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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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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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3
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González-Pech RA, Li VY, Garcia V, Boville E, Mammone M, Kitano H, Ritchie KB, Medina M. The Evolution, Assembly, and Dynamics of Marine Holobionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:443-466. [PMID: 37552896 DOI: 10.1146/annurev-marine-022123-104345] [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: 08/10/2023]
Abstract
The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.
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Affiliation(s)
- Raúl A González-Pech
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vivian Y Li
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vanessa Garcia
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Elizabeth Boville
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Marta Mammone
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina, Beaufort, South Carolina, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
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4
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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 PMCID: PMC11329227 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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5
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Steffen K, Proux-Wéra E, Soler L, Churcher A, Sundh J, Cárdenas P. Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae). G3 (BETHESDA, MD.) 2023; 13:jkad192. [PMID: 37619978 PMCID: PMC10542158 DOI: 10.1093/g3journal/jkad192] [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: 02/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023]
Abstract
Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes.
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Affiliation(s)
- Karin Steffen
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
| | - Estelle Proux-Wéra
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna SE-17121, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala 752 37, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå 901 87, Sweden
| | - John Sundh
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna SE-17121, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
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6
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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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7
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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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Chernogor L, Eliseikina M, Petrushin I, Chernogor E, Khanaev I, Belikov SI. Janthinobacterium sp. Strain SLB01 as Pathogenic Bacteria for Sponge Lubomirskia baikalensis. Pathogens 2022; 12:pathogens12010008. [PMID: 36678355 PMCID: PMC9860564 DOI: 10.3390/pathogens12010008] [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: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Sponges (phylum Porifera) are ancient, marine and inland water, filter feeding metazoans. In recent years, diseased sponges have been increasingly occurring in marine and freshwater environments. Endemic freshwater sponges of the Lubomirskiidae family are widely distributed in the coastal zone of Lake Baikal. The strain Janthinobacterium sp. SLB01 was isolated previously from the diseased sponge Lubomirskia baikalensis (Pallas, 1776), although its pathogenicity is still unknown. The aim of this study was to confirm whether the Janthinobacterium sp. strain SLB01 is the pathogen found in Baikal sponge. To address this aim, we infected the cell culture of primmorphs of the sponge L. baikalensis with strain SLB01 and subsequently reisolated and sequenced the strain Janthinobacterium sp. PLB02. The results showed that the isolated strain has more than 99% homology with strain SLB01. The genomes of both strains contain genes vioABCDE of violacein biosynthesis and floc formation, for strong biofilm, in addition to the type VI secretion system (T6SS) as the main virulence factor. Based on a comparison of complete genomes, we showed the similarity of the studied bacterial strains of Janthinobacterium spp. with the described strain of Janthinobacterium lividum MTR. This study will help expand our understanding of microbial interactions and determine one of the causes in the development of diseases and death in Baikal sponges.
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Affiliation(s)
- Lubov Chernogor
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
- Correspondence: (L.C.); (S.I.B.)
| | - Marina Eliseikina
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Ivan Petrushin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Ekaterina Chernogor
- Faculty of Business Communication and Informatics, Irkutsk State University, 664033 Irkutsk, Russia
| | - Igor Khanaev
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Sergei I. Belikov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
- Correspondence: (L.C.); (S.I.B.)
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de Menezes TA, de Freitas MAM, Lima MS, Soares AC, Leal C, Busch MDS, Tschoeke DA, de O Vidal L, Atella GC, Kruger RH, Setubal J, Vasconcelos AA, de Mahiques MM, Siegle E, Asp NE, Cosenza C, Hajdu E, de Rezende CE, Thompson CC, Thompson FL. Fluxes of the Amazon River plume nutrients and microbes into marine sponges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157474. [PMID: 35868367 DOI: 10.1016/j.scitotenv.2022.157474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/14/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km2 off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ13C and δ15N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.
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Affiliation(s)
- Tatiane A de Menezes
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mayanne A M de Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Michele S Lima
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ana Carolina Soares
- Bioinformatics Laboratory, Department of Biochemistry, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | - Camille Leal
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mileane de S Busch
- Laboratory of Lipids Biochemistry and Lipoprotein, Biochemistry Institute Leopoldo de Meis, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A Tschoeke
- Biomedical Engineering Program - COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciana de O Vidal
- Environmental Sciences Laboratory, Biosciences and Biotechnology Center, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil; Department of Ecology and Marine Resources, Institute of Biosciences, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Georgia C Atella
- Laboratory of Lipids Biochemistry and Lipoprotein, Biochemistry Institute Leopoldo de Meis, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ricardo H Kruger
- Laboratory of Enzymology, University of Brasilia (UNB), Brasilia, Brazil
| | - João Setubal
- Bioinformatics Laboratory, Department of Biochemistry, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | | | | | - Eduardo Siegle
- Oceanographic Institute (IO), University of São Paulo (USP), São Paulo, Brazil
| | - Nils Edvin Asp
- Federal University of Pará, Institute of Coastal Studies (IECOS), Bragança Campus, Bragança, PA, Brazil
| | - Carlos Cosenza
- Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Eduardo Hajdu
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carlos E de Rezende
- Environmental Sciences Laboratory, Biosciences and Biotechnology Center, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, 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; Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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10
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Lesser MP, Sabrina Pankey M, Slattery M, Macartney KJ, Gochfeld DJ. Microbiome diversity and metabolic capacity determines the trophic ecology of the holobiont in Caribbean sponges. ISME COMMUNICATIONS 2022; 2:112. [PMID: 37938762 PMCID: PMC9723761 DOI: 10.1038/s43705-022-00196-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 06/18/2023]
Abstract
Sponges are increasingly recognized as an ecologically important taxon on coral reefs, representing significant biomass and biodiversity where sponges have replaced scleractinian corals. Most sponge species can be divided into two symbiotic states based on symbiont community structure and abundance (i.e., the microbiome), and are characterized as high microbial abundance (HMA) or low microbial abundance (LMA) sponges. Across the Caribbean, sponge species of the HMA or LMA symbiotic states differ in metabolic capacity, as well as their trophic ecology. A metagenetic analysis of symbiont 16 S rRNA and metagenomes showed that HMA sponge microbiomes are more functionally diverse than LMA microbiomes, offer greater metabolic functional capacity and redundancy, and encode for the biosynthesis of secondary metabolites. Stable isotope analyses showed that HMA and LMA sponges primarily consume dissolved organic matter (DOM) derived from external autotrophic sources, or live particulate organic matter (POM) in the form of bacterioplankton, respectively, resulting in a low degree of resource competition between these symbiont states. As many coral reefs have undergone phase shifts from coral- to macroalgal-dominated reefs, the role of DOM, and the potential for future declines in POM due to decreased picoplankton productivity, may result in an increased abundance of chemically defended HMA sponges on tropical coral reefs.
