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Yamabe S, Yoshitake K, Ninomiya A, Piel J, Takeyama H, Matsunaga S, Takada K. Metagenomic Insights Reveal Unrecognized Diversity of Entotheonella in Japanese Theonella Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10350-8. [PMID: 39103714 DOI: 10.1007/s10126-024-10350-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024]
Abstract
Numerous biologically active natural products have been discovered from marine sponges, particularly from Theonella swinhoei, which is known to be a prolific source of natural products such as polyketides and peptides. Recent studies have revealed that many of these natural products are biosynthesized by Candidatus Entotheonella phylotypes, which are uncultivated symbionts within T. swinhoei. Consequently, Entotheonella is considered an untapped biochemical resource. In this study, we conducted metagenomic analyses to assess the diversity of Entotheonella in two T. swinhoei Y and two T. swinhoei W (Y and W referring to the yellow and white interior of the sponge, respectively), after separating filamentous bacteria using density gradient centrifugation. We obtained five Entotheonella metagenome-assembled genomes (MAGs) from filamentous bacteria-enriched fractions. Notably, one of these MAGs is significantly different from previously reported Entotheonella variants. Additionally, we identified closely related Entotheonella members present across different chemotypes of T. swinhoei. Thus, our metagenomic insights reveal that the diversity of Entotheonella within Theonella sponges is greater than previously recognized.
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Affiliation(s)
- Sota Yamabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Akihiro Ninomiya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-Ku, Tokyo, 162-8480, Japan
| | - Shigeki Matsunaga
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Kentaro Takada
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, 252-0373, Japan.
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Wang S, Li X, Yang W, Huang R. Exploring the secrets of marine microorganisms: Unveiling secondary metabolites through metagenomics. Microb Biotechnol 2024; 17:e14533. [PMID: 39075735 PMCID: PMC11286668 DOI: 10.1111/1751-7915.14533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024] Open
Abstract
Marine microorganisms are increasingly recognized as primary producers of marine secondary metabolites, drawing growing research interest. Many of these organisms are unculturable, posing challenges for study. Metagenomic techniques enable research on these unculturable microorganisms, identifying various biosynthetic gene clusters (BGCs) related to marine microbial secondary metabolites, thereby unveiling their secrets. This review comprehensively analyses metagenomic methods used in discovering marine microbial secondary metabolites, highlighting tools commonly employed in BGC identification, and discussing the potential and challenges in this field. It emphasizes the key role of metagenomics in unveiling secondary metabolites, particularly in marine sponges and tunicates. The review also explores current limitations in studying these metabolites through metagenomics, noting how long-read sequencing technologies and the evolution of computational biology tools offer more possibilities for BGC discovery. Furthermore, the development of synthetic biology allows experimental validation of computationally identified BGCs, showcasing the vast potential of metagenomics in mining marine microbial secondary metabolites.
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Affiliation(s)
- Shaoyu Wang
- Institute of Marine Science and TechnologyShandong UniversityQingdaoShandongChina
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission TechnologyShandong UniversityQingdaoChina
| | - Xinyan Li
- Institute of Marine Science and TechnologyShandong UniversityQingdaoShandongChina
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission TechnologyShandong UniversityQingdaoChina
| | - Weiqin Yang
- School of Computer Science and TechnologyShandong UniversityQingdaoShandongChina
| | - Ranran Huang
- Institute of Marine Science and TechnologyShandong UniversityQingdaoShandongChina
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission TechnologyShandong UniversityQingdaoChina
- Global Ocean Negative Carbon Emissions (ONCE) Program AllianceQingdaoChina
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Goldstein Ascer L, Nascimento-Silva G, Hardoim CCP, Custódio MR. Effects of plasticizer Di(2-ethylhexyl) phthalate (DEHP) on the microbiome of the marine sponge Hymeniacidon heliophila. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 273:107025. [PMID: 39032424 DOI: 10.1016/j.aquatox.2024.107025] [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: 03/18/2024] [Revised: 06/26/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Marine pollution research in the last 15 years focused on an emerging anthropogenic contaminant: plastic debris and more specifically, microplastics. Since, not only its physical impacts on marine invertebrates were studied, but also its additives. Phthalate, a plasticizer commonly found in the ocean and known endocrine disruptor was already observed in different aquatic invertebrates, but few is known about its presence and possible effects in Porifera physiology. Our study aimed to analyze potential shifts in Hymeniacidon heliophila (Desmosponge) microbiome after exposure to Di(2-ethylhexyl) phthalate (DEHP), the most common phthalate found in the ocean, in three different doses for 4 and 24 h. Results indicate that alpha diversity had significantly changed between control and exposed organisms but not in all multicomparisons. Microbial community structure changed after exposure as well although most abundant phyla did not vary along the experiment. The core microbiome between control and each exposed organisms contained the vast majority of total ASVs and a few ASVs were exclusive to each experimental group. After DEHP exposure, microbial classes had significant changes and species with phthalate degradation enzymes were identified in a specifically dose dependent manner pointing to a possible bacterial consortium responsible for the phthalate degradation. The bacterial detoxification activity may lead to H. heliophila resistance during DEHP exposure in polluted environmental conditions.
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Affiliation(s)
- Liv Goldstein Ascer
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Gabriel Nascimento-Silva
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Márcio Reis Custódio
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Moon YL, Kim KH, Park JS. Chengkuizengella axinellae sp. nov., a symbiotic bacterium isolated from a marine sponge of the genus Axinella. Antonie Van Leeuwenhoek 2024; 117:106. [PMID: 39060616 DOI: 10.1007/s10482-024-01998-2] [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: 03/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024]
Abstract
A Gram-stain-positive, strictly aerobic, creamy-white colored, endospore-forming and non-motile rods strain, designated as strain 2205SS18-9T, was isolated from a marine sponge, Axinella sp. collected from Seopseom Island, Republic of Korea. Optimal growth of strain 2205SS18-9T was observed at 25-30 °C, pH 6.5-7.0, and in the presence of 3.0% (w/v) NaCl. Cells were oxidase-positive and catalase-negative. Negative for nitrate reduction and indole production. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain 2205SS18-9T formed a distinct phyletic lineage in the genus Chengkuizengella, and it was most closely related to Chengkuizengella marina YPA3-1-1T and Chengkuizengella sediminis J15A17T with 97.1 and 96.6% 16S rRNA gene sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain 2205SS18-9T and Chengkuizengella marina YPA3-1-1T were 79.0 and 21.6%, respectively. The genomic DNA G + C content was 34.1%. The genome harbors a number of host-adhesion and transporter genes, suggested that strain 2205SS18-9T may interact with its sponge host as a symbiont. Menaquinone-7 was the sole isoprenoid quinone and antieiso-C15:0 (28.5%), iso-C16:0 (25.8%), C16:1 ω7c alcohol (15.0%), and iso-C15:0 (11.2%) were detected as the major fatty acids. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, and an unidentified lipid. The cell-wall peptidoglycan contained lysine, alanine, glutamate, and aspartate. Based on these analyses, strain 2205SS18-9T represents a novel species of the genus Chengkuizengella, for which the name Chengkuizengella axinellae sp. nov. is proposed. The type strain is 2205SS18-9T (= KACC 23238T = LMG 33063T).
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Affiliation(s)
- Yea-Lin Moon
- Department of Biological Sciences and Biotechnology, Hannam University, 1646,Yuseong-Daero, Yuseong-Gu, Daejeon, 34430, Republic of Korea
| | - Kyung Hyun Kim
- Department of Biological Sciences and Biotechnology, Hannam University, 1646,Yuseong-Daero, Yuseong-Gu, Daejeon, 34430, Republic of Korea
| | - Jin-Sook Park
- Department of Biological Sciences and Biotechnology, Hannam University, 1646,Yuseong-Daero, Yuseong-Gu, Daejeon, 34430, Republic of Korea.
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Shoham S, Keren R, Lavy A, Polishchuk I, Pokroy B, Ilan M. Out of the blue: Hyperaccumulation of molybdenum in the Indo-Pacific sponge Theonella conica. SCIENCE ADVANCES 2024; 10:eadn3923. [PMID: 39018411 PMCID: PMC466961 DOI: 10.1126/sciadv.adn3923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
Molybdenum is an essential micronutrient, but because of its toxicity at high concentrations, its accumulation in living organisms has not been widely demonstrated. In this study, we report that the marine sponge Theonella conica accumulates exceptionally high levels of molybdenum (46,793 micrograms per gram of dry weight) in a wide geographic distribution from the northern Red Sea to the reefs of Zanzibar, Indian Ocean. The element is found in various sponge body fractions and correlates to selenium. We further investigated the microbial composition of the sponge and compared it to its more studied congener, Theonella swinhoei. Our analysis illuminates the symbiotic bacterium Entotheonella sp. and its role in molybdenum accumulation. Through microscopic and analytical methods, we provide evidence of intracellular spheres within Entotheonella sp. that exhibit high molybdenum content, further unraveling the intricate mechanisms behind molybdenum accumulation in this sponge species and its significance in the broader context of molybdenum biogeochemical cycling.
