of 18 Phaeobacter strains isolated from biofilms on subtidal stones, with the aim of determining their potential to synthesize secondary metabolites. Based on whole-genome comparison and average nucleotide identity calculation, the isolated bacteria are classified as novel strains of Phaeobacter inhibens. Further analysis reveals a total of 153 biosynthetic gene clusters, which are assigned to 32 gene cluster families with low similarity to previously published ones. Complete TDA clusters are identified in 14 of the 18 strains, while in the other 4 strains the TDA clusters are rather incomplete and scattered across different chromosome and plasmid locations. Phylogenetic analysis suggests that their presence or absence may be potentially attributed to horizontal gene transfer. High-performance liquid chromatography-mass spectrometry analysis demonstrates the production of TDA in all the examined strains. Furthermore, the Phaeobacter strains have strong antibacterial activity against the pathogenic strain Vibrio owensii ems001, which is associated with acute hepatopancreatic necrosis in South American white shrimp. Altogether, this study ameliorates our knowledge of marine biofilm-associated Phaeobacter and offers new avenues for exploiting marine antimicrobial agents.
Collapse
Affiliation(s)
- Han Cui
- MOE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (H.C.); (J.L.)
| | - Jie Lu
- MOE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (H.C.); (J.L.)
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics & Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China;
| | - Weipeng Zhang
- MOE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (H.C.); (J.L.)
| |
Collapse
|
7
|
Arboleda-Baena C, Freilich M, Pareja CB, Logares R, De la Iglesia R, Navarrete SA. Microbial community and network responses across strong environmental gradients: How do they compare with macroorganisms? FEMS Microbiol Ecol 2024; 100:fiae017. [PMID: 38327185 PMCID: PMC10894034 DOI: 10.1093/femsec/fiae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/01/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
The way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems. Here, we characterize intertidal biofilm bacteria communities, comparing zonation at both the "species" and community levels, as well as network attributes, with co-occurring macroalgae and invertebrates in the same rocky shore system. The results revealed that the desiccation gradient has a more significant impact on smaller communities, while both desiccation and submersion gradients (surge) affect the larger, macroscopic communities. At the community level, we also confirmed the existence of distinct communities within each intertidal zone for microorganisms, similar to what has been previously described for macroorganisms. But our results indicated that dominant microbial organisms along the same environmental gradient exhibited less differentiation across tidal levels than their macroscopic counterparts. However, despite the substantial differences in richness, size and attributes of co-occurrence networks, both macro- and micro-communities respond to stress gradients, leading to the formation of similar zonation patterns in the intertidal rocky shore.
Collapse
Affiliation(s)
- Clara Arboleda-Baena
- Department of Ecology, Estación Costera de Investigaciones Marinas (ECIM), Pontificia Universidad Católica de Chile, El Tabo, 2690000, Chile
- Department of Molecular Genetics and Microbiology, Laboratorio de Microbiología Marina, Pontificia Universidad Católica de Chile, Santiago de Chile, 8320000, Chile
- Department of Hydrobiology, Laboratory of Microbial Processes & Biodiversity, Universidade Federal de São Carlos, São Carlos, 13565-905, Brazil
| | - Mara Freilich
- Department of Earth, Environmental, and Planetary Sciences and Division of Applied Mathematics, Brown University, Providence, RI, 02912, USA
| | - Claudia Belén Pareja
- Department of Molecular Genetics and Microbiology, Laboratorio de Microbiología Marina, Pontificia Universidad Católica de Chile, Santiago de Chile, 8320000, Chile
| | - Ramiro Logares
- Instituto de Ciencias del Mar – CSIC, Paseo Marítimo de la Barceloneta, Barcelona, 08003, Spain
| | - Rodrigo De la Iglesia
- Department of Molecular Genetics and Microbiology, Laboratorio de Microbiología Marina, Pontificia Universidad Católica de Chile, Santiago de Chile, 8320000, Chile
- Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, 8320000, Chile
| | - Sergio A Navarrete
- Department of Ecology, Estación Costera de Investigaciones Marinas (ECIM), Pontificia Universidad Católica de Chile, El Tabo, 2690000, Chile
- Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, 8320000, Chile
- Núcleo Milenio para la Ecología y la Conservación de los Ecosistemas de Arrecifes Mesofóticos Templados (NUTME), Pontificia Universidad Católica de Chile, Santiago de Chile, 8320000, Chile
- Center for Applied Ecology and Sustainability (CAPES) and Coastal Socioecologial Milenium Institute (SECOS), Pontificia Universidad Católica de Chile, Santiago de Chile, 8320000, Chile
- Center for Oceanographic Research, Copas Coastal, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| |
Collapse
|
8
|
Su X, Cui H, Zhang W. Copiotrophy in a Marine-Biofilm-Derived Roseobacteraceae Bacterium Can Be Supported by Amino Acid Metabolism and Thiosulfate Oxidation. Int J Mol Sci 2023; 24:ijms24108617. [PMID: 37239957 DOI: 10.3390/ijms24108617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Copiotrophic bacteria that respond rapidly to nutrient availability, particularly high concentrations of carbon sources, play indispensable roles in marine carbon cycling. However, the molecular and metabolic mechanisms governing their response to carbon concentration gradients are not well understood. Here, we focused on a new member of the family Roseobacteraceae isolated from coastal marine biofilms and explored the growth strategy at different carbon concentrations. When cultured in a carbon-rich medium, the bacterium grew to significantly higher cell densities than Ruegeria pomeroyi DSS-3, although there was no difference when cultured in media with reduced carbon. Genomic analysis showed that the bacterium utilized various pathways involved in biofilm formation, amino acid metabolism, and energy production via the oxidation of inorganic sulfur compounds. Transcriptomic analysis indicated that 28.4% of genes were regulated by carbon concentration, with increased carbon concentration inducing the expression of key enzymes in the EMP, ED, PP, and TCA cycles, genes responsible for the transformation of amino acids into TCA intermediates, as well as the sox genes for thiosulfate oxidation. Metabolomics showed that amino acid metabolism was enhanced and preferred in the presence of a high carbon concentration. Mutation of the sox genes decreased cell proton motive force when grown with amino acids and thiosulfate. In conclusion, we propose that copiotrophy in this Roseobacteraceae bacterium can be supported by amino acid metabolism and thiosulfate oxidation.
Collapse
Affiliation(s)
- Xiaoyan Su
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Han Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| |
Collapse
|
9
|
Cubillos VM, Ramírez FE, Mardones-Toledo DA, Valdivia N, Chaparro OR, Montory JA, Cruces EA. Specific plasticity of the anemone Anthopleura hermaphroditica to intertidal and subtidal environmental conditions of the Quempillén estuary. PLoS One 2023; 18:e0279482. [PMID: 36603008 PMCID: PMC9815623 DOI: 10.1371/journal.pone.0279482] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/08/2022] [Indexed: 01/06/2023] Open
Abstract
The cellular capacity of marine organisms to address rapid fluctuations in environmental conditions is decisive, especially when their bathymetric distribution encompasses intertidal and subtidal zones of estuarine systems. To understand how the bathymetric distribution determines the oxidative damage and antioxidant response of the estuarine anemone Anthopleura hermaphroditica, individuals were collected from upper intertidal and shallow subtidal zones of Quempillén River estuary (Chile), and their response analysed in a fully orthogonal, multifactorial laboratory experiment. The organisms were exposed to the effects of temperature (10°C and 30°C), salinity (10 ppt and 30 ppt) and radiation (PAR, > 400-700 nm; PAR+UV-A, > 320-700 nm; PAR+UV-A+UV-B, > 280-700 nm), and their levels of lipid peroxidation, protein carbonyl and total antioxidant capacity were determined. The results indicated that the intertidal individuals of A. hermaphroditica presented higher levels of tolerance to the stressful ranges of temperature, salinity, and radiation than individuals from the subtidal zone, which was evident from their lower levels of oxidative damage to lipids and proteins. These results were consistent with increased levels of total antioxidant capacity observed in subtidal organisms. Thus intertidal individuals could have greater plasticity to environmental variations than subtidal individuals. Future studies are needed to understand the mechanisms underlying stress adaptation in individuals from this estuarine anemone subjected to different environmental stressors during their life cycles.