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Affiliation(s)
- Michael P Lesser
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
| | - M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Marc Slattery
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, Oxford, MS, 38677, USA
| | - Keir J Macartney
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
- University of Texas Rio Grande Valley, School of Earth, Environmental and Marine Sciences, Port Isabel, TX, 78958, USA
| | - Deborah J Gochfeld
- National Center for Natural Products Research, University of Mississippi, Oxford, MS, 38677, USA
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11
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Díez-Vives C, Koutsouveli V, Conejero M, Riesgo A. Global patterns in symbiont selection and transmission strategies in sponges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1015592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sponges host dense and diverse communities of microbes (known as the microbiome) beneficial for the host nutrition and defense. Symbionts in turn receive shelter and metabolites from the sponge host, making their relationship beneficial for both partners. Given that sponge-microbes associations are fundamental for the survival of both, especially the sponge, such relationship is maintained through their life and even passed on to the future generations. In many organisms, the microbiome has profound effects on the development of the host, but the influence of the microbiome on the reproductive and developmental pathways of the sponges are less understood. In sponges, microbes are passed on to oocytes, sperm, embryos, and larvae (known as vertical transmission), using a variety of methods that include direct uptake from the mesohyl through phagocytosis by oocytes to indirect transmission to the oocyte by nurse cells. Such microbes can remain in the reproductive elements untouched, for transfer to offspring, or can be digested to make the yolky nutrient reserves of oocytes and larvae. When and how those decisions are made are fundamentally unanswered questions in sponge reproduction. Here we review the diversity of vertical transmission modes existent in the entire phylum Porifera through detailed imaging using electron microscopy, available metabarcoding data from reproductive elements, and macroevolutionary patterns associated to phylogenetic constraints. Additionally, we examine the fidelity of this vertical transmission and possible reasons for the observed variability in some developmental stages. Our current understanding in marine sponges, however, is that the adult microbial community is established by a combination of both vertical and horizontal (acquisition from the surrounding environment in each new generation) transmission processes, although the extent in which each mode shapes the adult microbiome still remains to be determined. We also assessed the fundamental role of filtration, the cellular structures for acquiring external microbes, and the role of the host immune system, that ultimately shapes the stable communities of prokaryotes observed in adult sponges.
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12
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Cleary DFR, Polónia ARM, Swierts T, Coelho FJRC, de Voogd NJ, Gomes NCM. Spatial and environmental variables structure sponge symbiont communities. Mol Ecol 2022; 31:4932-4948. [PMID: 35881675 PMCID: PMC9804187 DOI: 10.1111/mec.16631] [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: 06/11/2021] [Revised: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 01/05/2023]
Abstract
Understanding the maintenance and origin of beta diversity is a central topic in ecology. However, the factors that drive diversity patterns and underlying processes remain unclear, particularly for host-prokaryotic associations. Here, beta diversity patterns were studied in five prokaryotic biotopes, namely, two high microbial abundance (HMA) sponge taxa (Xestospongia spp. and Hyrtios erectus), one low microbial abundance (LMA) sponge taxon (Stylissa carteri), sediment and seawater sampled across thousands of kilometres. Using multiple regression on distance matrices (MRM), spatial (geographic distance) and environmental (sea surface temperature and chlorophyll α concentrations) variables proved significant predictors of beta diversity in all five biotopes and together explained from 54% to 82% of variation in dissimilarity of both HMA species, 27% to 43% of variation in sediment and seawater, but only 20% of variation of the LMA S. carteri. Variance partitioning was subsequently used to partition the variation into purely spatial, purely environmental and spatially-structured environmental components. The amount of variation in dissimilarity explained by the purely spatial component was lowest for S. carteri at 11% and highest for H. erectus at 55%. The purely environmental component, in turn, only explained from 0.15% to 2.83% of variation in all biotopes. In addition to spatial and environmental variables, a matrix of genetic differences between pairs of sponge individuals also proved a significant predictor of variation in prokaryotic dissimilarity of the Xestospongia species complex. We discuss the implications of these results for the HMA-LMA dichotomy and compare the MRM results with results obtained using constrained ordination and zeta diversity.
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Affiliation(s)
- Daniel F. R. Cleary
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Ana R. M. Polónia
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Thomas Swierts
- Marine Biodiversity, Naturalis Biodiversity CenterLeidenThe Netherlands,Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
| | - Francisco J. R. C. Coelho
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Nicole J. de Voogd
- Marine Biodiversity, Naturalis Biodiversity CenterLeidenThe Netherlands,Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
| | - Newton C. M. Gomes
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
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13
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The Porifera microeukaryome: Addressing the neglected associations between sponges and protists. Microbiol Res 2022; 265:127210. [PMID: 36183422 DOI: 10.1016/j.micres.2022.127210] [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: 05/02/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
Abstract
While bacterial and archaeal communities of sponges are intensively studied, given their importance to the animal's physiology as well as sources of several new bioactive molecules, the potential and roles of associated protists remain poorly known. Historically, culture-dependent approaches dominated the investigations of sponge-protist interactions. With the advances in omics techniques, these associations could be visualized at other equally important scales. Of the few existing studies, there is a strong tendency to focus on interactions with photosynthesizing taxa such as dinoflagellates and diatoms, with fewer works dissecting the interactions with other less common groups. In addition, there are bottlenecks and inherent biases in using primer pairs and bioinformatics approaches in the most commonly used metabarcoding studies. Thus, this review addresses the issues underlying this association, using the term "microeukaryome" to refer exclusively to protists associated with an animal host. We aim to highlight the diversity and community composition of protists associated with sponges and place them on the same level as other microorganisms already well studied in this context. Among other shortcomings, it could be observed that the biotechnological potential of the microeukaryome is still largely unexplored, possibly being a valuable source of new pharmacological compounds, enzymes and metabolic processes.
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14
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Indraningrat AAG, Steinert G, Becking LE, Mueller B, de Goeij JM, Smidt H, Sipkema D. Sponge holobionts shift their prokaryotic communities and antimicrobial activity from shallow to lower mesophotic depths. Antonie Van Leeuwenhoek 2022; 115:1265-1283. [PMID: 35998007 PMCID: PMC9534810 DOI: 10.1007/s10482-022-01770-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/07/2022] [Indexed: 11/05/2022]
Abstract
In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30–60 m (upper mesophotic), and 60–90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.
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Affiliation(s)
- Anak Agung Gede Indraningrat
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Faculty of Medicine and Health Sciences, Warmadewa University, Jln Terompong 24, 80235, Denpasar, Bali, Indonesia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Leontine E Becking
- Marine Animal Ecology Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Wageningen Marine Research, Wageningen University and Research, Ankerpark 27, 1781 AG, Den Helder, The Netherlands
| | - Benjamin Mueller
- Department of Freshwater and Marine Ecology, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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15
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Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification. mSystems 2022; 7:e0035722. [PMID: 35862823 PMCID: PMC9426513 DOI: 10.1128/msystems.00357-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.
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16
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Hanz U, Riekenberg P, de Kluijver A, van der Meer M, Middelburg JJ, de Goeij JM, Bart MC, Wurz E, Colaço A, Duineveld G, Reichart G, Rapp H, Mienis F. The important role of sponges in carbon and nitrogen cycling in a deep‐sea biological hotspot. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14117] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ulrike Hanz
- NIOZ‐Royal Netherlands Institute for Sea Research, Den Burg Texel Netherlands
| | - Philip Riekenberg
- NIOZ‐Royal Netherlands Institute for Sea Research, Den Burg Texel Netherlands
| | - Anna de Kluijver
- Department of Earth Sciences Utrecht University Utrecht Netherlands
| | - Marcel van der Meer
- NIOZ‐Royal Netherlands Institute for Sea Research, Den Burg Texel Netherlands
| | | | - Jasper M. de Goeij
- Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Martijn C. Bart
- Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Erik Wurz
- Wageningen University and Research Department of Animal Sciences Wageningen Netherlands
| | | | - Gerard Duineveld
- NIOZ‐Royal Netherlands Institute for Sea Research, Den Burg Texel Netherlands
| | - Gert‐Jan Reichart
- NIOZ‐Royal Netherlands Institute for Sea Research, Den Burg Texel Netherlands
- Department of Earth Sciences Utrecht University Utrecht Netherlands
| | - Hans‐Tore Rapp
- Department of Biology and K.G. Jebsen Centre for Deep Sea Research University of Bergen Bergen Norway
| | - Furu Mienis
- NIOZ‐Royal Netherlands Institute for Sea Research, Den Burg Texel Netherlands
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17
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Amelia TSM, Suaberon FAC, Vad J, Fahmi ADM, Saludes JP, Bhubalan K. Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:492-512. [PMID: 35567600 DOI: 10.1007/s10126-022-10130-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.