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Affiliation(s)
- Shani Shoham
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ray Keren
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Adi Lavy
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Iryna Polishchuk
- Faculty of Materials Engineering and the Russell Berrie Nanotechnology Institute, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Boaz Pokroy
- Faculty of Materials Engineering and the Russell Berrie Nanotechnology Institute, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Micha Ilan
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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Williams SE, Varliero G, Lurgi M, Stach JEM, Race PR, Curnow P. Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39073401 DOI: 10.1099/mic.0.001478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
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Affiliation(s)
- Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul R Race
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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7
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Liu T, Gui X, Zhang G, Luo L, Zhao J. Streptomyces-Fungus Co-Culture Enhances the Production of Borrelidin and Analogs: A Genomic and Metabolomic Approach. Mar Drugs 2024; 22:302. [PMID: 39057412 PMCID: PMC11278061 DOI: 10.3390/md22070302] [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: 05/22/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The marine Streptomyces harbor numerous biosynthetic gene clusters (BGCs) with exploitable potential. However, many secondary metabolites cannot be produced under laboratory conditions. Co-culture strategies of marine microorganisms have yielded novel natural products with diverse biological activities. In this study, we explored the metabolic profiles of co-cultures involving Streptomyces sp. 2-85 and Cladosporium sp. 3-22-derived from marine sponges. Combining Global Natural Products Social (GNPS) Molecular Networking analysis with natural product database mining, 35 potential antimicrobial metabolites annotated were detected, 19 of which were exclusive to the co-culture, with a significant increase in production. Notably, the Streptomyces-Fungus interaction led to the increased production of borrelidin and the discovery of several analogs via molecular networking. In this study, borrelidin was first applied to combat Saprolegnia parasitica, which caused saprolegniosis in aquaculture. We noted its superior inhibitory effects on mycelial growth with an EC50 of 0.004 mg/mL and on spore germination with an EC50 of 0.005 mg/mL compared to the commercial fungicide, preliminarily identifying threonyl-tRNA synthetase as its target. Further analysis of the associated gene clusters revealed an incomplete synthesis pathway with missing malonyl-CoA units for condensation within this strain, hinting at the presence of potential compensatory pathways. In conclusion, our findings shed light on the metabolic changes of marine Streptomyces and fungi in co-culture, propose the potential of borrelidin in the control of aquatic diseases, and present new prospects for antifungal applications.
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Affiliation(s)
- Tan Liu
- College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China; (T.L.); (X.G.)
| | - Xi Gui
- College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China; (T.L.); (X.G.)
| | - Gang Zhang
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361005, China; (G.Z.); (L.L.)
| | - Lianzhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Product Resources, Xiamen Medical College, Xiamen 361005, China; (G.Z.); (L.L.)
| | - Jing Zhao
- College of Ocean and Earth Science, Xiamen University, Xiamen 361005, China; (T.L.); (X.G.)
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Wen HM, Zhang YW, Feng FJ, Huang GB, Lv YH, Zhang ZY, Ding LJ. Antibacterial oxygenated ergostane-type steroids produced by the marine sponge-derived fungus Aspergillus sp. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:548-554. [PMID: 37712720 DOI: 10.1080/10286020.2023.2259317] [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: 05/22/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Two oxygenated ergostane-type steroids including one new compound, 3β-hydroxy-5α,6β-methoxyergosta-7,22-dien-15-one (1) along with a known analogue ergosta-6,22-dien-3β,5α,8α-triol (2) were isolated from the crude extracts of the marine sponge-derived fungus Aspergillus sp. Their structures were elucidated on the basis of combined NMR and MS spectroscopic methods. Compound 1 was a marine ergostane-type steroid with two methoxy groups at C-5 and C-6, respectively. These oxygenated ergostane-type steroids were evaluated for their antibacterial activities against human or aquatic pathogens. Among them, compound 1 exhibited antibacterial activity against Staphylococcus aureus.
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Affiliation(s)
- Hui-Min Wen
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
| | - Ya-Wen Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
| | - Fang-Jian Feng
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
| | - Guo-Bao Huang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
| | - Yu-Han Lv
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
| | - Zou-Yan Zhang
- National Clinical Trial Institute, The First Affiliated Hospital of Ningbo University, Ningbo University, Ningbo 315020, China
| | - Li-Jian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China
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Katoch M, Singh G, Bijarnia E, Gupta AP, Azeem M, Rani P, Kumar J. Biodiversity of endosymbiont fungi associated with a marine sponge Lamellodysidea herbacea and their potential as antioxidant producers. 3 Biotech 2024; 14:146. [PMID: 38706926 PMCID: PMC11068721 DOI: 10.1007/s13205-024-03972-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 03/01/2024] [Indexed: 05/07/2024] Open
Abstract
This study aims to isolate endosymbiontic fungi from the marine sponge Lamellodysidea herbacea and to explore their antioxidant potential. Marine-derived fungi, with their vast biodiversity, are considered a promising source of novel antioxidants which can replace synthetic ones. Marine sponges have previously reported bioactive properties that could ameliorate oxidative stress, particularly their associated fungi, producing high-frequency bioactive molecules (adaptogenic molecules) in response to stressors. 19 endosymbiont fungi associated with marine sponges were isolated, and their extracts were evaluated for their antioxidant capacities. Extract of an endosymbiont fungus, isolate SPG6, identified as Alternaria destruens, through surface electron microscopy (SEM) and ITS gene sequencing, showed broad range antioxidant activities (EC50 values) (free radical scavenging 32.54 mg L-1, Hydroxyl radical scavenging activity < 0.078 g L-1, total reducing power 0.114 g L-1, Chelating power 0.262 g L-1, H2O2 scavenging activity < 0.078 g L-1, and Superoxide radical scavenging activity > 5.0 g L-1). The extract of isolate SPG6 was fractioned and analyzed through GC-MS. Marine sponge-associated endosymbiont fungi are a rich source of antioxidant molecules. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03972-1.
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Affiliation(s)
- Meenu Katoch
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR, New Delhi, 110025 India
| | - Gurpreet Singh
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR, New Delhi, 110025 India
| | - Ekta Bijarnia
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
| | - A. P. Gupta
- Quality Control Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
| | - Mohd. Azeem
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
| | - Pragya Rani
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
| | - J. Kumar
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR, New Delhi, 110025 India
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Mazzella V, Dell'Anno A, Etxebarría N, González-Gaya B, Nuzzo G, Fontana A, Núñez-Pons L. High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits. Commun Biol 2024; 7:422. [PMID: 38589605 PMCID: PMC11001883 DOI: 10.1038/s42003-024-06109-5] [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: 08/04/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.
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Affiliation(s)
- Valerio Mazzella
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Ischia Marine Centre, 80077, Ischia, Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy
| | - Antonio Dell'Anno
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Néstor Etxebarría
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Belén González-Gaya
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia-Bld. 7, 80126, Napoli, Italy
| | - Laura Núñez-Pons
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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Walquist MJ, Eilertsen KE, Elvevoll EO, Jensen IJ. Marine-Derived Peptides with Anti-Hypertensive Properties: Prospects for Pharmaceuticals, Supplements, and Functional Food. Mar Drugs 2024; 22:140. [PMID: 38667757 PMCID: PMC11051484 DOI: 10.3390/md22040140] [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: 02/26/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Hypertension, a major health concern linked to heart disease and premature mortality, has prompted a search for alternative treatments due to side effects of existing medications. Sustainable harvesting of low-trophic marine organisms not only enhances food security but also provides a variety of bioactive molecules, including peptides. Despite comprising only a fraction of active natural compounds, peptides are ideal for drug development due to their size, stability, and resistance to degradation. Our review evaluates the anti-hypertensive properties of peptides and proteins derived from selected marine invertebrate phyla, examining the various methodologies used and their application in pharmaceuticals, supplements, and functional food. A considerable body of research exists on the anti-hypertensive effects of certain marine invertebrates, yet many species remain unexamined. The array of assessments methods, particularly for ACE inhibition, complicates the comparison of results. The dominance of in vitro and animal in vivo studies indicates a need for more clinical research in order to transition peptides into pharmaceuticals. Our findings lay the groundwork for further exploration of these promising marine invertebrates, emphasizing the need to balance scientific discovery and marine conservation for sustainable resource use.
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Affiliation(s)
- Mari Johannessen Walquist
- Faculty of Biosciences, Fisheries and Economics, The Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway; (K.-E.E.); (E.O.E.)
| | - Karl-Erik Eilertsen
- Faculty of Biosciences, Fisheries and Economics, The Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway; (K.-E.E.); (E.O.E.)
| | - Edel Oddny Elvevoll
- Faculty of Biosciences, Fisheries and Economics, The Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway; (K.-E.E.); (E.O.E.)
| | - Ida-Johanne Jensen
- Faculty of Biosciences, Fisheries and Economics, The Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway; (K.-E.E.); (E.O.E.)
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
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12
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Moreno-Pino M, Manrique-de-la-Cuba MF, López-Rodríguez M, Parada-Pozo G, Rodríguez-Marconi S, Ribeiro CG, Flores-Herrera P, Guajardo M, Trefault N. Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes. Sci Rep 2024; 14:6371. [PMID: 38493232 PMCID: PMC10944490 DOI: 10.1038/s41598-024-56480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.
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Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Génesis Parada-Pozo
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
- Millenium Nucleus in Marine Agronomy of Seaweed Holobionts (MASH), Puerto Montt, Chile
| | | | | | - Patricio Flores-Herrera
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
| | - Mariela Guajardo
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile.
