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Alghamdi AK, Parween S, Hirt H, Saad MM. Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina. BMC Genomics 2024; 25:672. [PMID: 38969999 PMCID: PMC11225332 DOI: 10.1186/s12864-024-10555-0] [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: 12/31/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium's adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.
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Affiliation(s)
- Amal Khalaf Alghamdi
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabiha Parween
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Max Perutz Laboratories, University of Vienna, Vienna, Austria.
| | - Maged M Saad
- DARWIN21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Han M, Zhou Z, Zhu T, Yu C, Si Q, Zhu C, Gao T, Jiang Q. Metabolomics and microbiome co-analysis reveals altered innate immune responses in Charybdis japonica following Aeromonas hydrophila infection. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101240. [PMID: 38718732 DOI: 10.1016/j.cbd.2024.101240] [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: 12/04/2023] [Revised: 04/13/2024] [Accepted: 05/03/2024] [Indexed: 05/27/2024]
Abstract
A comprehensive bioinformatics analysis was conducted to elucidate the innate immune response of Charybdis japonica following exposure to Aeromonas hydrophila. This study integrated metabolomics, 16S rRNA sequencing, and enzymatic activity data to dissect the immune mechanisms activated in response to infection. Infection with A. hydrophila resulted in an increased abundance of beneficial intestinal genera such as Photobacterium spp., Rhodobacter spp., Polaribacter spp., Psychrilyobacter spp., and Mesoflavibacter spp. These probiotics appear to suppress A. hydrophila colonization by competitively dominating the intestinal microbiota. Key metabolic pathways affected included fatty acid biosynthesis, galactose metabolism, and nitrogen metabolism, highlighting their role in the crab's intestinal response. Enzymatic analysis revealed a decrease in activities of hexokinase, phosphofructokinase, and pyruvate kinase, which are essential for energy homeostasis and ATP production necessary for stress responses. Additionally, reductions were observed in the activities of acetyl-CoA carboxylase and fatty acid synthase. Gene expression analysis showed downregulation in Peroxiredoxin 1 (PRDX1), Peroxiredoxin 2 (PRDX2), glutathione-S-transferase (GST), catalase (CAT), and glutathione (GSH), with concurrent increases in malondialdehyde (MDA) levels, indicating severe oxidative stress. This study provides insights into the molecular strategies employed by marine crabs to counteract bacterial invasions in their natural habitat.
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Affiliation(s)
- Mingming Han
- Centre for Marine and Coastal Studies, University Sains Malaysia, Minden, Penang 11800, Malaysia
| | - Zihan Zhou
- Centre for Marine and Coastal Studies, University Sains Malaysia, Minden, Penang 11800, Malaysia
| | - Tian Zhu
- Freshwater Fisheries Research Institute of Jiangsu Province, 79 Chating East Street, Nanjing 210017, China
| | - Cigang Yu
- Key Laboratory of Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210424, China
| | - Qin Si
- Key Laboratory of Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210424, China
| | - Chenxi Zhu
- Freshwater Fisheries Research Institute of Jiangsu Province, 79 Chating East Street, Nanjing 210017, China
| | - Tianheng Gao
- Institute of Marine Biology, College of Oceanography, Hohai University, China
| | - Qichen Jiang
- Freshwater Fisheries Research Institute of Jiangsu Province, 79 Chating East Street, Nanjing 210017, China; Low-temperature Germplasm Bank of Important Economic Fish (Freshwater Fisheries Research Institute of Jiangsu Province) of Jiangsu Provincial Science and Technology Resources (Agricultural Germplasm Resources) Coordination Service Platform, Nanjing 210017, China.
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Roager L, Athena-Vasileiadi D, Gram L, Sonnenschein EC. Antagonistic activity of Phaeobacter piscinae against the emerging fish pathogen Vibrio crassostreae in aquaculture feed algae. Appl Environ Microbiol 2024; 90:e0143923. [PMID: 38349149 PMCID: PMC10952492 DOI: 10.1128/aem.01439-23] [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: 08/21/2023] [Accepted: 12/21/2023] [Indexed: 03/21/2024] Open
Abstract
Aquaculture provides a rich resource of high-quality protein; however, the production is challenged by emerging pathogens such as Vibrio crassostreae. While probiotic bacteria have been proposed as a sustainable solution to reduce pathogen load in aquaculture, their application requires a comprehensive assessment across the aquaculture food chain. The purpose of this study was to determine the antagonistic effect of the potential probiotic bacterium Phaeobacter piscinae against the emerging fish pathogen V. crassostreae in aquaculture feed algae that can be an entry point for pathogens in fish and shellfish aquaculture. P. piscinae strain S26 produces the antibacterial compound tropodithietic acid (TDA). In a plate-based assay, P. piscinae S26 was equally to more effective than the well-studied Phaeobacter inhibens DSM17395 in its inhibition of the fish pathogens Vibrio anguillarum 90-11-286 and V. crassostreae DMC-1. When co-cultured with the microalgae Tetraselmis suecica and Isochrysis galbana, P. piscinae S26 reduced the maximum cell density of V. crassostreae DMC-1 by 2 log and 3-4 log fold, respectively. A TDA-deficient mutant of P. piscinae S26 inhibited V. crassostreae DMC-1 to a lesser extent than the wild type, suggesting that the antagonistic effect involves TDA and other factors. TDA is the prime antagonistic agent of the inhibition of V. anguillarum 90-11-286. Comparative genomics of V. anguillarum 90-11-286 and V. crassostreae DMC-1 revealed that V. crassostreae DMC-1 carries a greater arsenal of antibiotic resistance genes potentially contributing to the reduced effect of TDA. In conclusion, P. piscinae S26 is a promising new candidate for inhibition of emerging pathogens such as V. crassostreae DMC-1 in algal feed systems and could contribute to a more sustainable aquaculture industry.IMPORTANCEThe globally important production of fish and shellfish in aquaculture is challenged by disease outbreaks caused by pathogens such as Vibrio crassostreae. These outbreaks not only lead to substantial economic loss and environmental damage, but treatment with antibiotics can also lead to antibiotic resistance affecting human health. Here, we evaluated the potential of probiotic bacteria, specifically the newly identified strain Phaeobacter piscinae S26, to counteract these threats in a sustainable manner. Through a systematic assessment of the antagonistic effect of P. piscinae S26 against V. crassostreae DMC-1, particularly within the context of algal feed systems, the study demonstrates the effectiveness of P. piscinae S26 as probiotic and thereby provides a strategic pathway for addressing disease outbreaks in aquaculture. This finding has the potential of significantly contributing to the long-term stability of the industry, highlighting the potential of probiotics as an efficient and environmentally conscious approach to safeguarding aquaculture productivity against the adverse impact of pathogens.
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Affiliation(s)
- Line Roager
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Eva C. Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Swansea University, College of Science and Engineering, Swansea, Wales, United Kingdom
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Lu Z, Lin W, Li Q, Wu Q, Ren Z, Mu C, Wang C, Shi C, Ye Y. Recirculating aquaculture system as microbial community and water quality management strategy in the larviculture of Scylla paramamosain. WATER RESEARCH 2024; 252:121218. [PMID: 38330713 DOI: 10.1016/j.watres.2024.121218] [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: 11/13/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
The structure and function of the water microbial community can change dramatically between different rearing modes. Yet investigations into the relationships between microbial community and water quality remain obscure. We provide the first evidence that rearing modes alter bacterial community and water quality in the rearing water of the mud crab (Scylla paramamosain) larvae. The juveniles in the recirculating aquaculture system (RAS) had a higher viability than those in the water exchange system (WES). RAS had the significantly lower levels of total ammonia nitrogen (TAN), NH3, NO2--N, total nitrogen (TN), total dissolved solids (TDS), and chemical oxygen demand than those of WES. The number of significantly different amplicon sequence variants between rearing modes increased as the larvae developed. NH3, TAN, TDS, NO2--N, and TN were closely related to the late alterations in water bacterial community. Both the FAPROTAX tool and quantitative PCR analysis showed enhanced nitrogen cycling functional potential of water bacterial community of RAS. Random forest analysis identified the enriched water bacteria especially heterotrophic bacteria such as Phaeodactylibacter, Tenacibaculum, and Hydrogenophaga, which were vital in removing nitrogenous compounds via simultaneous nitrification and denitrification. Notably, RAS could save 18.5 m3 of seawater relative to WES in larviculture on the scale of 2.5 m3. Together, these data indicate that RAS could function as microbial community and water quality management strategy in the larviculture of crab.
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Affiliation(s)
- Zhibin Lu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Weichuan Lin
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Qiang Li
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Qingyang Wu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture (Co-construction by Ministry and Province), Ministry of Education; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315832, China
| | - Zhiming Ren
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture (Co-construction by Ministry and Province), Ministry of Education; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315832, China
| | - Changkao Mu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture (Co-construction by Ministry and Province), Ministry of Education; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315832, China
| | - Chunlin Wang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture (Co-construction by Ministry and Province), Ministry of Education; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315832, China
| | - Ce Shi
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture (Co-construction by Ministry and Province), Ministry of Education; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315832, China.
| | - Yangfang Ye
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture (Co-construction by Ministry and Province), Ministry of Education; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315832, China.
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Lee E, Lee KW, Kim MS, Park J, Park Y, Lee JS, Kang HM. An integrated transcriptome-microbiome host relationship associated with paraben toxicity in the brackish water flea Diaphanosoma celebensis. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133512. [PMID: 38232552 DOI: 10.1016/j.jhazmat.2024.133512] [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: 10/12/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Parabens, a group of alkyl esters of p-hydroxybenzoic acid, have been found in aquatic systems in particular, leading to concerns about their potential impact on ecosystems. This study investigated the effects of three commonly used parabens, methylparaben (MeP), ethylparaben (EtP), and propylparaben (PrP), on the brackish water flea Diaphanosoma celebensis. The results showed that PrP had the most adverse impact on survival rates, followed by EtP and MeP, while MeP and EtP induced significant adverse effects on reproductive performance. A transcriptome analysis revealed significant differential gene expression patterns in response to paraben exposure, with MeP associated with the most significant effects. MeP and EtP exposure produced greater disruption in the microbiota of D. celebensis than did PrP compared with control groups, and we identified eight key microbiota, including Ruegeria and Roseovarius. Correlation analysis between transcriptome and microbiome data revealed key interactions between specific microbiota and host gene expression. Certain microbial taxa were associated with specific genes (e.g. cuticle related genes) and toxicological pathways, shedding light on the complex molecular response and in vivo toxicity effects of parabens. These findings contribute to a deeper understanding of the molecular mechanisms underlying paraben toxicity and highlight the importance of considering the ecological impact of chemical contaminants in aquatic ecosystems.