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Affiliation(s)
- Tan Suet May Amelia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Ferr Angelus C Suaberon
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Johanne Vad
- Changing Oceans Research Group, School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Afiq Durrani Mohd Fahmi
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Jonel P Saludes
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
- Department of Chemistry, University of San Agustin, 5000, Iloilo City, Philippines
- Department of Science and Technology, Balik Scientist Program, Philippine Council for Health Research & Development (PCHRD), Bicutan, 1631, Taguig, Philippines
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
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18
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A genomic overview including polyphasic taxonomy of Thalassoroseus pseudoceratinae gen. nov., sp. nov. isolated from a marine sponge, Pseudoceratina sp. Antonie van Leeuwenhoek 2022; 115:843-856. [PMID: 35587321 DOI: 10.1007/s10482-022-01738-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
A pink-coloured, salt- and alkali-tolerant planctomycetal strain (JC658T) with oval to pear-shaped, motile, aerobic, Gram-negative stained cells was isolated from a marine sponge, Pseudoceratina sp. Strain JC658T shares the highest 16S rRNA gene sequence identity with Maioricimonas rarisocia Mal4T (< 89.2%) in the family Planctomycetaceae. The genomic analysis of the new strain indicates its biotechnological potential for the production of various industrially important enzymes, notably sulfatases and carbohydrate-active enzymes (CAZymes), and also potential antimicrobial compounds. Several genes encoding restriction-modification (RM) and CRISPR-CAS systems are also present. NaCl is obligate for growth, of which strain JC658T can tolerate a concentration up to 6% (w/v). Optimum pH and temperature for growth are 8.0 (range 7.0-9.0) and 25 ºC (range 10-40 °C), respectively. The major respiratory quinone of strain JC658T is MK6. Major fatty acids are C16:1ω7c/C16:1ω6c, C18:0 and C16:0. Major polar lipids are phosphatidylcholine, phosphatidyl-dimethylethanolamine and phosphatidyl-monomethylethanolamine. The genomic size of strain JC658T is 7.36 Mb with a DNA G + C content of 54.6 mol%. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strain JC658T belongs to a novel genus and constitutes a novel species within the family Planctomycetaceae, for which we propose the name Thalassoroseus pseudoceratinae gen. nov., sp. nov. The novel species is represented by the type strain JC658T (= KCTC 72881 T = NBRC 114371 T).
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Curdt F, Schupp PJ, Rohde S. Light Availability Affects the Symbiosis of Sponge Specific Cyanobacteria and the Common Blue Aquarium Sponge ( Lendenfeldia chondrodes). Animals (Basel) 2022; 12:1283. [PMID: 35625129 PMCID: PMC9137838 DOI: 10.3390/ani12101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Bacterial symbionts in marine sponges play a decisive role in the biological and ecological functioning of their hosts. Although this topic has been the focus of numerous studies, data from experiments under controlled conditions are rare. To analyze the ongoing metabolic processes, we investigated the symbiosis of the sponge specific cyanobacterium Synechococcus spongiarum and its sponge host Lendenfeldia chondrodes under varying light conditions in a defined aquarium setting for 68 days. Sponge clonal pieces were kept at four different light intensities, ranging from no light to higher intensities that were assumed to trigger light stress. Growth as a measure of host performance and photosynthetic yield as a proxy of symbiont photosynthetic activity were measured throughout the experiment. The lack of light prevented sponge growth and induced the expulsion of all cyanobacteria and related pigments by the end of the experiment. Higher light conditions allowed rapid sponge growth and high cyanobacteria densities. In addition, photosynthetically active radiation above a certain level triggered an increase in cyanobacteria's lutein levels, a UV absorbing protein, thus protecting itself and the host's cells from UV radiation damage. Thus, L. chondrodes seems to benefit strongly from hosting the cyanbacterium S. spongiarum and the relationship should be considered obligatory mutualistic.
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Affiliation(s)
- Franziska Curdt
- Department for Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhelmshaven, Germany; (F.C.); (P.J.S.)
| | - Peter J. Schupp
- Department for Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhelmshaven, Germany; (F.C.); (P.J.S.)
- Helmholtz Institute for Functional Marine Biodiversity, Carl-von-Ossietzky University of Oldenburg, 26129 Oldenburg, Germany
| | - Sven Rohde
- Department for Environmental Biochemistry, Institute for Chemistry and Biology of the Marine Environment Terramare, Carl-von-Ossietzky University Oldenburg, 26382 Wilhelmshaven, Germany; (F.C.); (P.J.S.)
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20
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González-Acosta B, Barraza A, Guadarrama-Analco C, Hernández-Guerrero CJ, Martínez-Díaz SF, Cardona-Félix CS, Aguila-Ramírez RN. Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs. PeerJ 2022; 10:e13133. [PMID: 35411254 PMCID: PMC8994493 DOI: 10.7717/peerj.13133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/26/2022] [Indexed: 01/12/2023] Open
Abstract
Background Sponge microbiomes are essential for the function and survival of their host and produce biologically active metabolites, therefore, they are ideal candidates for ecological, pharmacologic and clinical research. Next-generation sequencing (NGS) has revealed that many factors, including the environment and host, determine the composition and structure of these symbiotic communities but the controls of this variation are not well described. This study assessed the microbial communities associated with two marine sponges of the genera Aplysina (Nardo, 1834) and Ircinia (Nardo, 1833) in rocky reefs from Punta Arena de la Ventana (Gulf of California) and Pichilingue (La Paz Bay) in the coast of Baja California Sur, México to determine the relative importance of environment and host in structuring the microbiome of sponges. Methods Specimens of Aplysina sp were collected by scuba diving at 10 m and 2 m; Ircinia sp samples were collected at 2 m. DNA of sponge-associated prokaryotes was extracted from 1 cm3 of tissue, purified and sent for 16S amplicon sequencing. Primer trimmed pair-ended microbial 16S rDNA gene sequences were merged using Ribosomal Database Project (RDP) Paired-end Reads Assembler. Chao1, Shannon and Simpson (alpha) biodiversity indices were estimated, as well permutational analysis of variance (PERMANOVA), and Bray-Curtis distances. Results The most abundant phyla differed between hosts. Those phyla were: Proteobacteria, Acidobacteria, Cyanobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes. In Ircinia sp the dominant phylum was Acidobacteria. Depth was the main factor influencing the microbial community, as analysis of similarities (ANOSIM) showed a significant difference between the microbial communities from different depths. Conclusion Microbial diversity analysis showed that depth was more important than host in structuring the Aplysina sp and Ircinia sp microbiome. This observation contrast with previous reports that the sponge microbiome is highly host specific.
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Affiliation(s)
- Bárbara González-Acosta
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - César Guadarrama-Analco
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | | | | | | | - Ruth Noemí Aguila-Ramírez
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
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21
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Micaroni V, Strano F, McAllen R, Woods L, Turner J, Harman L, Bell JJ. Adaptive strategies of sponges to deoxygenated oceans. GLOBAL CHANGE BIOLOGY 2022; 28:1972-1989. [PMID: 34854178 DOI: 10.1111/gcb.16013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/08/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Ocean deoxygenation is one of the major consequences of climate change. In coastal waters, this process can be exacerbated by eutrophication, which is contributing to an alarming increase in the so-called 'dead zones' globally. Despite its severity, the effect of reduced dissolved oxygen has only been studied for a very limited number of organisms, compared to other climate change impacts such as ocean acidification and warming. Here, we experimentally assessed the response of sponges to moderate and severe simulated hypoxic events. We ran three laboratory experiments on four species from two different temperate oceans (NE Atlantic and SW Pacific). Sponges were exposed to a total of five hypoxic treatments, with increasing severity (3.3, 1.6, 0.5, 0.4 and 0.13 mg O2 L-1 , over 7-12-days). We found that sponges are generally very tolerant of hypoxia. All the sponges survived in the experimental conditions, except Polymastia crocea, which showed significant mortality at the lowest oxygen concentration (0.13 mg O2 L-1 , lethal median time: 286 h). In all species except Suberites carnosus, hypoxic conditions do not significantly affect respiration rate down to 0.4 mg O2 L-1 , showing that sponges can uptake oxygen at very low concentrations in the surrounding environment. Importantly, sponges displayed species-specific phenotypic modifications in response to the hypoxic treatments, including physiological, morphological and behavioural changes. This phenotypic plasticity likely represents an adaptive strategy to live in reduced or low oxygen water. Our results also show that a single sponge species (i.e., Suberites australiensis) can display different strategies at different oxygen concentrations. Compared to other sessile organisms, sponges generally showed higher tolerance to hypoxia, suggesting that sponges could be favoured and survive in future deoxygenated oceans.