- Millenium Nucleus in Marine Agronomy of Seaweed Holobionts (MASH), Puerto Montt, Chile.
- FONDAP Center IDEAL- Dynamics of High Latitude Marine Ecosystem, Valdivia, Chile.
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13
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Turon M, Ford M, Maldonado M, Sitjà C, Riesgo A, Díez-Vives C. Microbiome changes through the ontogeny of the marine sponge Crambe crambe. ENVIRONMENTAL MICROBIOME 2024; 19:15. [PMID: 38468324 DOI: 10.1186/s40793-024-00556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding. RESULTS Using 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics. CONCLUSIONS These findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.
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Affiliation(s)
- Marta Turon
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Madeline Ford
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Manuel Maldonado
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Cèlia Sitjà
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Cristina Díez-Vives
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
- Department of Systems Biology, Centro Nacional de Biotecnología, c/Darwin, 3, 28049, Madrid, Spain.
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14
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Stuij TM, Cleary DFR, Rocha RJM, Polónia ARM, Silva DAM, Louvado A, de Voogd NJ, Gomes NCM. Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp. FEMS Microbiol Ecol 2024; 100:fiae022. [PMID: 38366951 PMCID: PMC10939426 DOI: 10.1093/femsec/fiae022] [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: 06/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.
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Affiliation(s)
- Tamara M Stuij
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Rui J M Rocha
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Davide A M Silva
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Antonio Louvado
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Newton C M Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
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15
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Rosner A, Ballarin L, Barnay-Verdier S, Borisenko I, Drago L, Drobne D, Concetta Eliso M, Harbuzov Z, Grimaldi A, Guy-Haim T, Karahan A, Lynch I, Giulia Lionetto M, Martinez P, Mehennaoui K, Oruc Ozcan E, Pinsino A, Paz G, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring. Biol Rev Camb Philos Soc 2024; 99:131-176. [PMID: 37698089 DOI: 10.1111/brv.13015] [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: 08/31/2022] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, 28 avenue Valombrose, Nice, F-06107, France
| | - Ilya Borisenko
- Faculty of Biology, Department of Embryology, Saint Petersburg State University, Universitetskaya embankment 7/9, Saint Petersburg, 199034, Russia
| | - Laura Drago
- Department of Biology, University of Padova, via Ugo Bassi 58/B, Padova, I-35121, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, 1111, Slovenia
| | - Maria Concetta Eliso
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Zoya Harbuzov
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Haifa, 3498838, Israel
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant, Varese, 3-21100, Italy
| | - Tamar Guy-Haim
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli-Mersin, PO 28, 33731, Turkey
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Maria Giulia Lionetto
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via prov. le Lecce -Monteroni, Lecce, I-73100, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina, 61, Palermo, I-90133, Italy
| | - Pedro Martinez
- Department de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, Barcelona, 08010, Spain
| | - Kahina Mehennaoui
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
| | - Elif Oruc Ozcan
- Faculty of Arts and Science, Department of Biology, Cukurova University, Balcali, Saricam, Adana, 01330, Turkey
| | - Annalisa Pinsino
- National Research Council, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, PO 2336 Sha'ar Palmer 1, Haifa, 3102201, Israel
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, Milan, 20133, Italy
| | - Sébastien Cambier
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, Belvaux, L-4422, Luxembourg
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16
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Kim SB, Kim KH, Park JS. Parendozoicomonas callyspongiae sp. nov. Isolated from a Marine Sponge, Callyspongia elongate, and Reclassification of Sansalvadorimonas verongulae as Parendozoicomonas verongulae comb. nov. Curr Microbiol 2024; 81:85. [PMID: 38300357 DOI: 10.1007/s00284-023-03585-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 12/08/2023] [Indexed: 02/02/2024]
Abstract
A strictly aerobic Gram-negative bacterium, designated 2012CJ34-2T, was isolated from marine sponge to Chuja-do in Jeju-island, Republic of Korea and taxonomically characterized. Cells were catalase- and oxidase-positive, and non-motile rods (without flagella). Growth was observed at 15-42 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7), and in the presence of 0.5-10% (w/v) NaCl (optimum, 2-3%). The major cellular fatty acid and respiratory quinones were identified summed feature 3 (C16:1 ω7c/C16:1 ω6c), and Q-8 and Q-9, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified phospholipids, and three unidentified lipids. The DNA G+C content was 48.0 mol%. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences showed that strain 2012CJ34-2T formed a clade with Parendozoicomonas haliclonae S-B4-1UT and Sansalvadorimonas verongulae LMG 29871T within the family Endozoicomodaceae. Genome relatedness values, including dDDH, ANI and AF, and AAI and POCP, among strain 2012CJ34-2T, P. haliclonae S-B4-1UT, and S. verongulae LMG 29871T were within the range of the bacterial genus cut-off values. Based on the phylogenetic, chemotaxonomic, and genomic analyses, strain 2012CJ34-2T represents a novel bacterial species of the family Endozoicomodaceae, for which the name Parendozoicomonas callyspongiae sp. nov. is proposed. The type strain is 2012CJ34-2T (= KACC 22641T = LMG 32581T). Additionally, we proposed the reclassification of Sansalvadorimonas verongulae of the family Hahellaceae as Parendozoicomonas verongulae of the family Endozoicomonadaceae.
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Affiliation(s)
- Soo-Bin Kim
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon, 34430, Republic of Korea
| | - Kyung Hyun Kim
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon, 34430, Republic of Korea
| | - Jin-Sook Park
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon, 34430, Republic of Korea.
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17
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Skaraki K, Pavloudi C, Dailianis T, Lagnel J, Pantazidou A, Magoulas A, Kotoulas G. Microbial diversity in four Mediterranean irciniid sponges. Biodivers Data J 2024; 12:e114809. [PMID: 38283142 PMCID: PMC10819633 DOI: 10.3897/bdj.12.e114809] [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: 10/27/2023] [Accepted: 01/14/2024] [Indexed: 01/30/2024] Open
Abstract
This paper describes a dataset of microbial communities from four different sponge species: Irciniaoros (Schmidt, 1864), Irciniavariabilis (Schmidt, 1862), Sarcotragusspinosulus Schmidt, 1862 and Sarcotragusfasciculatus (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.
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Affiliation(s)
- Katerina Skaraki
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
- Department of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of Athens, Athens, GreeceDepartment of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of AthensAthensGreece
| | - Christina Pavloudi
- European Marine Biological Resource Centre (EMBRC-ERIC), Paris, FranceEuropean Marine Biological Resource Centre (EMBRC-ERIC)ParisFrance
| | - Thanos Dailianis
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
| | - Jacques Lagnel
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Centre de Recherche PACA, Montfavet, FranceINRAE, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), Centre de Recherche PACAMontfavetFrance
| | - Adriani Pantazidou
- Department of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of Athens, Athens, GreeceDepartment of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of AthensAthensGreece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, GreeceInstitute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine ResearchHeraklion, CreteGreece
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18
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Zhou K, Zhang T, Chen XW, Xu Y, Zhang R, Qian PY. Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:467-485. [PMID: 37647612 DOI: 10.1146/annurev-marine-021623-093133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.
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Affiliation(s)
- Kun Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Xiao-Wei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China;
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China;
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
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19
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Esposito R, Federico S, Sonnessa M, Reddel S, Bertolino M, Ruocco N, Zagami G, Giovine M, Pozzolini M, Guida M, Zupo V, Costantini M. Characterizing the bacterial communities associated with Mediterranean sponges: a metataxonomic analysis. Front Microbiol 2024; 14:1295459. [PMID: 38274771 PMCID: PMC10808595 DOI: 10.3389/fmicb.2023.1295459] [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: 10/02/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
The oceans cover over 70% of our planet, hosting a biodiversity of tremendous wealth. Sponges are one of the major ecosystem engineers on the seafloor, providing a habitat for a wide variety of species to be considered a good source of bioactive compounds. In this study, a metataxonomic approach was employed to describe the bacterial communities of the sponges collected from Faro Lake (Sicily) and Porto Paone (Gulf of Naples). Morphological analysis and amplification of the conserved molecular markers, including 18S and 28S (RNA ribosomal genes), CO1 (mitochondrial cytochrome oxidase subunit 1), and ITS (internal transcribed spacer), allowed the identification of four sponges. Metataxonomic analysis of sponges revealed a large number of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Cloroflexi, Dadabacteria, and Poribacteria. In particular, Myxilla (Myxilla) rosacea and Clathria (Clathria) toxivaria displayed several classes such as Alphaproteobacteria, Dehalococcoidia, Gammaproteobacteria, Cyanobacteria, and Bacteroidia. On the other hand, the sponges Ircinia oros and Cacospongia mollior hosted bacteria belonging to the classes Dadabacteriia, Anaerolineae, Acidimicrobiia, Nitrospiria, and Poribacteria. Moreover, for the first time, the presence of Rhizobiaceae bacteria was revealed in the sponge M. (Myxilla) rosacea, which was mainly associated with soil and plants and involved in biological nitrogen fixation.