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Affiliation(s)
- Euihyeon Lee
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Kyun-Woo Lee
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Min-Seok Kim
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Junewoo Park
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Yeun Park
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hye-Min Kang
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea.
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Byeon E, Jeong H, Lee YJ, Cho Y, Lee KW, Lee E, Jeong CB, Lee JS, Kang HM. Effects of microplastics and phenanthrene on gut microbiome and metabolome alterations in the marine medaka Oryzias melastigma. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132620. [PMID: 37757554 DOI: 10.1016/j.jhazmat.2023.132620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/10/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Plastic pollution of the oceans is increasing, and toxic interactions between microplastics (MPs) and organic pollutants have become a major environmental concern. However, the combined effects of organic pollutants and MPs on microbiomes and metabolomes have not been studied extensively. In the present study, to evaluate whether MPs and phenanthrene (Phe) act synergistically in the guts of marine medaka (Oryzias melastigma), we performed toxicity assessments, 16 S rRNA gene sequencing, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. Our investigations revealed increased toxicity induced by Phe, as well as disturbances in gut microbiota (known as dysbiosis) when MPs were present. Furthermore, combined exposure to Phe and MPs resulted in greater alterations to microbiota composition and metabolite profiles. Notably, MP exposure was distinctly associated with the abundance of Shewanella and Spongiibacteraceae, while Phe exposure was associated with the abundance of Marimicrobium. Among key microbiota, Marimicrobium and Roseibacillus were significantly correlated with metabolites responsible for coenzyme A and glycerophospholipid metabolism in medaka. These results suggest that interactions between Phe and MPs may have significant effects on the gut microbiota and metabolism of aquatic organisms and underscore the importance of acknowledging the interplay between MPs and contaminants in aquatic environments.
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Affiliation(s)
- Eunjin Byeon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Haksoo Jeong
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Yeon-Ju Lee
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Yeonwoo Cho
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Kyun-Woo Lee
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Euihyeon Lee
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea
| | - Chang-Bum Jeong
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hye-Min Kang
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; KIOST School, University of Science and Technology, Daejeon 34113, South Korea.
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Li M, Gou D, Gong P, Di W, Wang L, Ding J, Chang Y, Zuo R. An Investigation on the Effects of Dietary Vitamin E on Juvenile Sea Urchin ( Strongylocentrotus intermedius): Growth, Intestinal Microbiota, Immune Response, and Related Gene Expression. BIOLOGY 2023; 12:1523. [PMID: 38132349 PMCID: PMC10740812 DOI: 10.3390/biology12121523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
A 90 d feeding experiment was conducted to investigate the effects of vitamin E (VE) on growth, intestinal microbiota, immune response, and related gene expression of juvenile sea urchin (Strongylocentrotus intermedius). Six dry feeds were made to contain graded levels of VE (78, 105, 152, 235, 302, and 390 mg/kg); these were named E78, E105, E152, E235, E302, and E390, respectively. Dry feed E50 and fresh kelp (HD) were used as the control diets. There were six replicates of cages in each dietary group, and each cage held 20 sea urchins with an initial body weight of approximately 1.50 g. Results exhibited that weight gain rate and gonadosomatic index (GSI) of the sea urchins were not significantly affected by dietary VE ranging from 78 to 390 mg/kg. Sea urchins in the dry feed groups showed poorer growth performance, but significantly higher GSI than those in the fresh kelp groups. The pepsin and lipase activities were not significantly promoted by low or moderate VE, but were inhibited by a high level of VE (302-390 mg/kg), while amylase and cellulase activities were significantly increased by low or moderate VE, with the highest values observed in the E105 and E235 groups, respectively. VE addition at a low dosage (105-152 mg/kg) showed inhibitory effects on immune and antioxidant enzyme activities and expression of inflammation-related genes, but showed no beneficial effects at moderate or high dosage (235-390 mg/kg), while a moderate or relatively higher level of VE (235-302 mg/kg) significantly increased the expression of several immune-related genes. The relative abundance of Proteobacteria, Actinobacteria, Ruegeria, and Maliponia in the intestine of the sea urchins increased with the increase in VE in the dry feeds. On the contrary, the relative abundance of the Firmicutes, Bacteroidetes, Escherichia-Shigella, Bacteroides, and Clostridium sensu stricto 1 gradually decreased as VE content increased. These results indicated that a moderate level of VE (172.5-262.4) can achieve ideal digestive enzyme activities and growth performance, but a relatively higher level of VE (235-302 mg/kg) was beneficial for maintaining the immune and antioxidant capacity of juvenile S. intermedius by regulating the expression of inflammation- and immune-related genes and abundance of some bacteria to a healthy state.
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Affiliation(s)
- Min Li
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
- Department of Marine Biology, Weihai Ocean Vocational College, Weihai 264300, China
| | - Dan Gou
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
| | - Panke Gong
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
| | - Weixiao Di
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
| | - Lina Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
| | - Jun Ding
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
| | - Yaqing Chang
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
| | - Rantao Zuo
- Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea (Ministry of Agriculture and Rural Affairs), Dalian Ocean University, Dalian 116023, China; (M.L.); (Y.C.)
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Paralika V, Kokou F, Karapanagiotis S, Makridis P. Characterization of Host-Associated Microbiota and Isolation of Antagonistic Bacteria from Greater Amberjack ( Seriola dumerili, Risso, 1810) Larvae. Microorganisms 2023; 11:1889. [PMID: 37630449 PMCID: PMC10456766 DOI: 10.3390/microorganisms11081889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in the diet, and one without copepods (control). In addition, antagonistic bacteria were isolated from amberjack larvae and live food cultures. Proteobacteria was the most abundant phylum followed by Bacteroidota in amberjack larvae. The composition and diversity of the microbiota were influenced by age, but not by diet. Microbial community richness and diversity significantly increased over time. Rhodobacteraceae was the most dominant family followed by Vibrionaceae, which showed the highest relative abundance in larvae from the control group 31 days after hatching. Alcaligenes and Thalassobius genera exhibited a significantly higher relative abundance in the copepod group. Sixty-two antagonistic bacterial strains were isolated and screened for their ability to inhibit four fish pathogens (Aeromonas veronii, Vibrio harveyi, V. anguillarum, V. alginolyticus) using a double-layer test. Phaeobacter gallaeciensis, Phaeobacter sp., Ruegeria sp., and Rhodobacter sp. isolated from larvae and Artemia sp. inhibited the fish pathogens. These antagonistic bacteria could be used as host-derived probiotics to improve the growth and survival of the greater amberjack larvae.
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Affiliation(s)
| | - Fotini Kokou
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, 6700 AH Wageningen, The Netherlands;
| | | | - Pavlos Makridis
- Department of Biology, University of Patras, 26504 Rio, Greece;
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Panteli N, Feidantsis K, Demertzioglou M, Paralika V, Karapanagiotis S, Mylonas CC, Kormas KA, Mente E, Makridis P, Antonopoulou E. The Probiotic Phaeobacter inhibens Provokes Hypertrophic Growth via Activation of the IGF-1/Akt Pathway during the Process of Metamorphosis of Greater Amberjack ( Seriola dumerili, Risso 1810). Animals (Basel) 2023; 13:2154. [PMID: 37443952 DOI: 10.3390/ani13132154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/04/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Metamorphosis entails hormonally regulated morphological and physiological changes requiring high energy levels. Probiotics as feed supplements generate ameliorative effects on host nutrient digestion and absorption. Thereby, the aim of the present research was to investigate the impact of the probiotic Phaeobacter inhibens as a water additive on cellular signaling pathways in the metamorphosis of greater amberjack (Seriola dumerili). Activation of insulin-like growth factor type 1 receptor (IGF-1R), protein kinase B (Akt), mitogen-activated protein kinases (MAPKs) and AMP-activated protein kinase (AMPK), induction of heat shock proteins (Hsps), and programmed cell death were assessed through SDS-Page/immunoblot analysis, while energy metabolism was determined through enzymatic activities. According to the results, greater amberjack reared in P. inhibens-enriched water entered the metamorphic phase with greater body length, while protein synthesis was triggered to facilitate the hypertrophic growth as indicated by IGF-1/Akt activation and AMPK inhibition. Contrarily, MAPKs levels were reduced, whereas variations in Hsps response were evident in the probiotic treatment. Apoptosis and autophagy were mobilized potentially for the structural remodeling processes. Furthermore, the elevated enzymatic activities of intermediary metabolism highlighted the excess energy demands of metamorphosis. Collectively, the present findings demonstrate that P. inhibens may reinforce nutrient utilization, thus leading greater amberjack to an advanced growth and developmental state.
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Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Konstantinos Feidantsis
- Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Department of Fisheries & Aquaculture, University of Patras, 26504 Mesolonghi, Greece
| | - Maria Demertzioglou
- Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Vasiliki Paralika
- Department of Biology, University of Patras, 26504 Rio Achaias, Greece
| | | | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, P.O. Box 2214, 71003 Heraklion, Greece
| | - Konstantinos Ar Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 38221 Volos, Greece
| | - Eleni Mente
- Laboratory of Ichthyology-Culture and Pathology of Aquatic Animals, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Pavlos Makridis
- Department of Biology, University of Patras, 26504 Rio Achaias, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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10
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Callac N, Giraud C, Boulo V, Wabete N, Pham D. Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture. PeerJ 2023; 11:e15201. [PMID: 37214103 PMCID: PMC10198154 DOI: 10.7717/peerj.15201] [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: 10/04/2022] [Accepted: 03/17/2023] [Indexed: 05/24/2023] Open
Abstract
Background Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host's health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management. Methods In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage. Results We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected in the natural seawater. This highlights the great importance of the microbial composition of the lagoon on the rearing water microbiota. Considering the larval stage and larval survival we highlight that several genera: Nautella, Leisingera, Ruegerira, Alconivorax, Marinobacter and Tenacibaculum, could be beneficial for the larval survival and may, in the rearing water, overcome the r-strategist microorganisms and/or putative pathogens. Members of these genera might also act as probiotics for the larvae. Marivita, Aestuariicocccus, HIMB11 and Nioella, appeared to be unfavorable for the larval survival and could be associated with upcoming and occurring larval mortalities. All these specific biomarkers of healthy or unhealthy larvae, could be used as early routine detection proxies in the natural seawater and then during the first days of larval rearing, and might help to manage the rearing water microbiota and to select beneficial microorganisms for the larvae.