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Affiliation(s)
- Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Rob McAllen
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Lisa Woods
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington, New Zealand
| | - John Turner
- School of Ocean Sciences, Bangor University, Anglesey, UK
| | - Luke Harman
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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22
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Ho XY, Katermeran NP, Deignan LK, Phyo MY, Ong JFM, Goh JX, Ng JY, Tun K, Tan LT. Assessing the Diversity and Biomedical Potential of Microbes Associated With the Neptune's Cup Sponge, Cliona patera. Front Microbiol 2021; 12:631445. [PMID: 34267732 PMCID: PMC8277423 DOI: 10.3389/fmicb.2021.631445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sponges are known to host a complex microbial consortium that is essential to the health and resilience of these benthic invertebrates. These sponge-associated microbes are also an important source of therapeutic agents. The Neptune's Cup sponge, Cliona patera, once believed to be extinct, was rediscovered off the southern coast of Singapore in 2011. The chance discovery of this sponge presented an opportunity to characterize the prokaryotic community of C. patera. Sponge tissue samples were collected from the inner cup, outer cup and stem of C. patera for 16S rRNA amplicon sequencing. C. patera hosted 5,222 distinct OTUs, spanning 26 bacterial phyla, and 74 bacterial classes. The bacterial phylum Proteobacteria, particularly classes Gammaproteobacteria and Alphaproteobacteria, dominated the sponge microbiome. Interestingly, the prokaryotic community structure differed significantly between the cup and stem of C. patera, suggesting that within C. patera there are distinct microenvironments. Moreover, the cup of C. patera had lower diversity and evenness as compared to the stem. Quorum sensing inhibitory (QSI) activities of selected sponge-associated marine bacteria were evaluated and their organic extracts profiled using the MS-based molecular networking platform. Of the 110 distinct marine bacterial strains isolated from sponge samples using culture-dependent methods, about 30% showed quorum sensing inhibitory activity. Preliminary identification of selected QSI active bacterial strains revealed that they belong mostly to classes Alphaproteobacteria and Bacilli. Annotation of the MS/MS molecular networkings of these QSI active organic extracts revealed diverse classes of natural products, including aromatic polyketides, siderophores, pyrrolidine derivatives, indole alkaloids, diketopiperazines, and pyrone derivatives. Moreover, potential novel compounds were detected in several strains as revealed by unique molecular families present in the molecular networks. Further research is required to determine the temporal stability of the microbiome of the host sponge, as well as mining of associated bacteria for novel QS inhibitors.
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Affiliation(s)
- Xin Yi Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nursheena Parveen Katermeran
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Lindsey Kane Deignan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ma Yadanar Phyo
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Ji Fa Marshall Ong
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Jun Xian Goh
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Juat Ying Ng
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Karenne Tun
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
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23
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Moreno-Pino M, Ugalde JA, Valdés JH, Rodríguez-Marconi S, Parada-Pozo G, Trefault N. Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia. Front Microbiol 2021; 12:660779. [PMID: 34177840 PMCID: PMC8222686 DOI: 10.3389/fmicb.2021.660779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Antarctic sponges harbor a diverse range of microorganisms that perform unique metabolic functions for nutrient cycles. Understanding how microorganisms establish functional sponge-microbe interactions in the Antarctic marine ecosystem provides clues about the success of these ancient animals in this realm. Here, we use a culture-dependent approach and genome sequencing to investigate the molecular determinants that promote a dual lifestyle in three bacterial genera Sporosarcina, Cellulophaga, and Nesterenkonia. Phylogenomic analyses showed that four sponge-associated isolates represent putative novel bacterial species within the Sporosarcina and Nesterenkonia genera and that the fifth bacterial isolate corresponds to Cellulophaga algicola. We inferred that isolated sponge-associated bacteria inhabit similarly marine sponges and also seawater. Comparative genomics revealed that these sponge-associated bacteria are enriched in symbiotic lifestyle-related genes. Specific adaptations related to the cold Antarctic environment are features of the bacterial strains isolated here. Furthermore, we showed evidence that the vitamin B5 synthesis-related gene, panE from Nesterenkonia E16_7 and E16_10, was laterally transferred within Actinobacteria members. Together, these findings indicate that the genomes of sponge-associated strains differ from other related genomes based on mechanisms that may contribute to the life in association with sponges and the extreme conditions of the Antarctic environment.
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Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Juan A. Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Jorge H. Valdés
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Susana Rodríguez-Marconi
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Génesis Parada-Pozo
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
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24
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Mallott EK, Amato KR. Host specificity of the gut microbiome. Nat Rev Microbiol 2021; 19:639-653. [PMID: 34045709 DOI: 10.1038/s41579-021-00562-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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25
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Hudspith M, Rix L, Achlatis M, Bougoure J, Guagliardo P, Clode PL, Webster NS, Muyzer G, Pernice M, de Goeij JM. Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis. MICROBIOME 2021; 9:44. [PMID: 33583434 PMCID: PMC7883440 DOI: 10.1186/s40168-020-00984-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/16/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea. RESULTS The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome. CONCLUSIONS Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.
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Affiliation(s)
- Meggie Hudspith
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura Rix
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Michelle Achlatis
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Peta L. Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
- The UWA Oceans Institute, The University of Western Australia, Perth, Australia
- The UWA School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathieu Pernice
- Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, Australia
| | - Jasper M. de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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26
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Kumar G, Radha V, Jagadeeshwari U, Sasikala C, Venkata Ramana C. Bacterial communities of sponges from the wetland ecosystem of Little Rann of Kutch, India with particular reference to Planctomycetes. 3 Biotech 2020; 10:478. [PMID: 33094088 PMCID: PMC7568738 DOI: 10.1007/s13205-020-02449-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022] Open
Abstract
Five sponge specimens belonging to the genera Spongilla and Ciocalypta were collected from Little Rann of Kutch (in Gujarat, India) and analysed for associated microbiomes. Critical analysis was done with respect to members of the phylum Planctomycetes, using two different strategies; 1. Culture-independent metagenomic approach and 2. culture-dependent anaerobic enrichment for anammox-planctomycetes. The 16S rRNA gene (V1-V3 region) amplicon metagenome analysis revealed significant divergence in bacterial diversity, including Planctomycetes among the sponges analysed. Community metagenomics revealed a total of 376 Operational Taxonomic Units (OTUs) belonging to 41 different phyla. OTUs belonging to Proteobacteria was the most abundant (38%) among the sponge analysed. The KEGG annotation predicted a total of 6909 KEGG orthologs (KOs); most of the KOs are associated with membrane transport, xenobiotic degradation, production of secondary metabolites, amino acid metabolism and carbohydrate metabolism. In the culture-dependent study, FISH analysis confirmed the association of anammox-planctomycetes with sponges. Partial 16S rRNA gene sequences of two planctomycetes (JC545, JC543) were cladding with those of uncultured Phycisphaerae class. The other three putative anammox bacteria (JC541, JC542, JC544) formed a different clade with "Candidatus Brocadia anammoxidans". These three putative bacteria believably represent new species/genus related to "Candidatus Brocadia".