Collapse
Affiliation(s)
- Víctor M. Cubillos
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Laboratorio Costero de Recursos Acuáticos de Calfuco, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- * E-mail:
| | - Felipe E. Ramírez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Laboratorio Costero de Recursos Acuáticos de Calfuco, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Daniela A. Mardones-Toledo
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Laboratorio Costero de Recursos Acuáticos de Calfuco, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Nelson Valdivia
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Oscar R. Chaparro
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Edgardo A. Cruces
- Centro de Investigaciones Costeras, Universidad de Atacama (CIC-UDA), Copiapó, Chile
| |
Collapse
|
10
|
Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms. Microbiol Res 2022; 265:127207. [DOI: 10.1016/j.micres.2022.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/17/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022]
|
11
|
Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes. Genes (Basel) 2022; 13:genes13061050. [PMID: 35741812 PMCID: PMC9223118 DOI: 10.3390/genes13061050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 01/27/2023] Open
Abstract
Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies.
Collapse
|
12
|
Mandal A, Dutta A, Das R, Mukherjee J. Role of intertidal microbial communities in carbon dioxide sequestration and pollutant removal: A review. MARINE POLLUTION BULLETIN 2021; 170:112626. [PMID: 34153859 DOI: 10.1016/j.marpolbul.2021.112626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 05/16/2023]
Abstract
Intertidal microbial communities occur as biofilms or microphytobenthos (MPB) which are sediment-attached assemblages of bacteria, protozoa, fungi, algae, diatoms embedded in extracellular polymeric substances. Despite their global occurrence, they have not been reviewed in light of their structural and functional characteristics. This paper reviews the importance of such microbial communities and their importance in carbon dioxide sequestration as well as pollutant bioremediation. Global annual benthic microalgal productivity was 500 million tons of carbon, 50% of which contributed towards the autochthonous carbon fixation in the estuaries. Primary production by MPB was 27-234 gCm-2y-1 in the estuaries of Asia, Europe and the United States. Mechanisms of heavy metal removal remain to be tested in intertidal communities. Cyanobacteria facilitate hydrocarbon degradation in intertidal biofilms and microbial mats by supporting the associated sulfate-reducing bacteria and aerobic heterotrophs. Physiological cooperation between the microorganisms in intertidal communities imparts enhanced ability to utilize polycyclic aromatic hydrocarbon pollutants by these microorganisms than mono-species communities. Future research may be focused on biochemical characteristics of intertidal mats and biofilms, pollutant-microbial interactions and ecosystem influences.
Collapse
Affiliation(s)
- Abhishek Mandal
- School of Environmental Studies, Jadavpur University, 700032, India
| | - Ahana Dutta
- School of Environmental Studies, Jadavpur University, 700032, India
| | - Reshmi Das
- School of Environmental Studies, Jadavpur University, 700032, India.
| | - Joydeep Mukherjee
- School of Environmental Studies, Jadavpur University, 700032, India.
| |
Collapse
|
13
|
Mohapatra M, Yadav R, Rajput V, Dharne MS, Rastogi G. Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112738. [PMID: 34020306 DOI: 10.1016/j.jenvman.2021.112738] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 04/05/2021] [Accepted: 04/29/2021] [Indexed: 05/22/2023]
Abstract
Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.
Collapse
Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India.
| |
Collapse
|
14
|
Wiegand S, Rast P, Kallscheuer N, Jogler M, Heuer A, Boedeker C, Jeske O, Kohn T, Vollmers J, Kaster AK, Quast C, Glöckner FO, Rohde M, Jogler C. Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov. Microorganisms 2021; 9:microorganisms9071494. [PMID: 34361930 PMCID: PMC8303584 DOI: 10.3390/microorganisms9071494] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/31/2022] Open
Abstract
Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.
Collapse
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (J.V.); (A.-K.K.)
| | - Patrick Rast
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
- Institute of Bio- and Geosciences, Biotechnology (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich-Schiller University, 07743 Jena, Germany;
| | - Anja Heuer
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Christian Boedeker
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Olga Jeske
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Timo Kohn
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
| | - John Vollmers
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (J.V.); (A.-K.K.)
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (J.V.); (A.-K.K.)