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Affiliation(s)
- Nolwenn Callac
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Ifremer, Nouméa, New-Caledonia
| | - Carolane Giraud
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Ifremer, Nouméa, New-Caledonia
- Institut des Sciences Exactes et Appliquées, University of New Caledonia, Nouméa, New-Calédonia
| | - Viviane Boulo
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Ifremer, Nouméa, New-Caledonia
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan via Domitia, Ifremer, Montpellier, France
| | - Nelly Wabete
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Ifremer, Nouméa, New-Caledonia
| | - Dominique Pham
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Ifremer, Nouméa, New-Caledonia
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11
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Luo K, Liu Y, Qin G, Wang S, Wei C, Pan M, Guo Z, Liu Q, Tian X. A comparative study on effects of dietary three strains of lactic acid bacteria on the growth performance, immune responses, disease resistance and intestinal microbiota of Pacific white shrimp, Penaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108707. [PMID: 36966896 DOI: 10.1016/j.fsi.2023.108707] [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: 12/28/2022] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
The present study evaluated the growth performance, immune responses, disease resistance and intestinal microbiota in Penaeus vannamei fed diets supplemented with three strains of lactic acid bacteria (LAB). The basal diet (control, CO) supplemented with Lactobacillus plantarum W2 (LA), Pediococcus acidilactici Nj (PE), Enterococcus faecium LYB (EN) and florfenicol (FL), respectively, formed three LAB diets (1 × 1010 cfu kg-1) and a florfenicol diet (15 mg kg-1, positive control), were fed to shrimp for 42 days. Results indicated that specific growth rate, feed efficiency rate, and disease resistance of shrimp against Vibrio parahaemolyticus in the treatment groups were significantly improved versus the control (P < 0.05). Compared with the control, acid phosphatase, alkaline phosphatase, phenonoloxidase, total nitric oxide synthase, peroxidase, superoxide dismutase activities, total antioxidant capacity, and lysozyme content in the serum and the relative expression levels of SOD, LZM, proPO, LGBP, HSP70, Imd, Toll, Relish, TOR, 4E-BP, eIF4E1α and eIF4E2 genes in the hepatopancreas of LAB groups were enhanced to various extents. Intestinal microbiota analysis showed that the LA and EN groups significantly improved microbial diversity and richness, and LAB groups significantly altered intestinal microbial structure of shrimp. At the phylum level, the Verrucomicrobiota in the LA and PE groups, the Firmicutes in the EN group, and the Actinobacteriota in the PE and EN groups were enriched. Moreover, the CO group increased the proportion of potential pathogens (Vibrionaceae and Flavobacteriaceae). The potential pathogen (Vibrio) was reduced, and potential beneficial bacteria (Tenacibaculum, Ruegeria and Bdellovibrio) were enriched in response to dietary three strains of LAB. When the intestinal microbiota homeostasis of shrimp is considered, L. plantarum and E. faecium showed better effects than P. acidilactici. However, due to the concerns on the possible potential risks of E. faecium strains to human health, L. plantarum W2 is more suitable for application in aquaculture than E. faecium LYB. Considering collectively the above, Lactobacillus plantarum W2 could be applied as better probiotic to improve the growth performance, non-specific immunity, disease resistance and promote intestinal health of P. vannamei.
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Affiliation(s)
- Kai Luo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Yang Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Guangcai Qin
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Shishuang Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Cong Wei
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Miaojun Pan
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Zeyang Guo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | | | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.
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12
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Bech PK, Zhang SD, Henriksen NNSE, Bentzon-Tilia M, Strube ML, Gram L. The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater. NPJ Biofilms Microbiomes 2023; 9:12. [PMID: 36959215 PMCID: PMC10036634 DOI: 10.1038/s41522-023-00379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Microbial secondary metabolites play important roles in biotic interactions in microbial communities and yet, we do not understand how these compounds impact the assembly and development of microbial communities. To address the implications of microbial secondary metabolite production on biotic interactions in the assembly of natural seawater microbiomes, we constructed a model system where the assembly of a natural seawater biofilm community was influenced by the addition of the marine biofilm forming Phaeobacter inhibens that can produce the antibiotic secondary metabolite tropodithietic acid (TDA), or a mutant incapable of TDA production. Because of the broad antibiotic activity of TDA, we hypothesized that the potential of P. inhibens to produce TDA would strongly affect both biofilm and planktonic community assembly patterns. We show that 1.9 % of the microbial composition variance across both environments could be attributed to the presence of WT P. inhibens, and especially genera of the Bacteriodetes were increased by the presence of the TDA producer. Moreover, network analysis with inferred putative microbial interactions revealed that P. inhibens mainly displayed strong positive associations with genera of the Flavobacteriaceae and Alteromonadaceae, and that P. inhibens acts as a keystone OTU in the biofilm exclusively due to its potential to produce TDA. Our results demonstrate the potential impact of microbial secondary metabolites on microbial interactions and assembly dynamics of complex microbial communities.
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Affiliation(s)
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae. mSphere 2023; 8:e0051722. [PMID: 36622251 PMCID: PMC9942592 DOI: 10.1128/msphere.00517-22] [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] [Indexed: 01/10/2023] Open
Abstract
In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.
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Louvado A, Castro C, Silva DAM, Oliveira V, Conceição LEC, Cleary DFR, Gomes NCM. Assessing the Effects of Rotifer Feed Enrichments on Turbot ( Scophthalmus maximus) Larvae and Post-Larvae Gut-Associated Bacterial Communities. Microorganisms 2023; 11:microorganisms11020520. [PMID: 36838485 PMCID: PMC9962078 DOI: 10.3390/microorganisms11020520] [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: 01/19/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Live feed enrichments are often used in fish larvicultures as an optimized source of essential nutrients to improve larval growth and survival. In addition to this, they may also play an important role in structuring larval-associated microbial communities and may help improve their resistance to diseases. However, there is limited information available on how larval microbial communities and larviculture water are influenced by different live feed enrichments. In the present study, we investigated the effects of two commercial rotifer enrichments (ER) on turbot (Scophthalmus maximus) larval and post-larval gut-associated bacterial communities during larviculture production. We evaluated their effects on bacterial populations related to known pathogens and beneficial bacteria and their potential influence on the composition of bacterioplankton communities during larval rearing. High-throughput 16S rRNA gene sequencing was used to assess the effects of different rotifer enrichments (ER1 and ER2) on the structural diversity of bacterial communities of the whole turbot larvae 10 days after hatching (DAH), the post-larval gut 30 DAH, and the larviculture water. Our results showed that different rotifer feed enrichments were associated with significant differences in bacterial composition of turbot larvae 10 DAH, but not with the composition of larval gut communities 30 DAH or bacterioplankton communities 10 and 30 DAH. However, a more in-depth taxonomic analysis showed that there were significant differences in the abundance of Vibrionales in both 10 DAH larvae and in the 30 DAH post-larval gut fed different RE diets. Interestingly, the ER1 diet had a higher relative abundance of specific amplicon sequence variants (ASVs) related to potential Vibrio-antagonists belonging to the Roseobacter clade (e.g., Phaeobacter and Ruegeria at 10 DAH and Sulfitobacter at 30 DAH). In line with this, the diet was also associated with a lower relative abundance of Vibrio and a lower mortality. These results suggest that rotifer diets can affect colonization by Vibrio members in the guts of post-larval turbot. Overall, this study indicates that live feed enrichments can have modulatory effects on fish bacterial communities during the early stages of development, which includes the relative abundances of pathogenic and antagonist taxa in larviculture systems.
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Affiliation(s)
- Antonio Louvado
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carolina Castro
- Flatlantic—Actividades Piscícolas, SA 3070-732 Praia de Mira, Portugal
| | - Davide A. M. Silva
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Daniel F. R. Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Newton C. M. Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence:
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Du Y, Xu W, Wu T, Li H, Hu X, Chen J. Enhancement of growth, survival, immunity and disease resistance in Litopenaeus vannamei, by the probiotic, Lactobacillus plantarum Ep-M17. FISH & SHELLFISH IMMUNOLOGY 2022; 129:36-51. [PMID: 36041627 DOI: 10.1016/j.fsi.2022.08.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Green ecological prevention and control technology is a hot spot for aquatic disease research in recent years, and lactic acid bacteria is an important type of probiotic widely used in aquaculture. In this study, a strain of Lactobacillus plantarum Ep-M17 was isolated from the intestine of healthy grouper, which showed good antibacterial activity in vitro. To investigate the application prospects of Ep-M17 as a probiotic, we added it to the diet and fed Litopenaeus vannamei, and then detected its influence on the growth performance, survival rate, disease resistance, intestinal tissue structure, gene transcription, and the flora in the gut of shrimp. The results showed that feeding Ep-M17 increased the specific growth rate, reduced the feed conversion rate, improved the survival rate, and achieved a 76.9% relative protection rate after Vibrio parahaemolyticus E1 infection in shrimp. Histological examination displayed that Ep-M17-fed shrimp had a thick intestinal villi layer, which enhanced the protection against pathogen damage. It was also found that Ep-M17 significantly increased the activity levels of immune and digestion-related enzymes SOD, CAT, TRY, AKP, LIP, and AMS in the gut of shrimp, especially after V. parahaemolyticus E1 infection, these enzymes increased significantly higher than that of control. Transcriptome analysis revealed that Ep-M17 activated significantly differential expression of genes in immune, nutritional, metabolic, and Signal Transduction-related pathways in the gut of shrimp. In addition, Ep-M17 enriched the bacterial diversity of the shrimp gut, with a significant increase in many low-abundance bacterial species, a significant decrease in the number of pathogenic bacteria like Vibrio, and a significant increase in the number of beneficial bacteria. The above results evaluated that Ep-M17 as a potential probiotic can promote the growth and improve the disease resistance of shrimp by regulating the nutritional immune response and flora of the intestine.
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Affiliation(s)
- Yang Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Wenlong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Ting Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Hao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Xiaoman Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China.