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Affiliation(s)
- Gaurav Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Vaddavalli Radha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Uppadda Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
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27
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Bart MC, de Kluijver A, Hoetjes S, Absalah S, Mueller B, Kenchington E, Rapp HT, de Goeij JM. Differential processing of dissolved and particulate organic matter by deep-sea sponges and their microbial symbionts. Sci Rep 2020; 10:17515. [PMID: 33060808 PMCID: PMC7567089 DOI: 10.1038/s41598-020-74670-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/06/2020] [Indexed: 11/20/2022] Open
Abstract
Deep-sea sponges create hotspots of biodiversity and biological activity in the otherwise barren deep-sea. However, it remains elusive how sponge hosts and their microbial symbionts acquire and process food in these food-limited environments. Therefore, we traced the processing (i.e. assimilation and respiration) of 13C- and 15N-enriched dissolved organic matter (DOM) and bacteria by three dominant North Atlantic deep-sea sponges: the high microbial abundance (HMA) demosponge Geodia barretti, the low microbial abundance (LMA) demosponge Hymedesmia paupertas, and the LMA hexactinellid Vazella pourtalesii. We also assessed the assimilation of both food sources into sponge- and bacteria-specific phospholipid-derived fatty acid (PLFA) biomarkers. All sponges were capable of assimilating DOM as well as bacteria. However, processing of the two food sources differed considerably between the tested species: the DOM assimilation-to-respiration efficiency was highest for the HMA sponge, yet uptake rates were 4–5 times lower compared to LMA sponges. In contrast, bacteria were assimilated most efficiently and at the highest rate by the hexactinellid compared to the demosponges. Our results indicate that phylogeny and functional traits (e.g., abundance of microbial symbionts, morphology) influence food preferences and diet composition of sponges, which further helps to understand their role as key ecosystem engineers of deep-sea habitats.
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Affiliation(s)
- Martijn C Bart
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94248, 1090 GE, Amsterdam, The Netherlands.
| | - Anna de Kluijver
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Sean Hoetjes
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94248, 1090 GE, Amsterdam, The Netherlands
| | - Samira Absalah
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94248, 1090 GE, Amsterdam, The Netherlands
| | - Benjamin Mueller
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94248, 1090 GE, Amsterdam, The Netherlands
| | - Ellen Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Hans Tore Rapp
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94248, 1090 GE, Amsterdam, The Netherlands
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28
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Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. MICROBIOME 2020; 8:97. [PMID: 32576248 PMCID: PMC7313196 DOI: 10.1186/s40168-020-00877-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. RESULTS This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. CONCLUSIONS The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron Oliver
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, GU, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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29
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Helber SB, Steinert G, Wu YC, Rohde S, Hentschel U, Muhando CA, Schupp PJ. Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis. FEMS Microbiol Ecol 2020; 95:5369420. [PMID: 30830220 DOI: 10.1093/femsec/fiz026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/02/2019] [Indexed: 11/13/2022] Open
Abstract
Sponges are one of the most dominant organisms in marine ecosystems. One reason for their success is their association with microorganisms that are besides the host itself responsible for the chemical defence. Sponge abundances have been increasing on coral reefs in the Western Indian Ocean (WIO) and are predicted to increase further with rising anthropogenic impacts on coral reefs. However, there is a paucity of information on chemical ecology of sponges from the WIO and their prokaryotic community composition. We used a combination of Illumina sequencing and a predictive metagenomic analysis to (i) assess the prokaryotic community composition of sponges from Zanzibar, (ii) predict the presence of KEGG metabolic pathways responsible for bioactive compound production and (iii) relate their presence to the degree of observed chemical defence in their respective sponge host. We found that sponges from Zanzibar host diverse prokaryotic communities that are host species-specific. Sponge-species and respective specimens that showed strong chemical defences in previous studies were also predicted to be highly enriched in various pathways responsible for secondary metabolite production. Hence, the combined sequencing and predictive metagenomic approach proved to be a useful indicator for the metabolic potential of sponge holobionts.
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Affiliation(s)
- Stephanie B Helber
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.,Leibniz Center for Tropical Marine Research (ZMT) GmbH, Fahrenheitstr. 6, 28359 Bremen, Germany
| | - Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Yu-Chen Wu
- GEOMAR Helmholtz Centre for Ocean Research, Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Sven Rohde
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Christopher A Muhando
- Institute of Marine Sciences (IMS), Mizingani Road, P.O Box 668, Stonetown, Zanzibar, Tanzania
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Carl von Ossietzky University of Oldenburg, Ammerländer Heeerstr. 231, 26129 Oldenburg, Germany
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30
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Engelberts JP, Robbins SJ, de Goeij JM, Aranda M, Bell SC, Webster NS. Characterization of a sponge microbiome using an integrative genome-centric approach. THE ISME JOURNAL 2020; 14:1100-1110. [PMID: 31992859 PMCID: PMC7174397 DOI: 10.1038/s41396-020-0591-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
Marine sponges often host diverse and species-specific communities of microorganisms that are critical for host health. Previous functional genomic investigations of the sponge microbiome have focused primarily on specific symbiont lineages, which frequently make up only a small fraction of the overall community. Here, we undertook genome-centric analysis of the symbiont community in the model species Ircinia ramosa and analyzed 259 unique, high-quality metagenome-assembled genomes (MAGs) that comprised 74% of the I. ramosa microbiome. Addition of these MAGs to genome trees containing all publicly available microbial sponge symbionts increased phylogenetic diversity by 32% within the archaea and 41% within the bacteria. Metabolic reconstruction of the MAGs showed extensive redundancy across taxa for pathways involved in carbon fixation, B-vitamin synthesis, taurine metabolism, sulfite oxidation, and most steps of nitrogen metabolism. Through the acquisition of all major taxa present within the I. ramosa microbiome, we were able to analyze the functional potential of a sponge-associated microbial community in unprecedented detail. Critical functions, such as carbon fixation, which had previously only been assigned to a restricted set of sponge-associated organisms, were actually spread across diverse symbiont taxa, whereas other essential pathways, such as ammonia oxidation, were confined to specific keystone taxa.
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Affiliation(s)
- J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Institute of Marine Science, Townsville, QLD, Australia.
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31
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Savoca S, Lo Giudice A, Papale M, Mangano S, Caruso C, Spanò N, Michaud L, Rizzo C. Antarctic sponges from the Terra Nova Bay (Ross Sea) host a diversified bacterial community. Sci Rep 2019; 9:16135. [PMID: 31695084 PMCID: PMC6834628 DOI: 10.1038/s41598-019-52491-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/04/2019] [Indexed: 11/23/2022] Open
Abstract
Sponges represent important habitats for a community of associated (micro)organisms. Even if sponges dominate vast areas of the Antarctic shelves, few investigations have been performed on Antarctic sponge-associated bacteria. Using a culture-dependent approach, the composition of the bacterial communities associated with 14 Antarctic sponge species from different sites within the Terra Nova Bay (Ross Sea) area was analyzed. Overall, isolates were mainly affiliated to Gammaproteobacteria, followed by Actinobacteria and CF group of Bacteroidetes, being the genera Pseudoalteromonas, Arthrobacter and Gillisia predominant, respectively. Alphaproteobacteria and Firmicutes were less represented. Cluster analyses highlighted similarities/differences among the sponge-associated bacterial communities, also in relation to the sampling site. The gammaproteobacterial Pseudoalteromonas sp. SER45, Psychrobacter sp. SER48, and Shewanella sp. SER50, and the actinobacterial Arthrobacter sp. SER44 phylotypes occurred in association with almost all the analyzed sponge species. However, except for SER50, these phylotypes were retrieved also in seawater, indicating that they may be transient within the sponge body. The differences encountered within the bacterial communities may depend on the different sites of origin, highlighting the importance of the habitat in structuring the composition of the associated bacterial assemblages. Our data support the hypothesis of specific ecological interactions between bacteria and Porifera.
