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Judd M, Wira J, Place AR, Bachvaroff T. Long-Read Sequencing Unlocks New Insights into the Amphidinium carterae Microbiome. Mar Drugs 2024; 22:342. [PMID: 39195458 DOI: 10.3390/md22080342] [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: 06/21/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The impact of the microbiome on A. carterae growth and metabolite synthesis is not yet fully understood, nor is the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers during antibiotic treatment, bacterial sequences were still present. In this experiment, we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9 to 6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic treatment. Multiple antibiotic resistance genes were identified, as well as evidence that the bacterial population does not contribute to toxic secondary metabolite synthesis.
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Affiliation(s)
- Miranda Judd
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Jens Wira
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Allen R Place
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Tsvetan Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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Mustaq S, Moin A, Pandit B, Tiwary BK, Alam M. Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications. Folia Microbiol (Praha) 2024; 69:17-32. [PMID: 38038797 DOI: 10.1007/s12223-023-01107-2] [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: 07/27/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.
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Affiliation(s)
- Saqlain Mustaq
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, 700160, Kolkata, West Bengal, India
| | - Abdul Moin
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, 700160, Kolkata, West Bengal, India
| | - Baishali Pandit
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, 700160, Kolkata, West Bengal, India
- Department of Botany, Surendranath College, 24/2 MG Road, 700009, Kolkata, West Bengal, India
| | - Bipransh Kumar Tiwary
- Department of Microbiology, North Bengal St. Xavier's College, Rajganj, 735135, Jalpaiguri, West Bengal, India
| | - Masrure Alam
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, 700160, Kolkata, West Bengal, India.
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Zhang X, Xu J, Dai J, Zhang L, Feng L, Tian X, Yang Q. Taxonomic, Phylogenomic and Bioactivity Profiling of Novel Phycosphere Bacterium from Model Cyanobacterium Synechococcus elongatus PCC 7942. Mar Drugs 2024; 22:36. [PMID: 38248661 PMCID: PMC10817584 DOI: 10.3390/md22010036] [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: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Phycosphere niches host rich microbial consortia that harbor dynamic algae-bacteria interactions with fundamental significance in varied natural ecosystems. Hence, culturing the uncultured microbial majority of the phycosphere microbiota is vital for deep understanding of the intricate mechanisms governing the dynamic interactions, and also to provide novel and rich microbial resources, and to discover new natural bioactive metabolites. Synechococcus elongatus PCC 7942 is a robust model cyanobacterium widely used in environment, synthesis biology, and biotechnology research. To expand the number of novel phycosphere species that were brought into culture and to discover the natural bioactivities, we presented a new yellow-pigmented bacterium named ABI-127-1, which was recovered from the phycosphere of PCC 7942, using an optimized bacterial isolation procedure. Combined polyphasic taxonomic and phylogenomic characterization was performed to confidently identify the new isolate as a potential novel species belonging to the genus Qipengyuania. The observed bioactivity of strain ABI-127-1 with promoting potential towards the growth and CO2 fixation efficiency of the host microalgae was measured. Additionally, the bacterial production of active bioflocculant exopolysaccharides was evaluated after culture optimization. Thus, these findings revealed the potential environmental and biotechnological implications of this new microalgae growth-promoting bacterium isolated from the phycosphere microenvironment.
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Affiliation(s)
- Xiaoling Zhang
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
| | - Jiaquan Xu
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
| | - Jun Dai
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Lei Zhang
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lijuan Feng
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaoqing Tian
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Qiao Yang
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Marasco R, Michoud G, Sefrji FO, Fusi M, Antony CP, Seferji KA, Barozzi A, Merlino G, Daffonchio D. The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea. Front Microbiol 2023; 14:1155381. [PMID: 37200916 PMCID: PMC10185800 DOI: 10.3389/fmicb.2023.1155381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/04/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme-and unique-oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described. Methods To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria. Results and discussion This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.