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Kim SK, Song J, Rajeev M, Kim SK, Kang I, Jang IK, Cho JC. Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp ( Litopenaeus vannamei) aquaculture system. Front Microbiol 2022; 13:995699. [PMID: 36204630 PMCID: PMC9531771 DOI: 10.3389/fmicb.2022.995699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented. In this study, the Pacific white shrimp, Litopenaeus vannamei was cultivated in a greenhouse-enclosed BFT system. Rearing water samples were collected on a weekly basis for 5 months (152 days) and water quality variables such as physicochemical parameters and inorganic nutrients were monitored. In parallel, 16S rRNA gene pyrosequencing was employed to investigate the temporal patterns of rearing-water microbiota. The productivity, survival rate, and feed conversion ratio were 3.2-4.4 kg/m3, 74%-89%, and 1.2-1.3, respectively, representing successful super-intensive cultures. The metataxonomic results indicated a highly dynamic bacterioplankton community, with two major shifts over the culture. Members of the phylum Planctomycetes dominated in rearing water during the early stages, while Actinobacteria dominated during the middle stages, and Chloroflexi and TM7 dominated during the late stages of culture. The bacterioplankton community fluctuated more in the beginning but stabilized as the culture progressed. Intriguingly, we observed that certain bacterioplankton groups dominated in a culture-stage-specific manner; these groups include Rhodobacteraceae, Flavobacteriaceae, Actinobacteria, and Chloroflexi, which either contribute to water quality regulation or possess probiotic potential. Altogether, our results indicate that an operationally successful BFT-based aquaculture system favors the growth and dynamics of specific microbial communities in rearing water. Our study expands the scientific understanding of the practical utilization of microbes in sustainable aquaculture. A thorough understanding of rearing-water microbiota and factors influencing their dynamics will help to establish effective management strategies.
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Affiliation(s)
- Su-Kyoung Kim
- West Sea Mariculture Research Center, National Institute of Fisheries Science, Taean, South Korea
| | - Jaeho Song
- Division of Microbiology, Honam National Institute of Biological Resources, Mokpo, South Korea
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Meora Rajeev
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Su Kyoung Kim
- West Sea Mariculture Research Center, National Institute of Fisheries Science, Taean, South Korea
| | - Ilnam Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - In-Kwon Jang
- West Sea Mariculture Research Center, National Institute of Fisheries Science, Taean, South Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
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Xiao L, Chen Z, Yang Y, Liu Z. Growth promotion of Chlorella by symbiotic bacteria under adverse environments. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Onohuean H, Agwu E, Nwodo UU. A Global Perspective of Vibrio Species and Associated Diseases: Three-Decade Meta-Synthesis of Research Advancement. ENVIRONMENTAL HEALTH INSIGHTS 2022; 16:11786302221099406. [PMID: 35601189 PMCID: PMC9121474 DOI: 10.1177/11786302221099406] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/21/2022] [Indexed: 06/06/2023]
Abstract
Outbreaks of Vibrio infections have a long history of global public health concern and threat to the aquaculture industry. This 3-decade (1990-2019) meta-synthesis of global research progress in Vibrio species and associated disease outbreaks was undertaken to generate the knowledge needed to design effective interventions with policy implications. Using PRISMA protocol, we obtained data on the online version of the Institute for Scientific Information (ISI), Web of Science (WOS), and Scopus from January 1990 to September 2021 by title search of the keywords "Vibrio species OR Vibrio spp. OR vibriosis." On the 3-decade survey, the result has shown that a total of 776 publications document types were published on the subject, with an average of 24.25 ± 13.6 published documents per year with an annual growth rate of 4.71%. The year 2020 recorded the highest output of 52 published documents accounting for 6.70% of the total. The most prolific author, Blanch A., published 12 articles on the subject and has received citations of 1003 with an h-index of 10. While the most global cited paper author is the journal of J. Bacteriol (Bassler et al), receiving total citation (TC) (550) and per Year (22). The top active corresponding authors country is the United States of America with (92) articles, freq. 12.40%; TC of 3103. The observations in this study, such as the collaborations network map, and index, which have outlined a big difference between countries based on economic status, have underscored the need for a sustained research mentorship program that can define future policies.
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Affiliation(s)
- Hope Onohuean
- Biopharmaceutics Unit, Department of
Pharmacology and Toxicology, School of Pharmacy, Kampala International University,
Western Campus, Uganda
- Biomolecules, Metagenomics, Endocrine,
and Tropical Diseases Research Group (BMETDREG), Kampala International University,
Western Campus, Ishaka-Bushenyi, Uganda
| | - Ezera Agwu
- Biomolecules, Metagenomics, Endocrine,
and Tropical Diseases Research Group (BMETDREG), Kampala International University,
Western Campus, Ishaka-Bushenyi, Uganda
- Department of Microbiology and
Immunology, Kampala International University, Western Campus, Ishaka, Bushenyi,
Kampala, Uganda
| | - UU Nwodo
- SA-MRC Microbial Water Quality
Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology
Research Group (AEMREG), Department of Biochemistry and Microbiology, University of
Fort Hare, Alice, Eastern Cape, South Africa
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19
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Huang L, Guo H, Liu Z, Chen C, Wang K, Huang X, Chen W, Zhu Y, Yan M, Zhang D. Contrasting patterns of bacterial communities in the rearing water and gut of Penaeus vannamei in response to exogenous glucose addition. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:222-236. [PMID: 37073217 PMCID: PMC10077327 DOI: 10.1007/s42995-021-00124-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/18/2021] [Indexed: 05/03/2023]
Abstract
Supplementing exogenous carbon sources is a practical approach to improving shrimp health by manipulating the microbial communities of aquaculture systems. However, little is known about the microbiological processes and mechanisms of these systems. Here, the effects of glucose addition on shrimp growth performance and bacterial communities of the rearing water and the shrimp gut were investigated to address this knowledge gap. The results showed that glucose addition significantly improved the growth and survival of shrimp. Although the α-diversity indices of both bacterioplankton communities and gut microbiota were significantly decreased by adding glucose, both bacterial communities exhibited divergent response patterns to glucose addition. Glucose addition induced a dispersive bacterioplankton community but a more stable gut bacterial community. Bacterial taxa belonging to Ruegeria were significantly enriched by glucose in the guts, especially the operational taxonomic unit 2575 (OTU2575), which showed the highest relative importance to the survival rate and individual weight of shrimp, with the values of 43.8 and 40.6%, respectively. In addition, glucose addition increased the complexity of interspecies interactions within gut bacterial communities and the network nodes from Rhodobacteraceae accounted for higher proportions and linked more with the nodes from other taxa in the glucose addition group than that in control. These findings suggest that glucose addition may provide a more stable gut microbiota for shrimp by increasing the abundance of certain bacterial taxa, such as Ruegeria. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00124-9.
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Affiliation(s)
- Lei Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
- Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001 China
| | - Haipeng Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Zidan Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Chen Chen
- Zhejiang Mariculture Research Institute, Wenzhou, 325005 China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Xiaolin Huang
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
- Zhejiang Mariculture Research Institute, Wenzhou, 325005 China
| | - Wei Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Yueyue Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Mengchen Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
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20
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Bacterial controlled mitigation of dysbiosis in a seaweed disease. THE ISME JOURNAL 2022; 16:378-387. [PMID: 34341505 PMCID: PMC8776837 DOI: 10.1038/s41396-021-01070-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023]
Abstract
Disease in the marine environment is predicted to increase with anthropogenic stressors and already affects major habitat-formers, such as corals and seaweeds. Solutions to address this issue are urgently needed. The seaweed Delisea pulchra is prone to a bleaching disease, which is caused by opportunistic pathogens and involves bacterial dysbiosis. Bacteria that can inhibit these pathogens and/or counteract dysbiosis are therefore hypothesised to reduce disease. This study aimed to identify such disease-protective bacteria and investigate their protective action. One strain, Phaeobacter sp. BS52, isolated from healthy D. pulchra, was antagonistic towards bleaching pathogens and significantly increased the proportion of healthy individuals when applied before the pathogen challenge (pathogen-only vs. BS52 + pathogen: 41-80%), and to a level similar to the control. However, no significant negative correlations between the relative abundances of pathogens and BS52 on D. pulchra were detected. Instead, inoculation of BS52 mitigated pathogen-induced changes in the epibacterial community. These observations suggest that the protective activity of BS52 was due to its ability to prevent dysbiosis, rather than direct pathogen inhibition. This study demonstrates the feasibility of manipulating bacterial communities in seaweeds to reduce disease and that mitigation of dysbiosis can have positive health outcomes.
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21
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Roseobacter group probiotics exhibit differential killing of fish pathogenic Tenacibaculum species. Appl Environ Microbiol 2022; 88:e0241821. [PMID: 35080904 DOI: 10.1128/aem.02418-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fish pathogenic bacteria of the Tenacibaculum genus are a serious emerging concern in modern aquaculture, causing tenacibaculosis in a broad selection of cultured finfish. Data describing their virulence mechanisms are scarce and few means, antibiotic treatment aside, are available to control their proliferation in aquaculture systems. We genome sequenced a collection of 19 putative Tenacibaculum isolates from outbreaks at two aquaculture facilities and tested their susceptibility to treatment with tropodithietic acid (TDA)-producing Roseobacter group probiotics. We found that local outbreaks of Tenacibaculum can involve heterogeneous assemblages of species and strains with the capacity to produce multiple different virulence factors related to host invasion and infection. The probiotic Phaeobacter piscinae S26 proved efficient in killing pathogenic Tenacibaculum species such as T. maritimum, T. soleae, and some T. discolor strains. However, the T. mesophilum and T. gallaicum species exhibit natural tolerance towards TDA and are hence not likely to be easily killed by TDA-producing probiotics. Tolerance towards TDA in Tenacibaculum is likely involving multiple inherent physiological features pertaining to electron and proton transport, iron sequestration, and potentially also drug efflux mechanisms, as genetic determinants encoding such features were significantly associated with TDA tolerance. Collectively, our results support the use of TDA-producers to prevent tenacibaculosis, however, their efficacy is likely limited to some Tenacibaculum species. Importance A productive and sustainable aquaculture sector is needed to meet the UN sustainable development goals (SDGs) and supply the growing world population with high-protein food sources. A sustainable way to prevent disease outbreaks in the industry is the application of probiotic bacteria that can antagonize fish pathogens in the aquaculture systems. TDA-producing Roseobacter group probiotics have proven efficient in killing important vibrio pathogens and protecting fish larvae against infection, yet their efficacy against different fish pathogenic species of the Tenacibaculum genus has not been explored. Therefore, we tested the efficacy of such potential probiotics against a collection of different Tenacibaculum isolates and found the probiotic to efficiently kill a subset of relevant strains and species, supporting their use as sustainable disease control measure in aquaculture.