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Affiliation(s)
- Roberta Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Serena Federico
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | | | | | - Marco Bertolino
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Nadia Ruocco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Calabria Marine Centre, Amendolara, Italy
| | - Giacomo Zagami
- Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, Messina, Italy
| | - Marco Giovine
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Marina Pozzolini
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Valerio Zupo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Ischia Marine Centre, Naples, Italy
| | - Maria Costantini
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
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20
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Díez-Vives C, Riesgo A. High compositional and functional similarity in the microbiome of deep-sea sponges. THE ISME JOURNAL 2024; 18:wrad030. [PMID: 38365260 PMCID: PMC10837836 DOI: 10.1093/ismejo/wrad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/18/2024]
Abstract
Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Systems Biology, Centro Nacional de Biotecnología, c/ Darwin, 3, 28049 Madrid, Spain
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
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21
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Moghazy RM, Mahmoud RH. Microalgal-based macro-hollow loofah fiber bio-composite for methylene blue removal: A promising step for a green adsorbent. Int J Biol Macromol 2023; 253:127009. [PMID: 37734521 DOI: 10.1016/j.ijbiomac.2023.127009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
This study looked into how well the macro-hollow loofah fiber with and without the bio-attaching with green microalga (Chlamydomonas reinhardtii OR242521) was applied methylene blue elimination from water. Based on the results, the biosorption capacity of loofah sponge for methylene blue significantly increased with the increase of contact time, weight of microalgal biofilm, and methylene blue concentration. The maximum biosorption capacity was achieved after 120 min, after 0.042 mgg-1 biofilm weight, and MB concentration of 140 mgL-1. Furthermore, methylene blue's biosorption capacity was strongly affected by pH, reaching its maximum at pH 7. The biosorption capacity of the bio-attached loofah sponge was much higher than that of the loofah sponge, revealing that the microalgae bio-attachment enhanced the biosorption capacity of the loofah sponge. At the end of the MB biosorption process, the used bio-attached loofah sponge can still be utilized once more for the same purpose after the desorption of MB but with a lower biosorption capacity. Furthermore, the loofah sponge could also be applied as a bio-sorbent after domestic use. According to this study, the loofah sponge with or without algal biofilm attachment could be applied as a low-cost efficient bio-sorbent for methylene blue removal from water. However, the loofah sponge's ability for biosorption was dramatically increased by the bio-attachment of microalgae, making it a more potent bio-sorbent. Likewise, this study offers insights into the variables influencing the biosorption capacity of loofah sponges and bio-attached loofah sponges, which could be beneficial for enhancing the biosorption processes.
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Affiliation(s)
- Reda M Moghazy
- Water Pollution Research Department, National Research Centre (NRC), Dokki, Giza 12622, Egypt.
| | - Rehab H Mahmoud
- Water Pollution Research Department, National Research Centre (NRC), Dokki, Giza 12622, Egypt
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22
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Lo Giudice A, Rizzo C. Freshwater Sponges as a Neglected Reservoir of Bacterial Biodiversity. Microorganisms 2023; 12:25. [PMID: 38257852 PMCID: PMC10819713 DOI: 10.3390/microorganisms12010025] [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: 11/29/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Freshwater sponges (Spongillida: Demospongiae), including more than 240 described species, are globally distributed in continental waters (except for Antarctica), where they cover both natural and artificial surfaces. However, fragmentary studies have targeted their microbiome, making it difficult to test hypotheses about sponge-microbe specificity and metabolic relationships, along with the environmental factors playing key roles in structuring the associated microbial communities. To date, particular attention has been paid to sponges (family Lubomirskiidae) that are endemic to Lake Baikal. Few other freshwater sponge species (e.g., Ephydatia spp., Eunapius spp., and Spongilla lacustris), from lakes and rivers spanning from Europe to South and North America, have been targeted for microbiological studies. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria largely predominated, and high differences were reported between the microbiome of freshwater and marine sponges. Several bacterial strains isolated from freshwater sponges can produce bioactive compounds, mainly showing antibiotic activities, with potential application in biotechnology. Understanding the roles played by sponge microbiomes in freshwater ecosystems is still in its infancy and has yet to be clarified to disentangle the ecological and evolutionary significance of these largely under-investigated microbial communities. This review was aimed at providing the main available information on the composition and biotechnological potential of prokaryotic communities associated with healthy freshwater sponges, as a neglected component of the global sponge microbiome, to stimulate researchers interested in the field.
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Affiliation(s)
- Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy;
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy;
- Zoological Station “Anton Dohrn”, Department of Ecosustainable Marine Biotechnology, Villa Pace, Contrada Porticatello, 98168 Messina, Italy
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23
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Nnaji PT, Adukwu E, Morse HR, Chidugu-Ogborigbo RU. Amylase production from marine sponge Hymeniacidon perlevis; potentials sustainability benefits. PLoS One 2023; 18:e0294931. [PMID: 38127953 PMCID: PMC10734944 DOI: 10.1371/journal.pone.0294931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023] Open
Abstract
The marine sponge Hymeniacidon perlevis is a globally distributed and invasive species with extensive filter-feeding characteristics. The symbiotic relationship fostered between the sea sponge and the inhabiting microorganism is key in the production of metabolic enzymes which is the focus of this study. Sponge bacterial symbionts were grown on starch agar for 48hrs. Colourimetric analyses of amylase were conducted at 540nm using a spectrophotometric plate reader. Using an X-Bridge column (3.5μM, 4.6x150mm), 80/20 acetonitrile/water in 0.1% ammonium were the conditions used for the liquid chromatography-mass spectrometry (LC-MS) analyses. Seven reducing sugars were used to optimise LC-MS to determine the presence of the crude enzyme formed. Not all the bacterial symbionts isolated from H perlevis produced alpha and beta amylases to break down starch. From the statistical mean of crude enzyme concentrations from the hydrolysis of starch by amylase, isolate seven had the highest optical density (OD) at 0.43475 while isolate twelve had the lowest OD at 0.141417. From the LC-MS analysis, out of the seven sugars, Glucose and maltose constituted > 65% of the reducing sugars formed from the hydrolysis of starch by the amylases. Isolates 3,6 and 7 produced 6.906 mg/l, 12.309 mg/l, and 5.909 mg/l of glucose, while isolates 3,4,5,6 and 7 produced 203.391 mg/l, 176.238 mg/l, 139.938 mg/l, 39.030 mg/l, and 18.809 mg/l of maltose, respectively. Isolate two had the highest amount of maltose at a concentration of 267.237 mg/l while isolate four had the highest amount of glucose concentration of 53.084 mg/l. Enzymes from marine sponge bacteria offer greater potential for a green and sustainable production process. Amylase extraction from bacterial symbionts in H perlevis is sustainable and should be supported. They can serve as reliable sources of revenue for enzyme industries, and applications in food industries and biotechnological processes.
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Affiliation(s)
- Praise Tochukwu Nnaji
- School of Applied Sciences, College of Health, and Applied Sciences, The University of the West of England, Bristol, United Kingdom
| | - Emmanuel Adukwu
- Centre for Biosciences Research, School of Applied Sciences, The University of the West of England, Bristol, United Kingdom
| | - H. Ruth Morse
- Centre for Biosciences Research, School of Applied Sciences, The University of the West of England, Bristol, United Kingdom
| | - Rachael U. Chidugu-Ogborigbo
- School of Applied Sciences, College of Health, and Applied Sciences, The University of the West of England, Bristol, United Kingdom
- Centre for Biosciences Research, School of Applied Sciences, The University of the West of England, Bristol, United Kingdom
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24
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Montoya-Ciriaco N, Hereira-Pacheco S, Estrada-Torres A, Dendooven L, Méndez de la Cruz FR, Gómez-Acata ES, Díaz de la Vega-Pérez AH, Navarro-Noya YE. Maternal transmission of bacterial microbiota during embryonic development in a viviparous lizard. Microbiol Spectr 2023; 11:e0178023. [PMID: 37847033 PMCID: PMC10714757 DOI: 10.1128/spectrum.01780-23] [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: 05/09/2023] [Accepted: 09/08/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE We investigated the presence and diversity of bacteria in the embryos of the viviparous lizard Sceloporus grammicus and their amniotic environment. We compared this diversity to that found in the maternal intestine, mouth, and cloaca. We detected bacterial DNA in the embryos, albeit with a lower bacterial species diversity than found in maternal tissues. Most of the bacterial species detected in the embryos were also found in the mother, although not all of them. Interestingly, we detected a high similarity in the composition of bacterial species among embryos from different mothers. These findings suggest that there may be a mechanism controlling the transmission of bacteria from the mother to the embryo. Our results highlight the possibility that the interaction between maternal bacteria and the embryo may affect the development of the lizards.