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Affiliation(s)
- Serena Savoca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Angelina Lo Giudice
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy. .,Istituto di Scienze Polari, Consiglio Nazionale delle Ricerche (CNR-ISP), Spianata San Raineri 86, 98122, Messina, Italy.
| | - Maria Papale
- Istituto di Scienze Polari, Consiglio Nazionale delle Ricerche (CNR-ISP), Spianata San Raineri 86, 98122, Messina, Italy
| | - Santina Mangano
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Consolazione Caruso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Nunziacarla Spanò
- Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali, A.O.U. Policlinico "G. Martino", Torre Biologica, Via Consolare Valeria, 98125, Messina, Italy
| | | | - Carmen Rizzo
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
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32
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Bibi F, Alvi SA, Al-Sofyani A, Naseer MI, Yasir M, Azhar EI. Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea, Saudi Arabia. Saudi J Biol Sci 2019; 27:67-73. [PMID: 31889819 PMCID: PMC6933160 DOI: 10.1016/j.sjbs.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 11/16/2022] Open
Abstract
Bacterial communities of marine sponges are believed to be an important partner for host survival but remain poorly studied. Sponges show difference in richness and abundance of microbial population inhabiting them. Three marine sponges belonging to the species of Pione vastifica, Siphonochalina siphonella and Suberea mollis were collected from Red sea in Jeddah and were investigated using high throughput sequencing. Highly diverse communities containing 105 OTUs were identified in S. mollis host. Only 61 and 43 OTUs were found in P. vastifica and S. siphonella respectively. We identified 10 different bacterial phyla and 31 genera using 27,356 sequences. Most of the OTUs belong to phylum Proteobacteria (29%–99%) comprising of Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria where later two were only detected in HMA sponge, S. mollis. A number of 16S rRNA sequences (25%) were not identified to phylum level and may be novel taxa. Richness of bacterial community and Shannon, Simpson diversity revealed that sponge S. mollis harbors high diversity compared to other two LMA sponges. Dominance of Proteobacteria in sponges may indicate an ecological significance of this phylum in the Red sea sponges. These differences in bacterial composition may be due to difference in location site or host responses to environmental conditions. To the best of our knowledge, the microbial communities of these sponges have never been studied before and this is first attempt to unravel bacterial diversity using PCR-based 454-pyrosequencing method.
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Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Sana Akhtar Alvi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Abdulmohsin Al-Sofyani
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
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33
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Belikov S, Belkova N, Butina T, Chernogor L, Martynova-Van Kley A, Nalian A, Rorex C, Khanaev I, Maikova O, Feranchuk S. Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities. PLoS One 2019; 14:e0213926. [PMID: 30921366 PMCID: PMC6438488 DOI: 10.1371/journal.pone.0213926] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 03/04/2019] [Indexed: 01/01/2023] Open
Abstract
The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance in the studied microbial communities of diseased sponges is caused by several different conditionally pathogenic microorganisms that increase their negative effect by acting together and in concert, which leads to the death of photosynthetic microalgae and sponges. Sponges are an important component of coastal communities, and the massive loss of sponges can obviously affect the structure of benthic communities and the purity of water.
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Affiliation(s)
- Sergei Belikov
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- * E-mail:
| | - Natalia Belkova
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Tatiana Butina
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Lubov Chernogor
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | - Armen Nalian
- Department of Biology, Stephen F. Austin State University, Nacogdoches, Texas, United States of America
| | - Colin Rorex
- Department of Biology, Stephen F. Austin State University, Nacogdoches, Texas, United States of America
| | - Igor Khanaev
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Olga Maikova
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Sergey Feranchuk
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- Department of Informatics, National Research Technical University, Irkutsk, Russia
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Abstract
This review is intended as a comprehensive survey of iodinated metabolites possessing carbon–iodine covalent bond, which have been obtained from living organisms. Generally thought to be minor components produced by many different organisms these interesting compounds now number more than 110. Many from isolated and identified iodine-containing metabolites showed high biological activities. Recent research, especially in the marine area, indicates this number will increase in the future. Sources of iodinated metabolites include microorganisms, algae, marine invertebrates, and some animals. Their origin and possible biological significance have also been discussed.
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Affiliation(s)
- Valery M Dembitsky
- Department of Medicinal Chemistry and Natural Products, School of Pharmacy, P.O. Box 12065, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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35
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Lurgi M, Thomas T, Wemheuer B, Webster NS, Montoya JM. Modularity and predicted functions of the global sponge-microbiome network. Nat Commun 2019; 10:992. [PMID: 30824706 PMCID: PMC6397258 DOI: 10.1038/s41467-019-08925-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 02/08/2019] [Indexed: 11/10/2022] Open
Abstract
Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.
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Affiliation(s)
- Miguel Lurgi
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS-Paul Sabatier University, 09200, Moulis, France.
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, 4816, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jose M Montoya
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS-Paul Sabatier University, 09200, Moulis, France
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36
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Integrated Genomic and Metabolomic Approach to the Discovery of Potential Anti-Quorum Sensing Natural Products from Microbes Associated with Marine Samples from Singapore. Mar Drugs 2019; 17:md17010072. [PMID: 30669697 PMCID: PMC6356914 DOI: 10.3390/md17010072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 12/17/2022] Open
Abstract
With 70% of the Earth's surface covered in water, the marine ecosystem offers immense opportunities for drug discovery and development. Due to the decreasing rate of novel natural product discovery from terrestrial sources in recent years, many researchers are beginning to look seaward for breakthroughs in new therapeutic agents. As part of an ongoing marine drug discovery programme in Singapore, an integrated approach of combining metabolomic and genomic techniques were initiated for uncovering novel anti-quorum sensing molecules from bacteria associated with subtidal samples collected in the Singapore Strait. Based on the culture-dependent method, a total of 102 marine bacteria strains were isolated and the identities of selected strains were established based on their 16S rRNA gene sequences. About 5% of the marine bacterial organic extracts showed quorum sensing inhibitory (QSI) activity in a dose-dependent manner based on the Pseudomonas aeruginosa QS reporter system. In addition, the extracts were subjected to mass spectrometry-based molecular networking and the genome of selected strains were analysed for known as well as new biosynthetic gene clusters. This study revealed that using integrated techniques, coupled with biological assays, can provide an effective and rapid prioritization of marine bacterial strains for downstream large-scale culturing for the purpose of isolation and structural elucidation of novel bioactive compounds.
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37
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Olatunji OO, Petchoubon A, Thawai C, Plubrukarn A. Allocation of trisoxazole macrolides in the sponge Penares cf. nux and the impact on epiphytic bacterial cohabitants. Nat Prod Res 2018; 34:710-713. [PMID: 30445822 DOI: 10.1080/14786419.2018.1493589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The correlation between the allocation of trisoxazole macrolides in the capitums, appendages, and bases of the sponge Penares cf. nux and the surface-attached bacteria on the corresponding parts was examined. The kabiramide contents were highest in the capitums, followed by the appendages and bases. Conversely, direct counts of cultivable surface-attached bacteria showed that the bacteria aggregate more densely on the surfaces of the bases. This suggested the repelling effects of the kabiramides against the fouling bacteria, particularly on the capitums and appendages. Twenty-two bacterial strains were isolated and identified to 15 species; however, none has shown the potentials as a producer of any secondary metabolites in the sponge P. nux.