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22
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Henriksen NNSE, Lindqvist LL, Wibowo M, Sonnenschein EC, Bentzon-Tilia M, Gram L. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517774. [PMID: 35099011 PMCID: PMC9075582 DOI: 10.1093/femsre/fuac007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several of these metabolites also possess nonantimicrobial functions, both influencing the physiology of the producer and their ecological neighbors. An example of a versatile bacterial secondary metabolite with multiple functions is the tropone derivative tropodithietic acid (TDA). TDA is a broad-spectrum antimicrobial compound produced by several members of the Rhodobacteraceae family, a major marine bacterial lineage, within the genera Phaeobacter, Tritonibacter, and Pseudovibrio. The production of TDA is governed by the mode of growth and influenced by the availability of nutrient sources. The antibacterial effect of TDA is caused by disruption of the proton motive force of target microorganisms and, potentially, by its iron-chelating properties. TDA also acts as a signaling molecule, affecting gene expression in other bacteria, and altering phenotypic traits such as motility, biofilm formation, and antibiotic production in the producer. In microbial communities, TDA-producing bacteria cause a reduction of the relative abundance of closely related species and some fast-growing heterotrophic bacteria. Here, we summarize the current understanding of the chemical ecology of TDA, including the environmental niches of TDA-producing bacteria, and the molecular mechanisms governing the function and regulation of TDA.
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Affiliation(s)
| | | | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Lone Gram
- Corresponding author: Department of Bioechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark. Tel: +45 23688295; E-mail:
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23
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Toplak M, Teufel R. Three Rings to Rule Them All: How Versatile Flavoenzymes Orchestrate the Structural Diversification of Natural Products. Biochemistry 2021; 61:47-56. [PMID: 34962769 PMCID: PMC8772269 DOI: 10.1021/acs.biochem.1c00763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The structural diversification
of natural products is instrumental
to their versatile bioactivities. In this context, redox tailoring
enzymes are commonly involved in the modification and functionalization
of advanced pathway intermediates en route to the mature natural products.
In recent years, flavoprotein monooxygenases have been shown to mediate
numerous redox tailoring reactions that include not only (aromatic)
hydroxylation, Baeyer–Villiger oxidation, or epoxidation reactions
but also oxygenations that are coupled to extensive remodeling of
the carbon backbone, which are often central to the installment of
the respective pharmacophores. In this Perspective, we will highlight
recent developments and discoveries in the field of flavoenzyme catalysis
in bacterial natural product biosynthesis and illustrate how the flavin
cofactor can be fine-tuned to enable chemo-, regio-, and stereospecific
oxygenations via distinct flavin-C4a-peroxide and flavin-N5-(per)oxide
species. Open questions remain, e.g., regarding the breadth of chemical
reactions enabled particularly by the newly discovered flavin-N5-oxygen
adducts and the role of the protein environment in steering such cascade-like
reactions. Outstanding cases involving different flavin oxygenating
species will be exemplified by the tailoring of bacterial aromatic
polyketides, including enterocin, rubromycins, rishirilides, mithramycin,
anthracyclins, chartreusin, jadomycin, and xantholipin. In addition,
the biosynthesis of tropone natural products, including tropolone
and tropodithietic acid, will be presented, which features a recently
described prototypical flavoprotein dioxygenase that may combine flavin-N5-peroxide
and flavin-N5-oxide chemistry. Finally, structural and mechanistic
features of selected enzymes will be discussed as well as hurdles
for their application in the formation of natural product derivatives
via bioengineering.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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24
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Zhang YT, Chen H, He S, Wang F, Liu Y, Chen M, Yao G, Huang Y, Chen R, Xie L, Mu J. Subchronic toxicity of dietary sulfamethazine and nanoplastics in marine medaka (Oryzias melastigma): Insights from the gut microbiota and intestinal oxidative status. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 226:112820. [PMID: 34571422 DOI: 10.1016/j.ecoenv.2021.112820] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/06/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Antibiotics and nanoplastics are two prevalent pollutants in oceans, posing a great threat to marine ecosystems. As antibiotics and nanoplastics are highly bioconcentrated in lower trophic levels, evaluating their impacts on marine organisms via dietary exposure route is of great importance. In this study, the individual and joint effects of dietborne sulfamethazine (SMZ) and nanoplastic fragments (polystyrene, PS) in marine medaka (Oryzias melastigma) were investigated. After 30 days of dietary exposure, 4.62 mg/g SMZ decreased the Chao1 index (60.86% for females and 26.85% for males) and the Shannon index (68.95% for females and 65.05% for males) and significantly altered the structure of gut microbial communities in both sexes. The female fish exposed to 4.62 mg/g SMZ exhibited higher intestinal sod (43.5%), cat (38.5%) and gpx (39.6%) transcripts, indicating oxidative stress in the gut. PS alone at 3.45 mg/g slightly altered the composition of the gut microbiota. Interestingly, the mixture of SMZ and PS caused more modest effects on the gut microbiota and intestinal antioxidant physiology than the SMZ alone, suggesting that the presence of PS might alleviate the intestinal toxicity of SMZ in a scenario of dietary co-exposure. This study helps better understand the risk of antibiotics and nanoplastics to marine ecosystems.
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Affiliation(s)
- Yu Ting Zhang
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Hongxing Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Shuiqing He
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Feipeng Wang
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Yawen Liu
- State Key Laboratory of Marine Environmental Science, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Mengyun Chen
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Guangshan Yao
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Yaling Huang
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Ruanni Chen
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Lingtian Xie
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| | - Jingli Mu
- Fujian Key Laboratory of Functional Marine Sensing Materials, Institute of Oceanography, Minjiang University, Fuzhou 350108, China.
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25
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Pettersen JP, Gundersen MS, Almaas E. Robust bacterial co-occurence community structures are independent of r- and K-selection history. Sci Rep 2021; 11:23497. [PMID: 34873246 PMCID: PMC8648916 DOI: 10.1038/s41598-021-03018-z] [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: 08/04/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022] Open
Abstract
Selection for bacteria which are K-strategists instead of r-strategists has been shown to improve fish health and survival in aquaculture. We considered an experiment where microcosms were inoculated with natural seawater and the selection regime was switched from K-selection (by continuous feeding) to r-selection (by pulse feeding) and vice versa. We found the networks of significant co-occurrences to contain clusters of taxonomically related bacteria having positive associations. Comparing this with the time dynamics, we found that the clusters most likely were results of similar niche preferences of the involved bacteria. In particular, the distinction between r- or K-strategists was evident. Each selection regime seemed to give rise to a specific pattern, to which the community converges regardless of its prehistory. Furthermore, the results proved robust to parameter choices in the analysis, such as the filtering threshold, level of random noise, replacing absolute abundances with relative abundances, and the choice of similarity measure. Even though our data and approaches cannot directly predict ecological interactions, our approach provides insights on how the selection regime affects the composition of the microbial community, providing a basis for aquaculture experiments targeted at eliminating opportunistic fish pathogens.
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Affiliation(s)
- Jakob Peder Pettersen
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Madeleine S Gundersen
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.
- Department of Public Health and General Practice, K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.
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26
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Biosynthesis of Ditropolonyl Sulfide, an Antibacterial Compound Produced by Burkholderia cepacia Complex Strain R-12632. Appl Environ Microbiol 2021; 87:e0116921. [PMID: 34524894 DOI: 10.1128/aem.01169-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Burkholderia cepacia complex strain R-12632 produces ditropolonyl sulfide, an unusual sulfur-containing tropone, via a yet-unknown biosynthetic pathway. Ditropolonyl sulfide purified from a culture of strain R-12632 inhibits the growth of various Gram-positive and Gram-negative resistant bacteria, with MIC values as low as 16 μg/ml. In the present study, we used a transposon mutagenesis approach combined with metabolite analyses to identify the genetic basis for antibacterial activity of strain R-12632 against Gram-negative bacterial pathogens. Fifteen of the 8304 transposon mutants investigated completely lost antibacterial activity against Klebsiella pneumoniae LMG 2095. In these loss-of-activity mutants, nine genes were interrupted. Four of those genes were involved in assimilatory sulfate reduction, two were involved in phenylacetic acid (PAA) catabolism, and one was involved in glutathione metabolism. Via semipreparative fractionation and metabolite identification, it was confirmed that inactivation of the PAA degradation pathway or glutathione metabolism led to loss of ditropolonyl sulfide production. Based on earlier studies on the biosynthesis of tropolone compounds, the requirement for a functional PAA catabolic pathway for antibacterial activity in strain R-12632 indicated that this pathway likely provides the tropolone backbone for ditropolonyl sulfide. Loss of activity observed in mutants defective in assimilatory sulfate reduction and glutathione biosynthesis suggested that cysteine and glutathione are potential sources of the sulfur atom linking the two tropolone moieties. The demonstrated antibacterial activity of the unusual antibacterial compound ditropolonyl sulfide warrants further studies into its biosynthesis and biological role. IMPORTANCE Burkholderia bacteria are historically known for their biocontrol properties and have been proposed as a promising and underexplored source of bioactive specialized metabolites. Burkholderia cepacia complex strain R-12632 inhibits various Gram-positive and Gram-negative resistant pathogens and produces numerous specialized metabolites, among which is ditropolonyl sulfide. This unusual antimicrobial has been poorly studied and its biosynthetic pathway remains unknown. In the present study, we performed transposon mutagenesis of strain R-12632 and performed genome and metabolite analyses of loss-of-activity mutants to study the genetic basis for antibacterial activity. Our results indicate that phenylacetic acid catabolism, assimilatory sulfate reduction, and glutathione metabolism are necessary for ditropolonyl sulfide production. These findings contribute to understanding of the biosynthesis and biological role of this unusual antimicrobial.
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27
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Wang R, Gallant É, Wilson MZ, Wu Y, Li A, Gitai Z, Seyedsayamdost MR. Algal p-coumaric acid induces oxidative stress and siderophore biosynthesis in the bacterial symbiont Phaeobacter inhibens. Cell Chem Biol 2021; 29:670-679.e5. [PMID: 34437838 DOI: 10.1016/j.chembiol.2021.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/18/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
Abstract
The marine alpha-proteobacterium Phaeobacter inhibens engages in intermittent symbioses with microalgae. The symbiosis is biphasic and concludes in a parasitic phase, during which the bacteria release algaecidal metabolites in response to algal p-coumaric acid (pCA). The cell-wide effects of pCA on P. inhibens remain unknown. Herein, we report a microarray-based transcriptomic study and find that genes related to the oxidative stress response and secondary metabolism are upregulated most, while those associated with energy production and motility are downregulated in the presence of pCA. Among genes upregulated is a previously unannotated biosynthetic gene cluster and, using a combination of gene deletions and metabolic profiling, we show that it gives rise to an unreported siderophore, roseobactin. The simultaneous production of algaecides and roseobactin in the parasitic phase allows the bacteria to take up any iron that is released from dying algal cells, thereby securing a limited micronutrient.