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Affiliation(s)
- Nina Montoya-Ciriaco
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Stephanie Hereira-Pacheco
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Arturo Estrada-Torres
- Estación Científica La Malinche, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, CINVESTAV, Mexico City, Mexico
| | - Fausto R. Méndez de la Cruz
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elizabeth Selene Gómez-Acata
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Aníbal H. Díaz de la Vega-Pérez
- Consejo Nacional de Ciencia, Humanidades y Tecnología-Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala., Tlaxcala, Mexico
| | - Yendi E. Navarro-Noya
- Laboratorio de Interacciones Bióticas, Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
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25
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Cahyani NKD, Kasanah N, Kurnia DS, Hamann MT. Profiling Prokaryotic Communities and Aaptamines of Sponge Aaptos suberitoides from Tulamben, Bali. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1158-1175. [PMID: 38008858 DOI: 10.1007/s10126-023-10268-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/04/2023] [Indexed: 11/28/2023]
Abstract
Sponges (Porifera) harbor a diversity of microorganisms that contribute largely to the production a vast array of bioactive compounds. The microorganisms associated with sponge have an important impact on the chemical diversity of the natural products. Herein, our study focuses on an Aaptos suberitoides commonly found in Indonesia. The objective of this study was to investigate the profile of prokaryotic community and the presence of aaptamine metabolites in sponge Aaptos suberitoides. Sponges were collected from two site locations (Liberty Wreck and Drop Off) in Tulamben, Bali. The sponges were identified by barcoding DNA cytochrome oxidase subunit I (COI) gene. The profile of prokaryotic composition was investigated by amplifying the 16S rRNA gene using primers 515f and 806r to target the V4 region. The metabolites were analyzed using LC-MS, and dereplication was done to identify the aaptamines and its derivates. The barcoding DNA of the sponges confirmed the identity of samples as Aaptos suberitoides. The prokaryotic communities of samples A. suberitoides were enriched and dominated by taxa Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria. The chemical analysis showed that all sponges produce aaptamine and isoaaptamine except A. suberitoides S2421 produce analog of aaptamines. This is the first report on the profile of prokaryotic community and the aaptamine of tropical marine sponges, A. suberitoides, from Tulamben, Bali.
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Affiliation(s)
- Ni Kadek Dita Cahyani
- Biology Department, Faculty of Science and Mathematics, Diponegoro University, Semarang, Central Java, Indonesia
| | - Noer Kasanah
- Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Dewi Sri Kurnia
- Department of Biotechnology, Graduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mark T Hamann
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC, USA
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26
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Upender I, Yoshida O, Schrecengost A, Ranson H, Wu Q, Rowley DC, Kishore S, Cywes C, Miller EL, Whalen KE. A marine-derived fatty acid targets the cell membrane of Gram-positive bacteria. J Bacteriol 2023; 205:e0031023. [PMID: 37905811 PMCID: PMC10662121 DOI: 10.1128/jb.00310-23] [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: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE With the lack of new antibiotics in the drug discovery pipeline, coupled with accelerated evolution of antibiotic resistance, new sources of antibiotics that target pathogens of clinical importance are paramount. Here, we use bacterial cytological profiling to identify the mechanism of action of the monounsaturated fatty acid (Z)-13-methyltetra-4-decenoic acid isolated from the marine bacterium Olleya marilimosa with antibacterial effects against Gram-positive bacteria. The fatty acid antibiotic was found to rapidly destabilize the cell membrane by pore formation and membrane aggregation in Bacillus subtilis, suggesting that this fatty acid may be a promising adjuvant used in combination to enhance antibiotic sensitivity.
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Affiliation(s)
- Isha Upender
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Olivia Yoshida
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Anna Schrecengost
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Hilary Ranson
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Qihao Wu
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - David C. Rowley
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Shreya Kishore
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Claire Cywes
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Eric L. Miller
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | - Kristen E. Whalen
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
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27
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Gavriilidou A, Avcı B, Galani A, Schorn MA, Ingham CJ, Ettema TJG, Smidt H, Sipkema D. Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle. THE ISME JOURNAL 2023; 17:1808-1818. [PMID: 37587369 PMCID: PMC10579324 DOI: 10.1038/s41396-023-01484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 08/18/2023]
Abstract
Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
| | - Burak Avcı
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Anastasia Galani
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine BV, Verenigingstraat 36, 3515GJ, Utrecht, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
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28
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Zhang M, Song Q, Sang J, Li Z. Paenibacillus spongiae sp. nov. isolated from deep-water marine sponge Theonella swinhoei. Int J Syst Evol Microbiol 2023; 73. [PMID: 37910170 DOI: 10.1099/ijsem.0.006122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
A novel bacterial strain, designated as PHS-Z3T, was isolated from a marine sponge belonging to the genus Theonella on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3T were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3T showed 97.9 %, 96.7 %, and 96.2 % identities to Paenibacillus mendelii C/2T, Paenibacillus oenotherae DT7-4T and Paenibacillus aurantiacus RC11T, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3T formed an independent cluster with Paenibacillus mendelii C/2T. The total genome of PHS-Z3T was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3T and other type strains of species of the genus Paenibacillus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3T and those of members of the genus Paenibacillus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C15 : 0 and C16 : 0. The major polar lipids of PHS-Z3T consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3T was diamino heptanoic acid (meso-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus spongiae sp. nov. is proposed, with the type strain PHS-Z3T (=MCCC 1K07848T=KCTC 43443T).
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Affiliation(s)
- Mimi Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Qianqian Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jin Sang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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29
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Nugraha AS, Firli LN, Rani DM, Hidayatiningsih A, Lestari ND, Wongso H, Tarman K, Rahaweman AC, Manurung J, Ariantari NP, Papu A, Putra MY, Pratama ANW, Wessjohann LA, Keller PA. Indonesian marine and its medicinal contribution. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:38. [PMID: 37843645 PMCID: PMC10579215 DOI: 10.1007/s13659-023-00403-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
The archipelagic country of Indonesia is populated by the densest marine biodiversity in the world which has created strong global interest and is valued by both Indigenous and European settlements for different purposes. Nearly 1000 chemicals have been extracted and identified. In this review, a systematic data curation was employed to collate bioprospecting related manuscripts providing a comprehensive directory based on publications from 1988 to 2022. Findings with significant pharmacological activities are further discussed through a scoping data collection. This review discusses macroorganisms (Sponges, Ascidian, Gorgonians, Algae, Mangrove) and microorganism (Bacteria and Fungi) and highlights significant discoveries, including a potent microtubule stabilizer laulimalide from Hyattella sp., a prospective doxorubicin complement papuamine alkaloid from Neopetrosia cf exigua, potent antiplasmodial manzamine A from Acanthostrongylophora ingens, the highly potent anti trypanosomal manadoperoxide B from Plakortis cfr. Simplex, mRNA translation disrupter hippuristanol from Briareum sp, and the anti-HIV-1 (+)-8-hydroxymanzamine A isolated from Acanthostrongylophora sp. Further, some potent antibacterial extracts were also found from a limited biomass of bacteria cultures. Although there are currently no examples of commercial drugs from the Indonesian marine environment, this review shows the molecular diversity present and with the known understudied biodiversity, reveals great promise for future studies and outcomes.
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Affiliation(s)
- Ari Satia Nugraha
- Drug Utilisation and Discovery Research Group, Faculty of Pharmacy, Universitas Jember, Jember, 68121, Indonesia.
- Leibniz Institute Für Pflanzenbiochemie, Weinberg 3, 06120, Halle (Saale), Germany.
- School of Chemistry and Molecular Biosciences, Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia.
| | - Lilla Nur Firli
- Drug Utilisation and Discovery Research Group, Faculty of Pharmacy, Universitas Jember, Jember, 68121, Indonesia
| | - Dinar Mutia Rani
- Drug Utilisation and Discovery Research Group, Faculty of Pharmacy, Universitas Jember, Jember, 68121, Indonesia
| | - Ayunda Hidayatiningsih
- Drug Utilisation and Discovery Research Group, Faculty of Pharmacy, Universitas Jember, Jember, 68121, Indonesia
| | - Nadya Dini Lestari
- Drug Utilisation and Discovery Research Group, Faculty of Pharmacy, Universitas Jember, Jember, 68121, Indonesia
| | - Hendris Wongso
- Research Center for Radioisotope, Radiopharmaceutical, and Biodosimetry Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, Puspiptek, Banten, 15314, Indonesia
- Research Collaboration Center for Theranostic Radiopharmaceuticals, National Research and Innovation Agency, J1. Raya Bandung-Sumedang KM 21, Sumedang, 45363, Indonesia
| | - Kustiariyah Tarman
- Department of Aquatic Product Technology, Faculty of Fisheries and Marine Sciences; and Division of Marine Biotechnology, Centre for Coastal and Marine Resources Studies (CCMRS), IPB University, Bogor, 16680, Indonesia
| | | | - Jeprianto Manurung
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Ni Putu Ariantari
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Udayana University, Badung, Bali, 80361, Indonesia
| | - Adelfia Papu
- Biology Department, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, 95115, Indonesia
| | - Masteria Yunovilsa Putra
- Vaccine and Drug Research Center, National Research and Innovation Agency, Cibinong, Jawa Barat, 16911, Indonesia
| | | | - Ludger A Wessjohann
- Leibniz Institute Für Pflanzenbiochemie, Weinberg 3, 06120, Halle (Saale), Germany
| | - Paul A Keller
- School of Chemistry and Molecular Biosciences, Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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Bell JJ, Strano F, Broadribb M, Wood G, Harris B, Resende AC, Novak E, Micaroni V. Sponge functional roles in a changing world. ADVANCES IN MARINE BIOLOGY 2023; 95:27-89. [PMID: 37923539 DOI: 10.1016/bs.amb.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Sponges are ecologically important benthic organisms with many important functional roles. However, despite increasing global interest in the functions that sponges perform, there has been limited focus on how such functions will be impacted by different anthropogenic stressors. In this review, we describe the progress that has been made in our understanding of the functional roles of sponges over the last 15 years and consider the impacts of anthropogenic stressors on these roles. We split sponge functional roles into interactions with the water column and associations with other organisms. We found evidence for an increasing focus on functional roles among sponge-focused research articles, with our understanding of sponge-mediated nutrient cycling increasing substantially in recent years. From the information available, many anthropogenic stressors have the potential to negatively impact sponge pumping, and therefore have the potential to cause ecosystem level impacts. While our understanding of the importance of sponges has increased in the last 15 years, much more experimental work is required to fully understand how sponges will contribute to reef ecosystem function in future changing oceans.