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Affiliation(s)
- Oyenike O Olatunji
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
| | - Aekaphon Petchoubon
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
| | - Chitti Thawai
- Department of Biology, King Mongkut's Institute of Technology, Ladkrabang, Bangkok, Thailand.,Actinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology, Ladkrabang, Bangkok, Thailand
| | - Anuchit Plubrukarn
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
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38
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Pita L, Hoeppner MP, Ribes M, Hentschel U. Differential expression of immune receptors in two marine sponges upon exposure to microbial-associated molecular patterns. Sci Rep 2018; 8:16081. [PMID: 30382170 PMCID: PMC6208332 DOI: 10.1038/s41598-018-34330-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
The innate immune system helps animals to navigate the microbial world. The response to microbes relies on the specific recognition of microbial-associated molecular patterns (MAMPs) by immune receptors. Sponges (phylum Porifera), as early-diverging animals, provide insights into conserved mechanisms for animal-microbe crosstalk. However, experimental data is limited. We adopted an experimental approach followed by RNA-Seq and differential gene expression analysis in order to characterise the sponge immune response. Two Mediterranean species, Aplysina aerophoba and Dysidea avara, were exposed to a “cocktail” of MAMPs (lipopolysaccharide and peptidoglycan) or to sterile artificial seawater (control) and sampled 1 h, 3 h, and 5 h post-treatment for RNA-Seq. The response involved, first and foremost, a higher number of differentially-expressed genes in A. aerophoba than D. avara. Secondly, while both species constitutively express a diverse repertoire of immune receptors, they differed in their expression profiles upon MAMP challenge. The response in D. avara was mediated by increased expression of two NLR genes, whereas the response in A. aerophoba involved SRCR and GPCR genes. From the set of annotated genes we infer that both species activated apoptosis in response to MAMPs while in A. aerophoba phagocytosis was additionally stimulated. Our study assessed for the first time the transcriptomic responses of sponges to MAMPs and revealed conserved and species-specific features of poriferan immunity as well as genes potentially relevant to animal-microbe interactions.
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Affiliation(s)
- Lucía Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Marta Ribes
- Institute of Marine Science, CSIC, Barcelona, Spain
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Christian-Albrechts-University of Kiel (CAU), Kiel, Germany
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39
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Mehbub MF, Tanner JE, Barnett SJ, Bekker J, Franco CMM, Zhang W. A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens. Sci Rep 2018; 8:11801. [PMID: 30087404 PMCID: PMC6081443 DOI: 10.1038/s41598-018-30295-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/23/2018] [Indexed: 11/09/2022] Open
Abstract
Sponge-bacteria interactions are very important due to their ecological and biological significance. To understand the impact of interactions between sponges and bacteria (both associated with and external to sponges) on sponge-associated microbial diversity, sponge metabolite profiles and bioactivity, we used a controlled aquarium system and designed an experimental approach that allows the study of sponge-bacteria interactions in a well-defined manner. To test the feasibility of this approach, this system was used to study the interaction between a sponge Aplysilla rosea and a marine bacterium commonly found in seawater, Vibrio natriegens. Sponge explants were exposed to V. natriegens, at 5 × 106 cfu/ml, and changes were monitored for 48 hours. Pyro-sequencing revealed significant shifts in microbial communities associated with the sponges after 24 to 48 hours. Both the control (sponge only without added bacteria) and Vibrio-exposed sponges showed a distinct shift in bacterial diversity and abundance with time. Vibrio exposure significantly increased bacterial diversity, the abundance of a number of taxa compared to control sponges. The result experimentally supports the notion of dynamic and concerted responses by the sponge when interacting with a bacterium, and demonstrates the feasibility of using this controlled aquarium system for the study of sponge-bacteria interactions.
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Affiliation(s)
- Mohammad F Mehbub
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
| | - Jason E Tanner
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
- SARDI Aquatic Sciences, 2 Hamra Avenue, West Beach, SA, 5024, Adelaide, Australia
| | - Stephen J Barnett
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
| | - Jan Bekker
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
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40
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Castilla IA, Woods DF, Reen FJ, O'Gara F. Harnessing Marine Biocatalytic Reservoirs for Green Chemistry Applications through Metagenomic Technologies. Mar Drugs 2018; 16:E227. [PMID: 29973493 PMCID: PMC6071119 DOI: 10.3390/md16070227] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 01/24/2023] Open
Abstract
In a demanding commercial world, large-scale chemical processes have been widely utilised to satisfy consumer related needs. Chemical industries are key to promoting economic growth and meeting the requirements of a sustainable industrialised society. The market need for diverse commodities produced by the chemical industry is rapidly expanding globally. Accompanying this demand is an increased threat to the environment and to human health, due to waste produced by increased industrial production. This increased demand has underscored the necessity to increase reaction efficiencies, in order to reduce costs and increase profits. The discovery of novel biocatalysts is a key method aimed at combating these difficulties. Metagenomic technology, as a tool for uncovering novel biocatalysts, has great potential and applicability and has already delivered many successful achievements. In this review we discuss, recent developments and achievements in the field of biocatalysis. We highlight how green chemistry principles through the application of biocatalysis, can be successfully promoted and implemented in various industrial sectors. In addition, we demonstrate how two novel lipases/esterases were mined from the marine environment by metagenomic analysis. Collectively these improvements can result in increased efficiency, decreased energy consumption, reduced waste and cost savings for the chemical industry.
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Affiliation(s)
- Ignacio Abreu Castilla
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - F Jerry Reen
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
- Telethon Kids Institute, Perth, WA 6008, Australia.
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
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41
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Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. MICROBIOME 2018; 6:46. [PMID: 29523192 PMCID: PMC5845141 DOI: 10.1186/s40168-018-0428-1] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.
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Affiliation(s)
- L. Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - L. Rix
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - B. M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - A. Franke
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - U. Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts-University of Kiel (CAU), Kiel, Germany
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42
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Steinert G, Gutleben J, Atikana A, Wijffels RH, Smidt H, Sipkema D. Coexistence of poribacterial phylotypes among geographically widespread and phylogenetically divergent sponge hosts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:80-91. [PMID: 29194987 DOI: 10.1111/1758-2229.12609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
Marine sponges are benthic 'filter-feeding' invertebrates that can host dense and diverse bacterial, archaeal and eukaryotic communities. Due to the finding of several genes encoding symbiosis factors, such as adhesins, ankyrin repeats and tetratricopeptide repeats, the candidate phylum 'Poribacteria' is considered as a promising model microorganism for studying the origin of host-symbiont interactions in sponges. However, relatively little is known about its global diversity and phylogenetic distribution among different sponge hosts. Therefore, in this study we investigated phylogenetic relationships among poribacterial phylotypes and generated a phylogenetic network to examine the distribution and intraspecific diversity of the phylotypes between phylogenetically divergent host-sponges at a global scale. For this study 361 poribacterial 16S rRNA gene sequences obtained by Sanger sequencing from 15 different countries and 8 marine regions were gathered. We could demonstrate that the candidate phylum 'Poribacteria' is composed of diverse phylotypes, which are distributed among a wide range of phylogenetically divergent sponge hosts. The current phylogenetic analyses found neither conclusive evidence for co-speciation with its hosts, nor biogeographical correlation. Moreover, we identified a novel poribacterial clade, which might represent a link between the previously established four 'Poribacteria' clades.