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Affiliation(s)
- Rurun Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Étienne Gallant
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihan Wu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Anran Li
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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28
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Genomic evolution of the marine bacterium Phaeobacter inhibens during biofilm growth. Appl Environ Microbiol 2021; 87:e0076921. [PMID: 34288701 DOI: 10.1128/aem.00769-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
P. inhibens 2.10 is an effective biofilm former on marine surfaces and has the ability to outcompete other microorganisms, possibly due to the production of the plasmid-encoded, secondary metabolite tropodithietic acid (TDA). P. inhibens 2.10 biofilms produce phenotypic variants with reduced competitiveness compared to the wild-type. In the present study, we used longitudinal, genome-wide deep sequencing to uncover the genetic foundation that contributes to the emergent phenotypic diversity in P. inhibens 2.10 biofilm dispersants. Our results show that phenotypic variation is not due to the loss of plasmid that encodes the genes for the TDA synthesis, but instead show that P. inhibens 2.10 biofilm populations become rapidly enriched in single nucleotide variations in genes involved in the synthesis of TDA. While variants in genes previously linked to other phenotypes, such as lipopolysaccharide production (i.e. rfbA) and celluar persistence (i.e. metG), also appear to be selected for during biofilm dispersal, the number and consistency of variations found for genes involved in TDA production suggest that this metabolite imposes a burden for P. inhibens 2.10 cells. Our results indicate a strong selection pressure for the loss of TDA in mono-species biofilm populations and provide insight into how competition (or lack thereof) in biofilms might shape genome evolution in bacteria. Importance Statement Biofilm formation and dispersal are important survival strategies for environmental bacteria. During biofilm dispersal cells often display stable and heritable variants from the parental biofilm. Phaeobacter inhibens is an effective colonizer of marine surfaces, in which a subpopulation of its biofilm dispersal cells displays a non-competitive phenotype. This study aimed to elucidate the genetic basis of these phenotypic changes. Despite the progress made to date in characterizing the dispersal variants in P. inhibens, little is understood about the underlying genetic changes that result in the development of the specific variants. Here, P. inhibens phenotypic variation was linked to single nucleotide polymorphisms (SNPs), in particular in genes affecting the competitive ability of P. inhibens, including genes related to the production of the antibiotic tropodithietic acid (TDA) and bacterial cell-cell communication (e.g. quorum sensing). This work is significant as it reveals how the biofilm-lifestyle might shape genome evolution in a cosmopolitan bacterium.
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Effects of three probiotic strains (Bacillus coagulans, B. licheniformis and Paenibacillus polymyxa) on growth, immune response, gut morphology and microbiota, and resistance against Vibrio harveyi of northern whitings, Sillago sihama Forsskál (1775). Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.114958] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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The microbial profile of a tissue necrosis affecting the Atlantic invasive coral Tubastraea tagusensis. Sci Rep 2021; 11:9828. [PMID: 33972618 PMCID: PMC8110780 DOI: 10.1038/s41598-021-89296-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/22/2021] [Indexed: 02/03/2023] Open
Abstract
The Southwestern Atlantic rocky reef ecosystems are undergoing significant changes due to sun-corals (Tubastraea tagusensis and T. coccinea) invasion. At Búzios Island, on the northern coast of São Paulo State, where the abundance of T. tagusensis is particularly high, some colonies are displaying tissue necrosis, a phenomenon never reported for this invasive nor any other azooxanthellate coral species. Using next-generation sequencing, we sought to understand the relationship between T. tagusensis tissue necrosis and its microbiota. Thus, through amplicon sequencing, we studied both healthy and diseased coral colonies. Results indicate a wide variety of bacteria associated with healthy colonies and an even higher diversity associated with those corals presenting tissue necrosis, which displayed nearly 25% more microorganisms. Also, as the microbial community associated with the seven healthy colonies did not alter composition significantly, it was possible to verify the microbial succession during different stages of tissue necrosis (i.e., initial, intermediate, and advanced). Comparing the microbiome from healthy corals to those in early tissue necrosis suggests 21 potential pathogens, which might act as the promoters of such disease.
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The Roseobacter-Group Bacterium Phaeobacter as a Safe Probiotic Solution for Aquaculture. Appl Environ Microbiol 2021; 87:e0258120. [PMID: 33310713 DOI: 10.1128/aem.02581-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phaeobacter inhibens has been assessed as a probiotic bacterium for application in aquaculture. Studies addressing the efficacy and safety indicate that P. inhibens maintains its antagonistic activity against pathogenic vibrios in aquaculture live cultures (live feed and fish egg/larvae) while having no or a positive effect on the host organisms and a minor impact on the host microbiomes. While P. inhibens produces antibacterial and algicidal compounds, no study has so far found a virulent phenotype of P. inhibens cells against higher organisms. Additionally, an in silico search for antibiotic resistance genes using published genomes of representative strains did not raise concerns regarding the risk for antimicrobial resistance. P. inhibens occurs naturally in aquaculture systems, supporting its safe usage in this environment. In conclusion, at the current state of knowledge, P. inhibens is a "safe-to-use" organism.
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Turgay E, Steinum TM, Eryalçın KM, Yardımcı RE, Karataş S. The influence of diet on the microbiota of live-feed rotifers (Brachionus plicatilis) used in commercial fish larviculture. FEMS Microbiol Lett 2021; 367:5719568. [PMID: 32005987 DOI: 10.1093/femsle/fnaa020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
Live-feed is indispensable to commercial fish larviculture. However, high bacterial loads in rotifers could pose a biosecurity risk. While this may be true, live-feed associated bacteria could also be beneficial to fish larvae through improved feed utilization or pathogen inhibition following host microbiota modification. The study objective was to elucidate the largely unexplored microbiota of rotifers propagated on five different diets through bacterial community profiling by 16S rRNA gene amplicon sequencing. Investigated rotifer samples had a median observed alpha-diversity of 338 ± 87 bacterial species. Alpha- and Gamma-Proteobacteria dominated the rotifer microbiota followed by members of classes Flavobacteriia, Cytophagia, Mollicutes, Phycisphaerae and Bacteroidia. Different diets significantly altered the bacterial communities associated with rotifers according to PERMANOVA test results and beta dispersion calculations. A common core rotifer microbiome included 31 bacterial species present in relative abundances over 0.01%. We discuss the functional role of some microbiome members. Our data suggested the presence of several known fish pathogens in stock rotifers. However, we found no evidence for increased loads of these presumptive taxa in propagated live-feed rotifers during this field trial.
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Affiliation(s)
- Emre Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Terje Marken Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Kamil Mert Eryalçın
- Fish Nutrition & Phytoplankton-Zooplankton Culture Laboratory, Aquaculture Department, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Remziye Eda Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Süheyla Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
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Isolation of Phaeobacter sp. from Larvae of Atlantic Bonito ( Sarda sarda) in a Mesocosmos Unit, and Its Use for the Rearing of European Seabass Larvae ( Dicentrarchus labrax L.). Microorganisms 2021; 9:microorganisms9010128. [PMID: 33429891 PMCID: PMC7827910 DOI: 10.3390/microorganisms9010128] [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: 11/26/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022] Open
Abstract
The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p < 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration stopped. In a small challenge experiment, seabass larvae from probiotic treatment showed increased survival (p < 0.05) after experimental infection with a mild pathogen (Vibrio harveyi). Overall, our results showed that the use of an indigenous probiotic strain had a beneficial impact on larval rearing in industry-like conditions.
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Clean-in-place disinfection of dual-species biofilm (Listeria and Pseudomonas) by a green antibacterial product made from citrus extract. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Liu B, Eltanahy EE, Liu H, Chua ET, Thomas-Hall SR, Wass TJ, Pan K, Schenk PM. Growth-promoting bacteria double eicosapentaenoic acid yield in microalgae. BIORESOURCE TECHNOLOGY 2020; 316:123916. [PMID: 32768998 DOI: 10.1016/j.biortech.2020.123916] [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: 06/28/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 05/26/2023]
Abstract
High-yielding microalgae present an important commodity to sustainably satisfy burgeoning food, feed and biofuel demands. Because algae-associated bacteria can significantly enhance or reduce yields, we isolated, identified and selected highly-effective "probiotic" bacterial strains associated with Nannochloropsis oceanica, a high-yielding microalga rich in eicosapentaenoic acid (EPA). Xenic algae growth was significantly enhanced by co-cultivation with ten isolated bacteria that improved culture density and biomass by 2.2- and 1.56-fold, respectively (1.39 × 108 cells mL-1; 0.82 g L-1). EPA contents increased up to 2.25-fold (to 39.68% of total fatty acids). Added probiotic bacteria possessed multiple growth-stimulating characteristics, including atmospheric nitrogen fixation, growth hormone production and phosphorous solubilization. Core N. oceanica-dominant bacterial microbiomes at different cultivation scales included Sphingobacteria, Flavobacteria (Bacteroidetes), and α, γ-Proteobacteria, and added probiotic bacteria could be maintained. We conclude that the supplementation with probiotic algae-associated bacteria can significantly enhance biomass and EPA production of N. oceanica.
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Affiliation(s)
- Bingli Liu
- Laboratory of Applied Microalgae Biology, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eladl E Eltanahy
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Phycology Laboratory, Botany Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales 2751, Australia
| | - Elvis T Chua
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Skye R Thomas-Hall
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Taylor J Wass
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kehou Pan
- Laboratory of Applied Microalgae Biology, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Peer M Schenk
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
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Duan Y, Petzold M, Saleem‐Batcha R, Teufel R. Bacterial Tropone Natural Products and Derivatives: Overview of their Biosynthesis, Bioactivities, Ecological Role and Biotechnological Potential. Chembiochem 2020; 21:2384-2407. [PMID: 32239689 PMCID: PMC7497051 DOI: 10.1002/cbic.201900786] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/02/2020] [Indexed: 12/05/2022]
Abstract
Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.