| | - Christian Quast
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany;
| | - Frank Oliver Glöckner
- Alfred Wegener Institute Bremerhaven, MARUM, University of Bremen, 28359 Bremen, Germany;
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Christian Jogler
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
- Department of Microbial Interactions, Institute of Microbiology, Friedrich-Schiller University, 07743 Jena, Germany;
- Correspondence: ; Tel.: +49-364-194-9301
| |
Collapse
|
15
|
Kohn T, Rast P, Kallscheuer N, Wiegand S, Boedeker C, Jetten MSM, Jeske O, Vollmers J, Kaster AK, Rohde M, Jogler M, Jogler C. The Microbiome of Posidonia oceanica Seagrass Leaves Can Be Dominated by Planctomycetes. Front Microbiol 2020; 11:1458. [PMID: 32754127 PMCID: PMC7366357 DOI: 10.3389/fmicb.2020.01458] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Seagrass meadows are ubiquitous, fragile and endangered marine habitats, which serve as fish breeding grounds, stabilize ocean floor substrates, retain nutrients and serve as important carbon sinks, counteracting climate change. In the Mediterranean Sea, seagrass meadows are mostly formed by the slow-growing endemic plant Posidonia oceanica (Neptune grass), which is endangered by global warming and recreational motorboating. Despite its importance, surprisingly little is known about the leaf surface microbiome of P. oceanica. Using amplicon sequencing, we here show that species belonging to the phylum Planctomycetes can dominate the biofilms of young and aged P. oceanica leaves. Application of selective cultivation techniques allowed for the isolation of two novel planctomycetal strains belonging to two yet uncharacterized genera.
Collapse
Affiliation(s)
- Timo Kohn
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Patrick Rast
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | | | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Christian Boedeker
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Mike S. M. Jetten
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Olga Jeske
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
16
|
Wang B, Tan X, Du R, Zhao F, Zhang L, Han Y, Zhou Z. Bacterial composition of biofilms formed on dairy-processing equipment. Prep Biochem Biotechnol 2019; 49:477-484. [DOI: 10.1080/10826068.2019.1587623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Binbin Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Xiqian Tan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Renpeng Du
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Fangkun Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Lixia Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Ye Han
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Zhijiang Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| |
Collapse
|
17
|
Elshobary ME, Becker MG, Kalichuk JL, Chan AC, Belmonte MF, Piercey-Normore MD. Tissue-specific localization of polyketide synthase and other associated genes in the lichen, Cladonia rangiferina, using laser microdissection. PHYTOCHEMISTRY 2018; 156:142-150. [PMID: 30296707 DOI: 10.1016/j.phytochem.2018.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/25/2018] [Accepted: 09/28/2018] [Indexed: 02/05/2023]
Abstract
The biosynthesis of two polyketides, atranorin and fumarprotocetraric acid, produced from a lichen-forming fungus, Cladonia rangiferina (L.) F. H. Wigg. was correlated with the expression of eight fungal genes (CrPKS1, CrPKS3, CrPKS16, Catalase (CAT), Sugar Transporter (MFsug), Dioxygenase (YQE1), C2H2 Transcription factor (C2H2), Transcription Factor PacC (PacC), which are thought to be involved in polyketide biosynthesis, and one algal gene, NAD-dependent deacetylase sirtuin 2 (AsNAD)), using laser microdissection (LMD). The differential gene expression levels within the thallus tissue layers demonstrate that the most active region for potential polyketide biosynthesis within the lichen is the outer apical region proximal to the photobiont but some expression also occurs in reproductive tissue. This is the first study using laser microdissection to explore gene expression of these nine genes and their location of expression; it provides a proof-of-concept for future experiments exploring tissue-specific gene expression within lichens; and it highlights the utility of LMD for use in lichen systems.
Collapse
Affiliation(s)
| | - Michael G Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Jenna L Kalichuk
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Ainsley C Chan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Michele D Piercey-Normore
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada; School of Science and the Environment, Memorial University of Newfoundland (Grenfell Campus), Corner Brook, NL, A2H 5G4, Canada.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Lin J. Stress responses of Acinetobacter strain Y during phenol degradation. Arch Microbiol 2016; 199:365-375. [DOI: 10.1007/s00203-016-1310-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 08/10/2016] [Accepted: 10/17/2016] [Indexed: 12/14/2022]
|
20
|
Deciphering the recent phylogenetic expansion of the originally deeply rooted Mycobacterium tuberculosis lineage 7. BMC Evol Biol 2016; 16:146. [PMID: 27363525 PMCID: PMC4929747 DOI: 10.1186/s12862-016-0715-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/22/2016] [Indexed: 11/10/2022] Open
Abstract
Background A deeply rooted phylogenetic lineage of Mycobacterium tuberculosis (M. tuberculosis) termed lineage 7 was discovered in Ethiopia. Whole genome sequencing of 30 lineage 7 strains from patients in Ethiopia was performed. Intra-lineage genome variation was defined and unique characteristics identified with a focus on genes involved in DNA repair, recombination and replication (3R genes). Results More than 800 mutations specific to M. tuberculosis lineage 7 strains were identified. The proportion of non-synonymous single nucleotide polymorphisms (nsSNPs) in 3R genes was higher after the recent expansion of M. tuberculosis lineage 7 strain started. The proportion of nsSNPs in genes involved in inorganic ion transport and metabolism was significantly higher before the expansion began. A total of 22346 bp deletions were observed. Lineage 7 strains also exhibited a high number of mutations in genes involved in carbohydrate transport and metabolism, transcription, energy production and conversion. Conclusions We have identified unique genomic signatures of the lineage 7 strains. The high frequency of nsSNP in 3R genes after the phylogenetic expansion may have contributed to recent variability and adaptation. The abundance of mutations in genes involved in inorganic ion transport and metabolism before the expansion period may indicate an adaptive response of lineage 7 strains to enable survival, potentially under environmental stress exposure. As lineage 7 strains originally were phylogenetically deeply rooted, this may indicate fundamental adaptive genomic pathways affecting the fitness of M. tuberculosis as a species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0715-z) contains supplementary material, which is available to authorized users.