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Affiliation(s)
- Georg Steinert
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Wilhelmshaven, 26382, Germany
| | - Johanna Gutleben
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Akhirta Atikana
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Cibinong Science Center (CSC) Cibinong, Bogor, 16911, Indonesia
| | - Rene H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University, Wageningen, 6700 AA, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8026, Norway
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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43
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Astudillo-García C, Slaby BM, Waite DW, Bayer K, Hentschel U, Taylor MW. Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges. Environ Microbiol 2017; 20:561-576. [DOI: 10.1111/1462-2920.13965] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/20/2017] [Accepted: 10/19/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Carmen Astudillo-García
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Institute of Marine Science, University of Auckland; Auckland New Zealand
| | - Beate M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences, University of Würzburg; Würzburg Germany
| | - David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences; The University of Queensland; QLD, St Lucia Australia
| | - Kristina Bayer
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Christian-Albrechts-Universität zu Kiel; Kiel Germany
| | - Michael W. Taylor
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland; New Zealand
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44
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Liu J, Lopez N, Ahn Y, Goldberg T, Bromberg Y, Kerkhof LJ, Häggblom MM. Novel reductive dehalogenases from the marine sponge associated bacterium Desulfoluna spongiiphila. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:537-549. [PMID: 28618195 DOI: 10.1111/1758-2229.12556] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 05/08/2017] [Accepted: 06/03/2017] [Indexed: 06/07/2023]
Abstract
Desulfoluna spongiiphila strain AA1 is an organohalide respiring bacterium, isolated from the marine sponge Aplysina aerophoba, that can use brominated and iodinated phenols, in addition to sulfate and thiosulfate as terminal electron acceptors. The genome of Desulfoluna spongiiphila strain AA1 is approximately 6.5 Mb. Three putative reductive dehalogenase (rdhA) genes involved in respiratory metabolism of organohalides were identified within the sequence. Conserved motifs found in respiratory reductive dehalogenases (a twin arginine translocation signal sequence and two iron-sulfur clusters) were present in all three putative AA1 rdhA genes. Transcription of one of the three rdhA genes was significantly upregulated during respiration of 2,6-dibromophenol and sponge extracts. Strain AA1 appears to have the ability to synthesize cobalamin, the key cofactor of most characterized reductive dehalogenase enzymes. The genome contains genes involved in cobalamin synthesis and uptake and can grow without cobalamin supplementation. Identification of this target gene associated with debromination lays the foundation for understanding how dehalogenating bacteria control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle. In the sponge environment, D. spongiiphila strain AA1 may thus take advantage of both brominated compounds and sulfate as electron acceptors for respiration.
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Affiliation(s)
- Jie Liu
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Nora Lopez
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Youngbeom Ahn
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology, Technical University Munich, Garching, 85748, Germany
| | - Yana Bromberg
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Lee J Kerkhof
- Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Max M Häggblom
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
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45
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An Overview on Marine Sponge-Symbiotic Bacteria as Unexhausted Sources for Natural Product Discovery. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040040] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microbial symbiotic communities of marine macro-organisms carry functional metabolic profiles different to the ones found terrestrially and within surrounding marine environments. These symbiotic bacteria have increasingly been a focus of microbiologists working in marine environments due to a wide array of reported bioactive compounds of therapeutic importance resulting in various patent registrations. Revelations of symbiont-directed host specific functions and the true nature of host-symbiont interactions, combined with metagenomic advances detecting functional gene clusters, will inevitably open new avenues for identification and discovery of novel bioactive compounds of biotechnological value from marine resources. This review article provides an overview on bioactive marine symbiotic organisms with specific emphasis placed on the sponge-associated ones and invites the international scientific community to contribute towards establishment of in-depth information of the environmental parameters defining selection and acquisition of true symbionts by the host organisms.
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46
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Ramadan Y, Amro H, Nora F, Khaled AA. Quorum sensing signal production by sponge-associated bacteria isolated from the Red Sea, Egypt. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajb2017.16078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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47
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Ellis GA, Thomas CS, Chanana S, Adnani N, Szachowicz E, Braun DR, Harper MK, Wyche TP, Bugni TS. Brackish habitat dictates cultivable Actinobacterial diversity from marine sponges. PLoS One 2017; 12:e0176968. [PMID: 28692665 PMCID: PMC5503172 DOI: 10.1371/journal.pone.0176968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/20/2017] [Indexed: 11/29/2022] Open
Abstract
Bacterial communities associated with marine invertebrates such as sponges and ascidians have demonstrated potential as sources of bio-medically relevant small molecules. Metagenomic analysis has shown that many of these invertebrates harbor populations of Actinobacteria, many of which are cultivable. While some populations within invertebrates are transmitted vertically, others are obtained from the environment. We hypothesized that cultivable diversity from sponges living in brackish mangrove habitats have associations with Actinobacterial populations that differ from those found in clear tropical waters. In this study, we analyzed the cultivable Actinobacterial populations from sponges found in these two distinct habitats with the aim of understanding the secondary metabolite potential. Importantly, we wanted to broadly evaluate the potential differences among these groups to guide future Actinobacterial collection strategies for the purposes of drug discovery.
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Affiliation(s)
- Gregory A. Ellis
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris S. Thomas
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shaurya Chanana
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Navid Adnani
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Emily Szachowicz
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Doug R. Braun
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Thomas P. Wyche
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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48
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Moitinho-Silva L, Steinert G, Nielsen S, Hardoim CCP, Wu YC, McCormack GP, López-Legentil S, Marchant R, Webster N, Thomas T, Hentschel U. Predicting the HMA-LMA Status in Marine Sponges by Machine Learning. Front Microbiol 2017; 8:752. [PMID: 28533766 PMCID: PMC5421222 DOI: 10.3389/fmicb.2017.00752] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered “HMA indicators” and “LMA indicators.” Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Cristiane C P Hardoim
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Yu-Chen Wu
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
| | - Grace P McCormack
- Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, and Center for Marine Science, University of North CarolinaWilmington, NC, USA
| | - Roman Marchant
- Centre for Translational Data Science, School of Information Technologies, University of SydneySydney, NSW, Australia
| | - Nicole Webster
- Australian Institute of Marine ScienceTownsville, QLD, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of QueenslandSt. Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
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49
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Rozas EE, Mendes MA, Nascimento CAO, Espinosa DCR, Oliveira R, Oliveira G, Custodio MR. Bioleaching of electronic waste using bacteria isolated from the marine sponge Hymeniacidon heliophila (Porifera). JOURNAL OF HAZARDOUS MATERIALS 2017; 329:120-130. [PMID: 28131039 DOI: 10.1016/j.jhazmat.2017.01.037] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/13/2017] [Accepted: 01/20/2017] [Indexed: 06/06/2023]
Abstract
The bacteria isolated from Hymeniacidon heliophila sponge cells showed bioleaching activity. The most active strain, Hyhel-1, identified as Bacillus sp., was selected for bioleaching tests under two different temperatures, 30°C and 40°C, showing rod-shaped cells and filamentous growth, respectively. At 30°C, the bacteria secreted substances which linked to the leached copper, and at 40°C metallic nanoparticles were produced inside the cells. In addition, infrared analysis detected COOH groups and linear peptides in the tested bacteria at both temperatures. The Hyhel-1 strain in presence of electronic waste (e-waste) induced the formation of crust, which could be observed due to bacteria growing on the e-waste fragment. SEM-EDS measurements showed that the bacterial net surface was composed mostly of iron (16.1% w/w), while a higher concentration of copper was observed in the supernatant (1.7% w/w) and in the precipitated (49.8% w/w). The substances linked to copper in the supernatant were sequenced by MALDI-TOF-ms/ms and identified as macrocyclic surfactin-like peptides, similar to the basic sequence of Iturin, a lipopeptide from Bacillus subtilis. Finally, the results showed that Hyhel-1 is a bioleaching bacteria and cooper nanoparticles producer and that this bacteria could be used as a copper recovery tool from electronic waste.
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Affiliation(s)
- Enrique E Rozas
- LSCP, Chemical Engineering Department, University of São Paulo (USP), Brazil.
| | - Maria A Mendes
- LSCP, Chemical Engineering Department, University of São Paulo (USP), Brazil
| | | | - Denise C R Espinosa
- LAREX, Chemical Engineering Department, University of São Paulo (USP), Brazil
| | | | | | - Marcio R Custodio
- Departamento de Fisiologia Geral, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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50
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Jensen S, Fortunato SAV, Hoffmann F, Hoem S, Rapp HT, Øvreås L, Torsvik VL. The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle. MICROBIAL ECOLOGY 2017; 73:668-676. [PMID: 27664049 DOI: 10.1007/s00248-016-0836-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.
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Affiliation(s)
- Sigmund Jensen
- Department of Biology, University of Bergen, Bergen, Norway
| | - Sofia A V Fortunato
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Friederike Hoffmann
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway
| | - Solveig Hoem
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway
| | - Hans Tore Rapp
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway
| | - Lise Øvreås
- Department of Biology, University of Bergen, Bergen, Norway
| | - Vigdis L Torsvik
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway.
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