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Affiliation(s)
- Ying Duan
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Melanie Petzold
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | | | - Robin Teufel
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
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Lai KP, Lin X, Tam N, Ho JCH, Wong MKS, Gu J, Chan TF, Tse WKF. Osmotic stress induces gut microbiota community shift in fish. Environ Microbiol 2020; 22:3784-3802. [PMID: 32618094 DOI: 10.1111/1462-2920.15150] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.
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Affiliation(s)
- Keng Po Lai
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, 541004, China.,Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Xiao Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nathan Tam
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Jeff Cheuk Hin Ho
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Marty Kwok-Shing Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8564, Japan
| | - Jie Gu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Ting Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - William Ka Fai Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
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Wang Y, Wang K, Huang L, Dong P, Wang S, Chen H, Lu Z, Hou D, Zhang D. Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle. MICROBIOME 2020; 8:106. [PMID: 32620132 PMCID: PMC7334860 DOI: 10.1186/s40168-020-00879-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/08/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice. RESULTS Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery. CONCLUSIONS Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.
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Affiliation(s)
- Yanting Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Lei Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Pengsheng Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Sipeng Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Heping Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211 China
| | - Zheng Lu
- Huzhou Southern Taihu Lake Agricultural Biotechnology Institute, Huzhou, 313000 China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211 China
- School of Marine Sciences, Ningbo University, Ningbo, 315211 China
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Changes in the Microbiome of Mariculture Feed Organisms after Treatment with a Potentially Probiotic Strain of Phaeobacter inhibens. Appl Environ Microbiol 2020; 86:AEM.00499-20. [PMID: 32385083 DOI: 10.1128/aem.00499-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/03/2020] [Indexed: 01/04/2023] Open
Abstract
The Phaeobacter genus has been explored as probiotics in mariculture as a sustainable strategy for the prevention of bacterial infections. Its antagonistic effect against common fish pathogens is predominantly due to the production of the antibacterial compound tropodithietic acid (TDA), and TDA-producing strains have repeatedly been isolated from mariculture environments. Despite many in vitro trials targeting pathogens, little is known about its impact on host-associated microbiomes in mariculture. Hence, the purpose of this study was to investigate how the addition of a TDA-producing Phaeobacter inhibens strain affects the microbiomes of live feed organisms and fish larvae. We used 16S rRNA gene sequencing to characterize the bacterial diversity associated with live feed microalgae (Tetraselmis suecica), live feed copepod nauplii (Acartia tonsa), and turbot (Scophthalmus maximus) eggs/larvae. The microbial communities were unique to the three organisms investigated, and the addition of the probiotic bacterium had various effects on the diversity and richness of the microbiomes. The structure of the live feed microbiomes was significantly changed, while no effect was seen on the community structure associated with turbot larvae. The changes were seen primarily in particular taxa. The Rhodobacterales order was indigenous to all three microbiomes and decreased in relative abundance when P. inhibens was introduced in the copepod and turbot microbiomes, while it was unaffected in the microalgal microbiome. Altogether, the study demonstrates that the addition of P. inhibens in higher concentrations, as part of a probiotic regime, does not appear to cause major imbalances in the microbiome, but the effects were specific to closely related taxa.IMPORTANCE This work is an essential part of the risk assessment of the application of roseobacters as probiotics in mariculture. It provides insights into the impact of TDA-producing Phaeobacter inhibens on the commensal bacteria related to mariculture live feed and fish larvae. Also, the study provides a sequencing-based characterization of the microbiomes related to mariculture-relevant microalga, copepods, and turbot larvae.
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Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint. Appl Environ Microbiol 2019; 85:AEM.02095-19. [PMID: 31604772 DOI: 10.1128/aem.02095-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 11/20/2022] Open
Abstract
Growth energetics and metabolic efficiency contribute to the lifestyle and habitat imprint of microorganisms. Roseobacters constitute one of the most abundant and successful marine bacterioplankton groups. Here, we reflect on the energetics and metabolic efficiency of Phaeobacter inhibens DSM 17395, a versatile heterotrophic roseobacter. Fourteen different substrates (five sugars and nine amino acids) and their degradation pathways were assessed for energetic efficiencies based on catabolic ATP yields, calculated from net formed ATP and reducing equivalents. The latter were converted into ATP by employing the most divergent coupling ratios (i.e., ions per ATP) currently known for F1Fo ATP synthases in heterotrophic bacteria. The catabolic ATP yields of the pathways studied in P. inhibens differed ∼3-fold. The actual free energy costs for ATP synthesis were estimated at 81.6 kJ per mol ATP (3.3 ions per ATP) or 104.2 kJ per mol ATP (4.3 ions per ATP), yielding an average thermodynamic efficiency of ∼37.7% or ∼29.5%, respectively. Growth performance (rates, yields) and carbon assimilation efficiency were determined for P. inhibens growing in process-controlled bioreactors with 10 different single substrates (Glc, Man, N-acetylglucosamine [Nag], Phe, Trp, His, Lys, Thr, Val, or Leu) and with 2 defined substrate mixtures. The efficiencies of carbon assimilation into biomass ranged from ∼28% to 61%, with His/Trp and Thr/Leu yielding the lowest and highest levels. These efficiencies correlated with catabolic and ATP yields only to some extent. Substrate-specific metabolic demands and/or functions, as well as the compositions of the substrate mixtures, apparently affected the energetic costs of growth. These include energetic burdens associated with, e.g., slow growth, stress, and/or the production of tropodithietic acid.IMPORTANCE Heterotrophic members of the bacterioplankton serve the marine ecosystem by transforming organic matter, an activity that is governed by the bacterial growth efficiencies (BGEs) obtained under given environmental conditions. In marine ecology, the concept of BGE refers to the carbon assimilation efficiency within natural communities. The marine bacterium studied here, Phaeobacter inhibens DSM 17395, is a copiotrophic representative of the globally abundant Roseobacter group, and the 15 catabolic pathways investigated are widespread among these marine heterotrophs. Combining pathway-specific catabolic ATP yields with in-depth quantitative physiological data could (i) provide a new baseline for the study of growth energetics and efficiency in further Roseobacter group members and other copiotrophic marine bacteria in productive coastal ecosystems and (ii) contribute to a better understanding of the factors controlling BGE (including the additional energetic burden arising from widespread secondary-metabolite formation) based on laboratory studies with pure cultures.
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Nappi J, Soldi E, Egan S. Diversity and Distribution of Bacteria Producing Known Secondary Metabolites. MICROBIAL ECOLOGY 2019; 78:885-894. [PMID: 31016338 DOI: 10.1007/s00248-019-01380-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
There is an increasing interest in the utilisation of marine bioactive compounds as novel biopharmaceuticals and agrichemicals; however, little is known about the environmental distribution for many of these molecules. Here, we aimed to elucidate the environmental distribution and to detect the biosynthetic gene clusters in environmental samples of four bioactive compounds, namely violacein, tropodithietic acid (TDA), tambjamine and the antibacterial protein AlpP. Our database analyses revealed high bacterial diversity for AlpP and violacein producers, while TDA-producing bacteria were mostly associated with marine surfaces and all belonged to the roseobacter group. In contrast, the tambjamine cluster was only found in the genomes of two Pseudoalteromonas species and in one terrestrial species belonging to the Cupriavidus genus. Using a PCR-based screen of different marine samples, we detected TDA and violacein genes associated with the microbiome of Ulva and Protohyale niger and tambjamine genes associated with Nodilittorina unifasciata; however, alpP was not detected. These results highlight the variable distribution of the genes encoding these four bioactive compounds, including their detection from the surface of multiple marine eukaryotic hosts. Determining the natural distribution of these gene clusters will help to understand the ecological importance of these metabolites and the bacteria that produce them.
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Affiliation(s)
- Jadranka Nappi
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia
| | - Erika Soldi
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia.
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Dittmann KK, Porsby CH, Goncalves P, Mateiu RV, Sonnenschein EC, Bentzon-Tilia M, Egan S, Gram L. Tropodithietic acid induces oxidative stress response, cell envelope biogenesis and iron uptake in Vibrio vulnificus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:581-588. [PMID: 31102321 DOI: 10.1111/1758-2229.12771] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
The Roseobacter group is a widespread marine bacterial group, of which some species produce the broad-spectrum antibiotic tropodithietic acid (TDA). A mode of action for TDA has previously been proposed in Escherichia coli, but little is known about its effect on non-producing marine bacteria at in situ concentrations. The purpose of this study was to investigate how a sub-lethal level of TDA affects Vibrio vulnificus at different time points (30 and 60 min) using a transcriptomic approach. Exposure to TDA for as little as 30 min resulted in the differential expression of genes associated with cell regeneration, including the up-regulation of those involved in biogenesis of the cell envelope. Defence mechanisms including oxidative stress defence proteins and iron uptake systems were also up-regulated in response to TDA, while motility-related genes were down-regulated. Gene expression data and scanning electron microscopy imaging revealed a switch to a biofilm phenotype in the presence of TDA. Our study shows that a low concentration of this antibiotic triggers a defence response to reactive oxygen species and iron depletion in V. vulnificus, which indicates that the mode of action of TDA is likely more complex in this bacterium than what is known for E. coli.
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Affiliation(s)
- Karen K Dittmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Randwick, NSW, 2052, Australia
| | - Cisse H Porsby
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Priscila Goncalves
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Randwick, NSW, 2052, Australia
| | - Ramona Valentina Mateiu
- Center for Electron Nanoscopy, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Suhelen Egan
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Randwick, NSW, 2052, Australia
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
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Dittmann KK, Sonnenschein EC, Egan S, Gram L, Bentzon-Tilia M. Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:401-413. [PMID: 30277320 DOI: 10.1111/1758-2229.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
Bacteria-host interactions are universal in nature and have significant effects on host functionality. Bacterial secondary metabolites are believed to play key roles in such interactions as well as in interactions within the host-associated microbial community. Hence, prominent secondary metabolite-producing bacteria may be strong drivers of microbial community composition in natural host-associated microbiomes. This has, however, not been rigorously tested, and the purpose of this study was to investigate how the secondary metabolite producer Phaeobacter inhibens affects the diversity and composition of microbiomes associated with the microalga Emiliania huxleyi and the European flat oyster, Ostrea edulis. Roseobacters were indigenous to both communities exhibiting relative abundances between 2.8% and 7.0%. Addition of P. inhibens caused substantial changes in the overall structure of the low-complexity microbiome of E. huxleyi, but did not shape microbial community structure to the same degree in the more complex oyster microbiomes. Species-specific interactions occurred in both microbiomes and specifically the abundances of other putative secondary metabolite-producers such as vibrios and pseudoalteromonads were reduced. Thus, the impact of a bioactive strain like P. inhibens on host-associated microbiomes depends on the complexity and composition of the existing microbiome.