Collapse
|
21
|
Intraspecific Variation in Microbial Symbiont Communities of the Sun Sponge, Hymeniacidon heliophila, from Intertidal and Subtidal Habitats. Appl Environ Microbiol 2015; 82:650-8. [PMID: 26567307 DOI: 10.1128/aem.02980-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/07/2015] [Indexed: 11/20/2022] Open
Abstract
Sponges host diverse and complex communities of microbial symbionts that display a high degree of host specificity. The microbiomes of conspecific sponges are relatively constant, even across distant locations, yet few studies have directly examined the influence of abiotic factors on intraspecific variation in sponge microbial community structure. The contrast between intertidal and subtidal environments is an ideal system to assess the effect of environmental variation on sponge-microbe symbioses, producing two drastically different environments on a small spatial scale. Here, we characterized the microbial communities of individual intertidal and subtidal Hymeniacidon heliophila sponges, ambient seawater, and sediment from a North Carolina oyster reef habitat by partial (Illumina sequencing) and nearly full-length (clone libraries) 16S rRNA gene sequence analyses. Clone library sequences were compared to H. heliophila symbiont communities from the Gulf of Mexico and Brazil, revealing strong host specificity of dominant symbiont taxa across expansive geographic distances. Sediment and seawater samples yielded clearly distinct microbial communities from those found in H. heliophila. Despite the close proximity of the sponges sampled, significant differences between subtidal and intertidal sponges in the diversity, structure, and composition of their microbial communities were detected. Differences were driven by changes in the relative abundance of a few dominant microbial symbiont taxa, as well as the presence or absence of numerous rare microbial taxa. These findings suggest that extreme abiotic fluctuations, such as periodic air exposure in intertidal habitats, can drive intraspecific differences in complex host-microbe symbioses.
Collapse
|
22
|
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
| |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Bo Yang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong,
| | | | | | | | | |
Collapse
|
24
|
Zhang W, Sun J, Ding W, Lin J, Tian R, Lu L, Liu X, Shen X, Qian PY. Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development. Front Cell Infect Microbiol 2015; 5:40. [PMID: 26029669 PMCID: PMC4429628 DOI: 10.3389/fcimb.2015.00040] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/27/2015] [Indexed: 12/13/2022] Open
Abstract
Though the essential role of extracellular matrix in biofilm development has been extensively documented, the function of matrix-associated proteins is elusive. Determining the dynamics of matrix-associated proteins would be a useful way to reveal their functions in biofilm development. Therefore, we applied iTRAQ-based quantitative proteomics to evaluate matrix-associated proteins isolated from different phases of Pseudomonas aeruginosa ATCC27853 biofilms. Among the identified 389 proteins, 54 changed their abundance significantly. The increased abundance of stress resistance and nutrient metabolism-related proteins over the period of biofilm development was consistent with the hypothesis that biofilm matrix forms micro-environments in which cells are optimally organized to resist stress and use available nutrients. Secreted proteins, including novel putative effectors of the type III secretion system were identified, suggesting that the dynamics of pathogenesis-related proteins in the matrix are associated with biofilm development. Interestingly, there was a good correlation between the abundance changes of matrix-associated proteins and their expression. Further analysis revealed complex interactions among these modulated proteins, and the mutation of selected proteins attenuated biofilm development. Collectively, this work presents the first dynamic picture of matrix-associated proteins during biofilm development, and provides evidences that the matrix-associated proteins may form an integral and well regulated system that contributes to stress resistance, nutrient acquisition, pathogenesis and the stability of the biofilm.