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Affiliation(s)
- James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Manon Broadribb
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gabriela Wood
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Ben Harris
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Anna Carolina Resende
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Emma Novak
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Lagopati N, Pippa N, Gatou MA, Papadopoulou-Fermeli N, Gorgoulis VG, Gazouli M, Pavlatou EA. Marine-Originated Materials and Their Potential Use in Biomedicine. APPLIED SCIENCES 2023; 13:9172. [DOI: 10.3390/app13169172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
Aquatic habitats cover almost 70% of the Earth, containing several species contributing to marine biodiversity. Marine and aquatic organisms are rich in chemical compounds that can be widely used in biomedicine (dentistry, pharmacy, cosmetology, etc.) as alternative raw biomaterials or in food supplements. Their structural characteristics make them promising candidates for tissue engineering approaches in regenerative medicine. Thus, seaweeds, marine sponges, arthropods, cnidaria, mollusks, and the biomaterials provided by them, such as alginate, vitamins, laminarin, collagen, chitin, chitosan, gelatin, hydroxyapatite, biosilica, etc., are going to be discussed focusing on the biomedical applications of these marine-originated biomaterials. The ultimate goal is to highlight the sustainability of the use of these biomaterials instead of conventional ones, mainly due to the antimicrobial, anti-inflammatory, anti-aging and anticancer effect.
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Affiliation(s)
- Nefeli Lagopati
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Natassa Pippa
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Maria-Anna Gatou
- Laboratory of General Chemistry, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15772 Athens, Greece
| | - Nefeli Papadopoulou-Fermeli
- Laboratory of General Chemistry, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15772 Athens, Greece
| | - Vassilis G. Gorgoulis
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National Kapodistrian University of Athens (NKUA), 11527 Athens, Greece
- Clinical Molecular Pathology, Medical School, University of Dundee, Dundee DD1 9SY, UK
- Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M20 4GJ, UK
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, Surrey GU2 7YH, UK
| | - Maria Gazouli
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- School of Science and Technology, Hellenic Open University, 26335 Patra, Greece
| | - Evangelia A. Pavlatou
- Laboratory of General Chemistry, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15772 Athens, Greece
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Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M. Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta. THE ISME JOURNAL 2023; 17:1208-1223. [PMID: 37188915 PMCID: PMC10356861 DOI: 10.1038/s41396-023-01420-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.
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Affiliation(s)
- Florian U Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cherie Motti
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bettina Glasl
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, St Lucia, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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35
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Stuij T, Cleary DFR, Polónia ARM, Putchakarn S, Pires ACC, Gomes NCM, de Voogd NJ. Exploring Prokaryotic Communities in the Guts and Mucus of Nudibranchs, and Their Similarity to Sediment and Seawater Microbiomes. Curr Microbiol 2023; 80:294. [PMID: 37481620 PMCID: PMC10363043 DOI: 10.1007/s00284-023-03397-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 07/01/2023] [Indexed: 07/24/2023]
Abstract
In the present study, we compared mucus and gut-associated prokaryotic communities from seven nudibranch species with sediment and seawater from Thai coral reefs using high-throughput 16S rRNA gene sequencing. The nudibranch species were identified as Doriprismatica atromarginata (family Chromodorididae), Jorunna funebris (family Discodorididae), Phyllidiella nigra, Phyllidiella pustulosa, Phyllidia carlsonhoffi, Phyllidia elegans, and Phyllidia picta (all family Phyllidiidae). The most abundant bacterial phyla in the dataset were Proteobacteria, Tenericutes, Chloroflexi, Thaumarchaeota, and Cyanobacteria. Mucus and gut-associated communities differed from one another and from sediment and seawater communities. Host phylogeny was, furthermore, a significant predictor of differences in mucus and gut-associated prokaryotic community composition. With respect to higher taxon abundance, the order Rhizobiales (Proteobacteria) was more abundant in Phyllidia species (mucus and gut), whereas the order Mycoplasmatales (Tenericutes) was more abundant in D. atromarginata and J. funebris. Mucus samples were, furthermore, associated with greater abundances of certain phyla including Chloroflexi, Poribacteria, and Gemmatimonadetes, taxa considered to be indicators for high microbial abundance (HMA) sponge species. Overall, our results indicated that nudibranch microbiomes consisted of a number of abundant prokaryotic members with high sequence similarities to organisms previously detected in sponges.
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Affiliation(s)
- Tamara Stuij
- Department of Biology, CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology, CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology, CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Sumaitt Putchakarn
- Institute of Marine Science, Burapha University, Chon Buri, 20131, Thailand
| | - Ana C C Pires
- Department of Biology, CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology, CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.
- Environmental Biology Department, Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
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36
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Caudal F, Rodrigues S, Dufour A, Artigaud S, Le Blay G, Petek S, Bazire A. Extracts from Wallis Sponges Inhibit Vibrio harveyi Biofilm Formation. Microorganisms 2023; 11:1762. [PMID: 37512934 PMCID: PMC10383632 DOI: 10.3390/microorganisms11071762] [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: 06/09/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Pathogenic bacteria and their biofilms are involved in many human and animal diseases and are a major public health problem with, among other things, the development of antibiotic resistance. These biofilms are known to induce chronic infections for which classical treatments using antibiotic therapy are often ineffective. Sponges are sessile filter-feeding marine organisms known for their dynamic symbiotic partnerships with diverse microorganisms and their production of numerous metabolites of interest. In this study, we investigated the antibiofilm efficacy of different extracts from sponges, isolated in Wallis, without biocidal activity. Out of the 47 tested extracts, from 28 different genera, 11 showed a strong activity against Vibrio harveyi biofilm formation. Moreover, one of these extracts also inhibited two quorum-sensing pathways of V. harveyi.
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Affiliation(s)
- Flore Caudal
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Sophie Rodrigues
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
| | - Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
| | | | | | - Sylvain Petek
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Alexis Bazire
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
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37
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Hamoda AM, Hamdy R, Fayed B, Abouleish M, Sulaiman A, Hamad M, Soliman SSM. Evolutionary relevance of metabolite production in relation to marine sponge bacteria symbiont. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12649-3. [PMID: 37358811 DOI: 10.1007/s00253-023-12649-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/14/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Sponges are habitats for a diverse community of microorganisms. Sponges provide shelter, whereas microbes provide a complementary defensive mechanism. Here, a symbiotic bacterium, identified as Bacillus spp., was isolated from a marine sponge following culture enrichment. Fermentation-assisted metabolomics using thin-layer chromatography (TLC) and gas chromatography-mass spectrometry (GC-MS) indicated that marine simulated nutrition and temperature was the optimum in metabolite production represented by the highest number of metabolites and the diverse chemical classes when compared to other culture media. Following large-scale culture in potato dextrose broth (PDB) and dereplication, compound M1 was isolated and identified as octadecyl-1-(2',6'-di-tert-butyl-1'-hydroxyphenyl) propionate. M1, at screening concentrations up to 10 mg/ml, showed no activity against prokaryotic bacteria including Staphylococcus aureus and Escherichia coli, while 1 mg/ml of M1 was sufficient to cause a significant killing effect on eukaryotic cells including Candida albicans, Candida auris, and Rhizopus delemar fungi and different mammalian cells. M1 exhibited MIC50 0.97 ± 0.006 and 7.667 ± 0.079 mg/ml against C. albicans and C. auris, respectively. Like fatty acid esters, we hypothesize that M1 is stored in a less harmful form and upon pathogenic attack is hydrolyzed to a more active form as a defensive metabolite. Subsequently, [3-(3,5-di-tert-butyl-4-hydroxyphenyl)-propionic acid] (DTBPA), the hydrolysis product of M1, exhibited ~ 8-fold and 18-fold more antifungal activity than M1 against C. albicans and C. auris, respectively. These findings indicated the selectivity of that compound as a defensive metabolite towards the eukaryotic cells particularly the fungi, a major infectious agent to sponges. Metabolomic-assisted fermentation can provide a significant understanding of a triple marine-evolved interaction. KEY POINTS: • Bacillus species, closely related to uncultured Bacillus, is isolated from Gulf marine sponge • Metabolomic-assisted fermentations showed diverse metabolites • An ester with a killing effect against eukaryotes but not prokaryotes is isolated.