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Affiliation(s)
- Karen K Dittmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Copenhagen, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Copenhagen, Denmark
| | - Suhelen Egan
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Randwick, NSW, Australia
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Copenhagen, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Copenhagen, Denmark
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Du Y, Zhou S, Liu M, Wang B, Jiang K, Fang H, Wang L. Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2019; 86:1194-1206. [PMID: 30599258 DOI: 10.1016/j.fsi.2018.12.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 06/09/2023]
Abstract
The interactions of microbiota in the intestines play an important role in promoting or maintaining the health of hosts. The present study aim to investigate the effects of the surface proteins of Lactobacillus pentosus HC-2 on the immune response and the bacterial composition of Litopenaeus vannamei, thus, the immune-related genes, surface condition, HC-2 numbers and the bacteria diversity in midgut were explored after shrimp feeding the normal HC-2 and 5 M - lithium chloride (LiCl) treated HC-2 for four weeks. Obvious improvements in the intestinal surface were observed in R group than the control group and L group. qPCR analysis demonstrated that the selected immune-related genes of lysozyme, proPO, LGBP, PEN-3α, crustin, and lvLec were significantly up-regulated in group R than in group L. Meanwhile, in the challenge test, shrimp in R group received 72% relative percent survival, which was significantly higher than the L group (RPS = 9%). The bacteria composition analysis showed that the abundance of Proteobacteria were significantly higher in group R and L than in group C, and the Bacteroidetes were significantly higher in group C than in group R and L, whereas the numbers of Chloroflexi were significantly higher in group R than in group C and L. The bacterial community difference analysis revealed that the harmful bacteria such as genus of Vibrio, Tenacibaculu and Thalassobius were decreased and the beneficial bacterium as Ruegeria and Lactobacillus were increased in R group, whereas this phenomenon were not found in L group. Taken together, above results indicating that the surface proteins were indispensable for L. pentosus HC-2 adhesion and colonization in shrimp intestines to improve intestine condition, enhance immune response, competitively exclude the pathogens, and promote the beneficial bacteria growth to protect the shrimp from pathogens infection. The findings in this work will help to promote the understanding of the roles of probiotics in shrimp intestines displaying probiotic-function by regulating the intestinal bacteria.
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Affiliation(s)
- Yang Du
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shuhong Zhou
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Mei Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Baojie Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Keyong Jiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Han Fang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Lei Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266400, China.
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Turgay E, Steinum T, Colquhoun D, Karataş S. Environmental biofilm communities associated with early‐stage common dentex (Dentex dentex) culture. J Appl Microbiol 2019; 126:1032-1043. [DOI: 10.1111/jam.14205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 01/03/2019] [Accepted: 01/14/2019] [Indexed: 11/29/2022]
Affiliation(s)
- E. Turgay
- Faculty of Aquatic Sciences Istanbul University Istanbul Turkey
| | - T.M. Steinum
- Faculty of Sciences Department of Molecular Biology and Genetics Istanbul University Istanbul Turkey
| | - D. Colquhoun
- Fish Health Research Group Norwegian Veterinary Institute Oslo Norway
| | - S. Karataş
- Faculty of Aquatic Sciences Istanbul University Istanbul Turkey
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46
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Tinta T, Kogovšek T, Klun K, Malej A, Herndl GJ, Turk V. Jellyfish-Associated Microbiome in the Marine Environment: Exploring Its Biotechnological Potential. Mar Drugs 2019; 17:E94. [PMID: 30717239 PMCID: PMC6410321 DOI: 10.3390/md17020094] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
Despite accumulating evidence of the importance of the jellyfish-associated microbiome to jellyfish, its potential relevance to blue biotechnology has only recently been recognized. In this review, we emphasize the biotechnological potential of host⁻microorganism systems and focus on gelatinous zooplankton as a host for the microbiome with biotechnological potential. The basic characteristics of jellyfish-associated microbial communities, the mechanisms underlying the jellyfish-microbe relationship, and the role/function of the jellyfish-associated microbiome and its biotechnological potential are reviewed. It appears that the jellyfish-associated microbiome is discrete from the microbial community in the ambient seawater, exhibiting a certain degree of specialization with some preferences for specific jellyfish taxa and for specific jellyfish populations, life stages, and body parts. In addition, different sampling approaches and methodologies to study the phylogenetic diversity of the jellyfish-associated microbiome are described and discussed. Finally, some general conclusions are drawn from the existing literature and future research directions are highlighted on the jellyfish-associated microbiome.
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Affiliation(s)
- Tinkara Tinta
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Tjaša Kogovšek
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Alenka Malej
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, The Netherlands.
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia.
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Kos Kramar M, Tinta T, Lučić D, Malej A, Turk V. Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic). PLoS One 2019; 14:e0198056. [PMID: 30645606 PMCID: PMC6333360 DOI: 10.1371/journal.pone.0198056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/24/2018] [Indexed: 12/16/2022] Open
Abstract
Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on ‘outer’ body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure.
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Affiliation(s)
- Maja Kos Kramar
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Davor Lučić
- Institute for Marine and Coastal Research, University of Dubrovnik, Dubrovnik, Croatia
| | - Alenka Malej
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- * E-mail:
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48
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Microbial embryonal colonization during pipefish male pregnancy. Sci Rep 2019; 9:3. [PMID: 30626884 PMCID: PMC6327025 DOI: 10.1038/s41598-018-37026-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 11/08/2018] [Indexed: 02/06/2023] Open
Abstract
While originally acquired from the environment, a fraction of the microbiota is transferred from parents to offspring. The immune system shapes the microbial colonization, while commensal microbes may boost host immune defences. Parental transfer of microbes in viviparous animals remains ambiguous, as the two transfer routes (transovarial vs. pregnancy) are intermingled within the maternal body. Pipefishes and seahorses (syngnathids) are ideally suited to disentangle transovarial microbial transfer from a contribution during pregnancy due to their maternal egg production and their unique male pregnancy. We assessed the persistency and the changes in the microbial communities of the maternal and paternal reproductive tracts over proceeding male pregnancy by sequencing microbial 16S rRNA genes of swabs from maternal gonads and brood pouches of non-pregnant and pregnant fathers. Applying parental immunological activation with heat-killed bacteria, we evaluated the impact of parental immunological status on microbial development. Our data indicate that maternal gonads and paternal brood pouches harbor distinct microbial communities, which could affect embryonal development in a sex-specific manner. Upon activation of the immune system, a shift of the microbial community was observed. The activation of the immune system induced the expansion of microbiota richness during late pregnancy, which corresponds to the time point of larval mouth opening, when initial microbial colonization must take place.
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49
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Su Y, Tang K, Liu J, Wang Y, Zheng Y, Zhang XH. Quorum Sensing System of Ruegeria mobilis Rm01 Controls Lipase and Biofilm Formation. Front Microbiol 2019; 9:3304. [PMID: 30687283 PMCID: PMC6333666 DOI: 10.3389/fmicb.2018.03304] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 12/19/2018] [Indexed: 01/02/2023] Open
Abstract
Quorum sensing (QS) promotes in situ extracellular enzyme (EE) activity via the exogenous signal N-acylhomoserine lactone (AHL), which facilitates marine particle degradation, but the species that engage in this regulatory mechanism remain unclear. Here, we obtained AHL-producing and AHL-degrading strains from marine particles. The strain Ruegeria mobilis Rm01 of the Roseobacter group (RBG), which was capable of both AHL producing and degrading, was chosen to represent these strains. We demonstrated that Rm01 possessed a complex QS network comprising AHL-based QS and quorum quenching (QQ) systems and autoinducer-2 (AI-2) perception system. Rm01 was able to respond to multiple exogenous QS signals through the QS network. By applying self-generated AHLs and non-self-generated AHLs and AI-2 QS signal molecules, we modulated biofilm formation and lipase production in Rm01, which reflected the coordination of bacterial metabolism with that of other species via eavesdropping on exogenous QS signals. These results suggest that R. mobilis might be one of the participators that could regulate EE activities by responding to QS signals in marine particles.
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Affiliation(s)
- Ying Su
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Weifang Engineering Vocational College, Weifang, China
| | - Kaihao Tang
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yan Wang
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yanfen Zheng
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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50
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Majzoub ME, McElroy K, Maczka M, Thomas T, Egan S. Causes and Consequences of a Variant Strain of Phaeobacter inhibens With Reduced Competition. Front Microbiol 2018; 9:2601. [PMID: 30450086 PMCID: PMC6224355 DOI: 10.3389/fmicb.2018.02601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/11/2018] [Indexed: 11/13/2022] Open
Abstract
Phaeobacter inhibens 2.10 is an effective biofilm former and colonizer of marine surfaces and has the ability to outcompete other microbiota. During biofilm dispersal P. inhibens 2.10 produces heritable phenotypic variants, including those that have a reduced ability to inhibit the co-occurring bacterium Pseudoalteromonas tunicata. However, the genetic changes that underpin the phenotypic variation and what the ecological consequences are for variants within the population are unclear. To answer these questions we sequenced the genomes of strain NCV12a1, a biofilm variant of P. inhibens 2.10 with reduced inhibitory activity and the P. inhibens 2.10 WT parental strain. Genome wide analysis revealed point mutations in genes involved in synthesis of the antibacterial compound tropodithietic acid (TDA) and indirectly in extracellular polymeric substances (EPS) production. However, confocal laser scanning microscopy analyses found little differences in biofilm growth between P. inhibens 2.10 WT (parental) and NCV12a1. P. inhibens NCV12a1 was also not outcompeted in co-cultured biofilms with P. tunicata, despite its reduced inhibitory activity, rather these biofilms were thicker than those produced when the WT strain was co-cultured with P. tunicata. Notably, dispersal populations from biofilms of P. inhibens NCV12a1 had a higher proportion of WT-like morphotypes when co-cultured with P. tunicata. These observations may explain why the otherwise non-inhibiting variant persists in the presence of a natural competitor, adding to our understanding of the relative importance of genetic diversification in microbial biofilms.
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Affiliation(s)
- Marwan E Majzoub
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Kerensa McElroy
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Michael Maczka
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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