Collapse
Affiliation(s)
- Weipeng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Jin Sun
- Department of Biology, Hong Kong Baptist University Hong Kong, China
| | - Wei Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A & F University Yangling, China
| | - Jinshui Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A & F University Yangling, China
| | - Renmao Tian
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Liang Lu
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Xiaofen Liu
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A & F University Yangling, China
| | - Pei-Yuan Qian
- Division of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| |
Collapse
|
25
|
Fierer N, Barberán A, Laughlin DC. Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities. Front Microbiol 2014; 5:614. [PMID: 25429288 PMCID: PMC4228856 DOI: 10.3389/fmicb.2014.00614] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/28/2014] [Indexed: 02/03/2023] Open
Abstract
Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities.
Collapse
Affiliation(s)
- Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA ; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
| | - Albert Barberán
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
| | - Daniel C Laughlin
- Environmental Research Institute, School of Science, University of Waikato Hamilton, New Zealand
| |
Collapse
|
26
|
Zhang WP, Wang Y, Tian RM, Bougouffa S, Yang B, Cao HL, Zhang G, Wong YH, Xu W, Batang Z, Al-Suwailem A, Zhang XX, Qian PY. Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system. Sci Rep 2014; 4:6647. [PMID: 25323200 PMCID: PMC4200420 DOI: 10.1038/srep06647] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/07/2014] [Indexed: 11/09/2022] Open
Abstract
Studies focusing on biofilm assembly in deep-sea environments are rarely conducted. To examine the effects of substrate type on microbial community assembly, biofilms were developed on different substrates for different durations at two locations in the Red Sea: in a brine pool and in nearby bottom water (NBW) adjacent to the Thuwal cold seep II. The composition of the microbial communities in 51 biofilms and water samples were revealed by classification of pyrosequenced 16S rRNA gene amplicons. Together with the microscopic characteristics of the biofilms, the results indicate a stronger selection effect by the substrates on the microbial assembly in the brine pool compared with the NBW. Moreover, the selection effect by substrate type was stronger in the early stages compared with the later stages of the biofilm development. These results are consistent with the hypotheses proposed in the framework of species sorting theory, which states that the power of species sorting during microbial community assembly is dictated by habitat conditions, duration and the structure of the source community. Therefore, the results of this study shed light on the control strategy underlying biofilm-associated marine fouling and provide supporting evidence for ecological theories important for understanding the formation of deep-sea biofilms.
Collapse
Affiliation(s)
- Wei Peng Zhang
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Yong Wang
- 1] KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong [2] Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, San Ya, Hai Nan, China
| | - Ren Mao Tian
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Salim Bougouffa
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Bo Yang
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Hui Luo Cao
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Gen Zhang
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Yue Him Wong
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Wei Xu
- King Abdullah University of Science and Technology, Thuwal, The Kingdom of Saudi Arabia
| | - Zenon Batang
- 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
| | - Xi Xiang Zhang
- 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
| |
Collapse
|
27
|
Lee OO, Wang Y, Tian R, Zhang W, Shek CS, Bougouffa S, Al-Suwailem A, Batang ZB, Xu W, Wang GC, Zhang X, Lafi FF, Bajic VB, Qian PY. In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system. Sci Rep 2014; 4:3587. [PMID: 24399144 PMCID: PMC5378041 DOI: 10.1038/srep03587] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/05/2013] [Indexed: 02/05/2023] Open
Abstract
Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.
Collapse
Affiliation(s)
- On On Lee
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
- These authors contribute equally to this work
| | - Yong Wang
- Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, San Ya, Hai Nan, China
- These authors contribute equally to this work
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Chun Shum Shek
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Salim Bougouffa
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
- Computational Biosciences Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abdulaziz Al-Suwailem
- Coastal and Marine Resources Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zenon B. Batang
- Coastal and Marine Resources Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Wei Xu
- Advanced Nanofabrication, Imaging, and Characterization Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Guang Chao Wang
- Advanced Nanofabrication, Imaging, and Characterization Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xixiang Zhang
- Advanced Nanofabrication, Imaging, and Characterization Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Feras F. Lafi
- Computational Biosciences Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Vladmir B. Bajic
- Computational Biosciences Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| |
Collapse
|