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Affiliation(s)
- Alshaimaa M Hamoda
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- College of Medicine, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut-71526, Egypt
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Bahgat Fayed
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Chemistry of Natural and Microbial Product Department, National Research Centre, Cairo, Egypt
| | - Mohamed Abouleish
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Ashna Sulaiman
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Mohamad Hamad
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Medical Laboratory Sciences, Collage of Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Sameh S M Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
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38
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Freitas MAMD, Cunha-Ferreira IC, Leal CV, Fernandez JCC, Omachi CY, Campos LS, Masi BP, Krüger RH, Hajdu E, Thompson CC, Thompson FL. Microbiome diversity from sponges biogeographically distributed between South America and Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163256. [PMID: 37011689 DOI: 10.1016/j.scitotenv.2023.163256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Sponges from South America and Antarctica are evolutionarily closely related. Specific symbiont signatures that could differentiate these two geographic regions are unknown. This study aimed to investigate the microbiome diversity of sponges from South America and Antarctica. In total 71 sponge specimens were analyzed (Antarctica: N = 59, 13 different species; South America: N = 12, 6 different species). Illumina 16S rRNA sequences were generated (2.88 million sequences; 40K ± 29K/sample). The most abundant symbionts were heterotrophic (94.8 %) and belonged mainly to Proteobacteria and Bacteroidota. EC94 was the most abundant symbiont and dominated the microbiome of some species (70-87 %), comprising at least 10 phylogroups. Each of the EC94 phylogroups was specific to one genus or species of sponge. Furthermore, South America sponges had higher abundance of photosynthetic microorganisms (2.3 %) and sponges from Antarctica, the highest abundance of chemosynthetic (5.5 %). Sponge symbionts may contribute to the function of their hosts. The unique features from each of these two regions (e.g., light, temperature, and nutrients) possibly stimulate distinct microbiome diversity from sponges biogeographically distributed across continents.
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Affiliation(s)
- Mayanne A M de Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Camille V Leal
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Julio C C Fernandez
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Claudia Y Omachi
- Laboratory of Environmental Indicators, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Lucia S Campos
- Department of Zoology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno P Masi
- Laboratory of Marine Ecology and Fishery Oceanography of the Amazon (LEMOPA), Socio environmental and Water Resources Institute (ISARH), Federal Rural University of the Amazon (UFRA), Belém, PA, Brazil
| | - Ricardo H Krüger
- Laboratory of Enzymology, Biology Institute, University of Brasília (UNB), Brasília, Brazil
| | - Eduardo Hajdu
- Laboratory of Environmental Indicators, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Cristiane C Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Botté ES, Bennett H, Engelberts JP, Thomas T, Bell JJ, Webster NS, Luter HM. Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis. ISME COMMUNICATIONS 2023; 3:53. [PMID: 37311801 PMCID: PMC10264452 DOI: 10.1038/s43705-023-00247-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 04/14/2023] [Indexed: 06/15/2023]
Abstract
Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.
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Affiliation(s)
- Emmanuelle S Botté
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Victoria University of Wellington, Wellington, New Zealand
- Cawthron Institute, Nelson, New Zealand
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - James J Bell
- Victoria University of Wellington, Wellington, New Zealand
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Heidi M Luter
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
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40
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Roveta C, Calcinai B, Girolametti F, Fernandes Couceiro J, Puce S, Annibaldi A, Costa R. The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection. ZOOLOGY 2023; 158:126091. [PMID: 37003141 DOI: 10.1016/j.zool.2023.126091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Microbial communities inhabiting sponges are known to take part in many metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of 16S rRNA genes to characterize the prokaryotic communities present in the cortex and choanosome, respectively the external and internal body region of Chondrosia reniformis, and in the surrounding seawater. Furthermore, we estimated the total mercury content (THg) in these body regions of the sponge and in the corresponding microbial cell pellets. Fifteen prokaryotic phyla were detected in association with C. reniformis, 13 belonging to the domain Bacteria and two to the Archaea. No significant differences between the prokaryotic community composition of the two regions were found. Three lineages of ammonium-oxidizing organisms (Cenarchaeum symbiosum, Nitrosopumilus maritimus, and Nitrosococcus sp.) co-dominated the prokaryotic community, suggesting ammonium oxidation/nitrification as a key metabolic pathway within the microbiome of C. reniformis. In the sponge fractions, higher THg levels were found in the choanosome compared to the cortex. In contrast, comparable THg levels found in the microbial pellets obtained from both regions were significantly lower than those observed in the corresponding sponge fractions. Our work provides new insights into the prokaryotic communities and TEs distribution in different body parts of a model organism relevant for marine conservation and biotechnology. In this sense, this study paves the way for scientists to deepen the possible application of sponges not only as bioindicators, but also as bioremediation tools of metal polluted environments.
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Affiliation(s)
- Camilla Roveta
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Barbara Calcinai
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Federico Girolametti
- Department of Industrial Engineering and Mathematical Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Joana Fernandes Couceiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Stefania Puce
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna Annibaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Portugal
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Gantt SE, Erwin PM. Effects of sponge-to-sponge contact on the microbiomes of three spatially competing Caribbean coral reef species. Microbiologyopen 2023; 12:e1354. [PMID: 37379422 DOI: 10.1002/mbo3.1354] [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: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 06/30/2023] Open
Abstract
Sponges perform important ecosystem functions, host diverse microbial symbiont communities (microbiomes), and have been increasing in density on Caribbean coral reefs over the last decade. Sponges compete for space in coral reef communities through both morphological and allelopathic strategies, but no studies of microbiome impacts during these interactions have been conducted. Microbiome alterations mediate spatial competition in other coral reef invertebrates and may similarly impact competitive outcomes for sponges. In this study, we characterized the microbiomes of three common Caribbean sponges (Agelas tubulata, Iotrochota birotulata, and Xestospongia muta) observed to naturally interact spatially in Key Largo, Florida (USA). For each species, replicate samples were collected from sponges in contact with neighbors at the site of contact (contact) and distant from the site of contact (no contact), and from sponges spatially isolated from neighbors (control). Next-generation amplicon sequencing (V4 region of 16S rRNA) revealed significant differences in microbial community structure and diversity among sponge species, but no significant effects were observed within sponge species across all contact states and competitor pairings, indicating no large community shifts in response to direct contact. At a finer scale, particular symbiont taxa (operational taxonomic units at 97% sequence identity, OTUs) were shown to decrease significantly in some interaction pairings, suggesting localized effects for specific sponge competitors. Overall, these results revealed that direct contact during spatial competition does not significantly alter microbial community composition or structure of interacting sponges, suggesting that allelopathic interactions and competitive outcomes are not mediated by microbiome damage or destabilization.
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Affiliation(s)
- Shelby E Gantt
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Patrick M Erwin
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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Peters EE, Cahn JKB, Lotti A, Gavriilidou A, Steffens UAE, Loureiro C, Schorn MA, Cárdenas P, Vickneswaran N, Crews P, Sipkema D, Piel J. Distribution and diversity of 'Tectomicrobia', a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites. ISME COMMUNICATIONS 2023; 3:50. [PMID: 37248312 PMCID: PMC10227082 DOI: 10.1038/s43705-023-00259-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus 'Entotheonella' has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested 'Entotheonella' as the first members of a new candidate phylum, 'Tectomicrobia'. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that 'Entotheonella' and other 'Tectomicrobia' are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described 'Entotheonella' lineage can be more accurately divided into at least three different candidate genera with the terrestrial 'Candidatus Prasianella', the largely terrestrial 'Candidatus Allonella', the 'Candidatus Thalassonella' comprising sponge-associated members, and the more widely distributed 'Candidatus Entotheonella'. Genomic characterization of 'Thalassonella' members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to 'Entotheonella' regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised 'Entotheonella' 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich 'Entotheonella' variants, and led to the identification of the first 'Entotheonella' symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of 'Entotheonella'-based chemical symbiosis.
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Affiliation(s)
- Eike E Peters
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Jackson K B Cahn
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Alessandro Lotti
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Ursula A E Steffens
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, BioMedical Center, Uppsala University, Husargatan 3, 75124, Uppsala, Sweden
| | - Nilani Vickneswaran
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.
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43
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Segaran TC, Azra MN, Lananan F, Wang Y. Microbe, climate change and marine environment: Linking trends and research hotspots. MARINE ENVIRONMENTAL RESEARCH 2023:106015. [PMID: 37291004 DOI: 10.1016/j.marenvres.2023.106015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 06/10/2023]
Abstract
Microbes, or microorganisms, have been the foundation of the biosphere for over 3 billion years and have played an essential role in shaping our planet. The available knowledge on the topic of microbes associated with climate change has the potential to reshape upcoming research trends globally. As climate change impacts the ocean or marine ecosystem, the responses of these "unseen life" will heavily influence the achievement of a sustainable evolutionary environment. The present study aims to identify microbial-related research under changing climate within the marine environment through the mapping of visualized graphs of the available literature. We used scientometric methods to retrieve documents from the Web of Science platform in the Core Collection (WOSCC) database, analyzing a total of 2767 documents based on scientometric indicators. Our findings show that this research area is growing exponentially, with the most influential keywords being "microbial diversity," "bacteria," and "ocean acidification," and the most cited being "microorganism" and "diversity." The identification of influential clusters in the field of marine science provides insight into the hot spots and frontiers of research in this area. Prominent clusters include "coral microbiome," "hypoxic zone," "novel Thermoplasmatota clade," "marine dinoflagellate bloom," and "human health." Analyzing emerging trends and transformative changes in this field can inform the creation of special issues or research topics in selected journals, thus increasing visibility and engagement among the scientific community.
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Affiliation(s)
- Thirukanthan Chandra Segaran
- Climate Change Adaptation Laboratory, Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Mohamad Nor Azra
- Climate Change Adaptation Laboratory, Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), 21030, Kuala Nerus, Terengganu, Malaysia; Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Organization, National Research and Innovation Agency (BRIN), Pemenang, West Nusa Tenggara, 83352, Indonesia.
| | - Fathurrahman Lananan
- East Coast Environmental Research Institute, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia.
| | - Youji Wang
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China.