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Taxonomic and Bioactivity Characterizations of Mameliella alba Strain LZ-28 Isolated from Highly Toxic Marine Dinoflagellate Alexandrium catenella LZT09. Mar Drugs 2022; 20:md20050321. [PMID: 35621971 PMCID: PMC9147911 DOI: 10.3390/md20050321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/15/2023] Open
Abstract
Microalgae host varied microbial consortium harboring cross-kingdom interactions with fundamental ecological significance in aquatic ecosystems. Revealing the complex biofunctions of the cultivable bacteria of phycosphere microbiota is one vital basis for deeply understanding the mechanisms governing these dynamic associations. In this study, a new light-yellow pigmented bacterial strain LZ-28 was isolated from the highly-toxic and harmful algal bloom-forming dinoflagellate Alexandrium catenella LZT09. Collective phenotypic and genotypic profiles were obtained to confidently identify this strain as a new Mameliellaalba member. Comparative genomic analysis showed that strain LZ-28 shared highly similar functional features with other four marine algae-derived M. alba strains in spite of their distinctive isolation sources. Based on the bioactivity assaying, the mutual growth-promoting effects between bacterial strain LZ-28 and algal strain LZT09 were observed. After the culture conditions were optimized, strain LZ-28 demonstrated an extraordinary production ability for its bioflocculanting exopolysaccharides (EPS). Moreover, the portions of two monosaccharides glucose and fucose of the EPS were found to positively contribute to the bioflocculanting capacity. Therefore, the present study sheds light on the similar genomic features among the selected M. alba strains, and it also reveals the potential pharmaceutical, environmental and biotechnological implications of active EPS produced by this new Mameliella alba strain LZ-28 recovered from toxic bloom-forming marine dinoflagellate.
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Kim KH, Kristyanto S, Kim HM, Kim KR, Jeon CO. Nitratireductor rhodophyticola sp. nov., isolated from marine red algae. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, strictly aerobic bacteria, strains L1-7-SET and R6, isolated from marine red algae, were characterized. They shared 99.9 % 16S rRNA gene sequence similarity and a 100 % digital DNA–DNA hybridization (DDH) value, representing members of a single species. Cells of strains L1-7-SET and R6 were catalase- and oxidase-positive motile rods with a single polar flagellum. Strains L1-7-SET and R6 optimally grew at 30–35 °C, pH 7.0–8.0 and with 1.0–2.0 % (w/v) NaCl. Ubiquinone-10 was the sole isoprenoid quinone and C19 : 0 cyclo ω8c and summed feature 8 (comprising C18 : 1
ω7c and/or C18 : 1
ω6c) were detected as the major cellular fatty acids. The DNA G+C contents of strains L1-7-SET and R6 were both 61.62 mol%. The polar lipids of strain L1-7-SET consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and two unidentified polar lipids. Phylogenetic analyses based on 16S rRNA gene and 120 protein marker sequences revealed that strains L1-7-SET and R6 formed a phyletic lineage within the genus
Nitratireductor
and they were most closely related to
Nitratireductor aquibiodomus
NL21T and
Nitratireductor kimnyeongensis
KY 101T with both 98.8 % 16S rRNA gene sequence similarities. Digital DDH values between strain L1-7-SET and the type strains of
N. aquibiodomus
and
N. kimnyeongensis
were 60.3 and 29.5 %, respectively. The phenotypic, chemotaxonomic and molecular features support that strains L1-7-SET and R6 represents a novel species of the genus
Nitratireductor
, for which the name Nitratireductor rhodophyticola sp. nov. is proposed. The type strain is L1-7-SET (=KACC 19076T=KCTC 92231T=JCM 31802T).
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Affiliation(s)
- Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sylvia Kristyanto
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyung Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyeong Ryeol Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Limnobacter alexandrii sp. nov., a thiosulfate-oxidizing, heterotrophic and EPS-bearing Burkholderiaceae isolated from cultivable phycosphere microbiota of toxic Alexandrium catenella LZT09. Antonie van Leeuwenhoek 2020; 113:1689-1698. [PMID: 32955707 DOI: 10.1007/s10482-020-01473-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
A novel Gram-negative, aerobic, motile and short rod-shaped bacterium with exopolysaccharides production, designated as LZ-4T, was isolated from cultivable phycosphere microbiota of harmful algal blooms-causing marine dinoflagellate Alexandrium catenella LZT09 which produces paralytic shellfish poisoning toxins. Strain LZ-4T was able to use thiosulfate (optimum concentration 10 mM) as energy source for bacterial growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LZ-4T belonged to the genus Limnobacter, showing high 16S rRNA gene sequences similarities with L. thiooxidans DSM 13612T (99.4%), L. humi NBRC 11650T (98.2%) and L. litoralis NBRC 105857T (97.2%), respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between LZ-4T and L. thiooxidans DSM 13612T were 78.9 and 21.9%, respectively. Both values were far lower than the thresholds (95-96% for ANI and 70% for dDDH) generally accepted for new species delineation. The respiratory quinone of strain LZ-4T was Q-8. The dominant cellular fatty acids were determined as summed feature 3 (C16:1 ω6c/ω7c), summed feature 8 (C18:1 ω6c/ω7c) and C16:0. Polar lipids profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and three unidentified polar lipids. The genomic DNA G+C content of strain LZ-4T was 52.5 mol%. Based on polyphasic characterization, strain LZ-4T represents a novel species of the genus Limnobacter, for which the name Limnobacter alexandrii sp. nov. is proposed. The type strain is LZ-4T (=CCTCC AB 2019004T =KCTC 72281T).
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