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Carr CM, Keller MB, Paul B, Schubert SW, Clausen KSR, Jensen K, Clarke DJ, Westh P, Dobson ADW. Purification and biochemical characterization of SM14est, a PET-hydrolyzing enzyme from the marine sponge-derived Streptomyces sp. SM14. Front Microbiol 2023; 14:1170880. [PMID: 37250061 PMCID: PMC10213408 DOI: 10.3389/fmicb.2023.1170880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
The successful enzymatic degradation of polyester substrates has fueled worldwide investigation into the treatment of plastic waste using bio-based processes. Within this realm, marine-associated microorganisms have emerged as a promising source of polyester-degrading enzymes. In this work, we describe the hydrolysis of the synthetic polymer PET by SM14est, a polyesterase which was previously identified from Streptomyces sp. SM14, an isolate of the marine sponge Haliclona simulans. The PET hydrolase activity of purified SM14est was assessed using a suspension-based assay and subsequent analysis of reaction products by UV-spectrophotometry and RP-HPLC. SM14est displayed a preference for high salt conditions, with activity significantly increasing at sodium chloride concentrations from 100 mM up to 1,000 mM. The initial rate of PET hydrolysis by SM14est was determined to be 0.004 s-1 at 45°C, which was increased by 5-fold to 0.02 s-1 upon addition of 500 mM sodium chloride. Sequence alignment and structural comparison with known PET hydrolases, including the marine halophile PET6, and the highly efficient, thermophilic PHL7, revealed conserved features of interest. Based on this work, SM14est emerges as a useful enzyme that is more similar to key players in the area of PET hydrolysis, like PHL7 and IsPETase, than it is to its marine counterparts. Salt-tolerant polyesterases such as SM14est are potentially valuable in the biological degradation of plastic particles that readily contaminate marine ecosystems and industrial wastewaters.
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Affiliation(s)
- Clodagh M. Carr
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
| | - Malene B. Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Bijoya Paul
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sune W. Schubert
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Kristine S. R. Clausen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - David J. Clarke
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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45
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Bibi F, Naseer MI, Azhar EI. Exploring bioactive compounds from a symbiotic bacterial strain of Spongiobacter sp. Bioinformation 2023; 19:369-374. [PMID: 37822833 PMCID: PMC10563573 DOI: 10.6026/97320630019369] [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: 04/01/2023] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 10/13/2023] Open
Abstract
Marine sponges are a host of different symbiotic groups of bacteria playing crucial roles in the protection and survival of marine sponges. Marine symbiotic bacteria from sponges are promising sources of bioactive chemicals and are increasingly being investigated. Therefore, the present study was undertaken to analyze total compounds from active symbiotic bacterial strain from sponge, Pione vastifical. Potential bacterial strain EA276 previously isolated from P. vastifical and was identified as Spongiobacter sp. Among 57 isolates, only 42% exhibited antagonistic activity. Four major classes of bacteria were reported previously where γ-Proteobacteria, was the dominant class. From these active antagonistic bacterial isolates, a potential bacterial strain Spongiobacter sp. EA276 was selected, and total metabolites were identified using GC and LC-MS analyses. Using LC-MS analysis bioactive compounds Dichlorphenamide, Amifloxacin and Carbenicillin are identified in both positive and negative mode. Plant growth hormones, Indole-3-acetic acid and Methyl jasmonate were identified using GC-MS analysis from culture extract of strain Spongiobacter sp. EA276. Our results highlighted the significance of marine flora inhabiting sponges from the Red Sea as potential source of bioactive compounds and plant growth hormones of biological and agricultural significance.
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Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Fang G, Yu H, Zhang Y, Liang J, Tang Y, Liang Z. Diversities and Shifts of Microbial Communities Associated with Farmed Oysters ( Crassostrea gigas) and Their Surrounding Environments in Laoshan Bay Marine Ranching, China. Microorganisms 2023; 11:1167. [PMID: 37317141 DOI: 10.3390/microorganisms11051167] [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: 03/05/2023] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Pacific oysters (Crassostrea gigas) are widely cultured in Chinese marine ranching with high economic value. However, mass death of farmed oysters has occurred frequently in recent years because of diseases and environmental disturbance (e.g., high temperatures). In order to analyze the potential relationships between microorganisms and the death of farmed oysters, we compared the dynamics of bacterial and protist communities in oysters at different growth phases using high-throughput sequencing. The results showed that the microbial communities in farmed oysters significantly changed and were markedly different from microbes in natural oysters and the surrounding environments. The number of biomarker taxa among farmed oysters and their surrounding environments decreased gradually with the growth of oysters. During the mass death of farmed oysters, the microbial communities' abundance of ecological function genes changed, and the correlations among microorganisms disappeared. These results enrich our understanding of the dynamics of microbial communities in farmed oysters at different growth phases, illustrating the characteristics of interactions among microorganisms during the mass death of farmed oysters. Our study is beneficial to promote the healthy aquaculture of oysters.
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Affiliation(s)
- Guangjie Fang
- Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resources of Zhejiang Province, Zhoushan 316021, China
- Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhoushan 316021, China
| | - Haolin Yu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yazhou Zhang
- Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resources of Zhejiang Province, Zhoushan 316021, China
- Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhoushan 316021, China
| | - Jun Liang
- Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resources of Zhejiang Province, Zhoushan 316021, China
- Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Zhoushan 316021, China
| | - Yanli Tang
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Zhenlin Liang
- Marine College, Shandong University, Weihai 264209, China
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47
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Nguyen VH, Wemheuer B, Song W, Bennett H, Webster N, Thomas T. Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species. Syst Appl Microbiol 2023; 46:126426. [PMID: 37141831 DOI: 10.1016/j.syapm.2023.126426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Brown MO, Olagunju BO, Giner JL, Welander PV. Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations. Nat Commun 2023; 14:1859. [PMID: 37012227 PMCID: PMC10070321 DOI: 10.1038/s41467-023-37552-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Sterane molecular fossils are broadly interpreted as eukaryotic biomarkers, although diverse bacteria also produce sterols. Steranes with side-chain methylations can act as more specific biomarkers if their sterol precursors are limited to particular eukaryotes and are absent in bacteria. One such sterane, 24-isopropylcholestane, has been attributed to demosponges and potentially represents the earliest evidence for animals on Earth, but enzymes that methylate sterols to give the 24-isopropyl side-chain remain undiscovered. Here, we show that sterol methyltransferases from both sponges and yet-uncultured bacteria function in vitro and identify three methyltransferases from symbiotic bacteria each capable of sequential methylations resulting in the 24-isopropyl sterol side-chain. We demonstrate that bacteria have the genomic capacity to synthesize side-chain alkylated sterols, and that bacterial symbionts may contribute to 24-isopropyl sterol biosynthesis in demosponges. Together, our results suggest bacteria should not be dismissed as potential contributing sources of side-chain alkylated sterane biomarkers in the rock record.
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Affiliation(s)
- Malory O Brown
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Babatunde O Olagunju
- Department of Chemistry, State University of New York-Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - José-Luis Giner
- Department of Chemistry, State University of New York-Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
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Nascimento-Silva G, Costa CM, Lobo-Hajdu G, Custódio MR, Hardoim CCP. Diversity and structure of bacterial and archaeal communities associated with the vulnerable sponge Halichondria cebimarensis. Antonie Van Leeuwenhoek 2023; 116:367-382. [PMID: 36646940 DOI: 10.1007/s10482-023-01808-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023]
Abstract
Sponges are essential components of the marine benthos and well known for their complex and abundant associated microbial communities. There are five endemic species of the genus Halichondria on the Brazilian coast and H. cebimarensis is one of the least studied. This sponge has a very limited geographic distribution and is classified as vulnerable. In order to understand the bacterial and archaeal communities associated with this sponge, samples of H. cebimarensis were collected from the southwestern Atlantic coast (Brazil, São Paulo state). Choanosome samples were separated and processed to be (i) inoculated in three different culture media; (ii) investigated by transmission electron microscopy; (iii) submitted to 16S rRNA metabarcoding. Forty isolates were obtained and 12 were identified as belonging to the Bacilli class. The culture-dependent approaches allowed us to access unique members of the microbial community. Our analyses revealed that this animal belongs to the Low Microbial Abundance group of sponges. Culture-independent approaches showed that the H. cebimarensis microbiome is dominated by the heterotrophic Gammaproteobacteria AqS2 ("Ca. Amphirhobacter heronislandensis"). This is the first study to reveal details of the microbiome of this vulnerable sponge and is an important step in understanding how this sponge functions, its biotechnological potential and a contribution to conservation efforts.
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Affiliation(s)
| | | | - Gisele Lobo-Hajdu
- Departament of Genetic, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Márcio Reis Custódio
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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50
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Nguyen VH, Wemheuer B, Song W, Bennett H, Palladino G, Burgsdorf I, Sizikov S, Steindler L, Webster NS, Thomas T. Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges. Syst Appl Microbiol 2023; 46:126401. [PMID: 36774720 DOI: 10.1016/j.syapm.2023.126401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Cawthron Institute, Nelson, New Zealand
| | - Giorgia Palladino
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | | | | | | | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia; Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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