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Meunier L, Costa R, Keller-Costa T, Cannella D, Dechamps E, George IF. Selection of marine bacterial consortia efficient at degrading chitin leads to the discovery of new potential chitin degraders. Microbiol Spectr 2024:e0088624. [PMID: 39315806 DOI: 10.1128/spectrum.00886-24] [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: 04/06/2024] [Accepted: 07/13/2024] [Indexed: 09/25/2024] Open
Abstract
Chitin degradation is a keystone process in the oceans, mediated by marine microorganisms with the help of several enzymes, mostly chitinases. Sediment, seawater, and filter-feeding marine invertebrates, such as sponges, are known to harbor chitin-degrading bacteria and are presumably hotspots for chitin turnover. Here, we employed an artificial selection process involving enrichment cultures derived from microbial communities associated with the marine sponge Hymeniacidon perlevis, its surrounding seawater and sediment, to select bacterial consortia capable of degrading raw chitin. Throughout the artificial selection process, chitin degradation rates and the taxonomic composition of the four successive enrichment cultures were followed. To the best of our knowledge, chitin degradation was characterized for the first time using size exclusion chromatography, which revealed significant shifts in the numbered average chitin molecular weight, strongly suggesting the involvement of endo-chitinases in the breakdown of the chitin polymer during the enrichment process. Concomitantly with chitin degradation, the enrichment cultures exhibited a decrease in alpha diversity compared with the environmental samples. Notably, some of the dominant taxa in the enriched communities, such as Motilimonas, Arcobacter, and Halarcobacter, were previously unknown to be involved in chitin degradation. In particular, the analysis of published genomes of these genera suggests a pivotal role of Motilimonas in the hydrolytic cleavage of chitin. This study provides context to the microbiome of the marine sponge Hymeniacidon perlevis in light of its environmental surroundings and opens new ground to the future discovery and characterization of novel enzymes of marine origin involved in chitin degradation processes.IMPORTANCEChitin is the second most abundant biopolymer on Earth after cellulose, and the most abundant in the marine environment. At present, industrial processes for the conversion of seafood waste into chitin, chitosan, and chitooligosaccharide (COS) rely on the use of high amounts of concentrated acids or strong alkali at high temperature. Developing bio-based methods to transform available chitin into valuable compounds, such as chitosan and COS, holds promise in promoting a more sustainable, circular bioeconomy. By employing an artificial selection procedure based on chitin as a sole C and N source, we discovered microorganisms so-far unknown to metabolize chitin in the rare microbial biosphere of several marine biotopes. This finding represents a first important step on the path towards characterizing and exploiting potentially novel enzymes of marine origin with biotechnological interest, since products of chitin degradation may find applications across several sectors, such as agriculture, pharmacy, and waste management.
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Affiliation(s)
- Laurence Meunier
- Laboratory of Ecology of Aquatic Systems, Brussels Bioengineering School, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB) and Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB) and Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal
| | - David Cannella
- PhotoBioCatalysis Unit, Crop Nutrition and Biostimulation Lab (CPBL) and Biomass Transformation Lab (BTL), Brussels Bioengineering School, Université Libre de Bruxelles, Brussels, Belgium
| | - Etienne Dechamps
- Laboratory of Ecology of Aquatic Systems, Brussels Bioengineering School, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Isabelle F George
- Laboratory of Ecology of Aquatic Systems, Brussels Bioengineering School, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Hamamoto K, Mizuyama M, Nishijima M, Maeda A, Gibu K, Poliseno A, Iguchi A, Reimer JD. Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan. ENVIRONMENTAL MICROBIOME 2024; 19:54. [PMID: 39080706 PMCID: PMC11290285 DOI: 10.1186/s40793-024-00594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions. RESULTS The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation. CONCLUSION Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.
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Affiliation(s)
- Kohei Hamamoto
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
- Department of Health Informatics, Faculty of Human Health Sciences, Meio University, Nago, Okinawa, 905-8585, Japan
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Ayumi Maeda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-Conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
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3
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Chen X, Liu L, Wang Y, Zhou L, Xiao J, Yan W, Li M, Li Q, He X, Zhang L, You X, Zhu D, Yan J, Wang B, Hang X. The combined effects of lanthanum-modified bentonite and Vallisneria spiralis on phosphorus, dissolved organic matter, and heavy metal(loid)s. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170502. [PMID: 38301791 DOI: 10.1016/j.scitotenv.2024.170502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/10/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
The use of lanthanum-modified bentonite (LMB) combined with Vallisneria spiralis (V∙s) (LMB + V∙s) is a common method for controlling internal phosphorus (P) release from sediments. However, the behaviors of iron (Fe) and manganese (Mn) under LMB + V∙s treatments, as well as the associated coupling effect on P, dissolved organic matter (DOM), and heavy metal(loid)s (HMs), require further investigations. Therefore, we used in this study a microelectrode system and high-resolution dialysis technology (HR-Peeper) to study the combined effects of LMB and V∙s on P, DOM, and HMs through a 66-day incubation experiment. The LMB + V∙s treatment increased the sediment DO concentration, promoting in-situ formations of Fe (III)/Mn (IV) oxyhydroxides, which, in turn, adsorbed P, soluble tungsten (W), DOM, and HMs. The increase in the concentrations of HCl-P, amorphous and poorly crystalline (oxyhydr) oxides-bound W, and oxidizable HMs forms demonstrated the capacity of the LMB + V∙s treatment to transform mobile P, W, and other HMs forms into more stable forms. The significant positive correlations between SRP, soluble W, UV254, and soluble Fe (II)/Mn, and the increased concentrations of the oxidizable HMs forms suggested the crucial role of the Fe/Mn redox in controlling the release of SRP, DOM, and HMs from sediments. The LMB + V∙s treatment resulted in SRP, W, and DOM removal rates of 74.49, 78.58, and 54.78 %, which were higher than those observed in the control group (without LMB and V∙s applications). On the other hand, the single and combined uses of LMB and V·s influenced the relative abundances of the sediment microbial communities without exhibiting effects on microbial diversity. This study demonstrated the key role of combined LMB and V∙s applications in controlling the release of P, W, DOM, and HMs in eutrophic lakes.
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Affiliation(s)
- Xiang Chen
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Ling Liu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yan Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Li Zhou
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Jing Xiao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Wenming Yan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Minjuan Li
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Qi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Xiangyu He
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Lan Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xiaohui You
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Dongdong Zhu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Jiabao Yan
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Bin Wang
- Zhongyifeng Construction Group Co., Ltd., Suzhou 215131, China
| | - Xiaoshuai Hang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
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4
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Chen X, Liu L, Wang Y, You X, Yan W, Li M, Li Q, He X, Zhang L, Zhou L, Xiao J, Zhu D, Yan J, Hang X. Combining lanthanum-modified bentonite and calcium peroxide to enhance phosphorus removal from lake sediments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 353:120150. [PMID: 38278118 DOI: 10.1016/j.jenvman.2024.120150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
Lanthanum-modified bentonite (LMB) and calcium peroxide (CP) are known for their effective removal phosphorus (P) capacities. The present study aims to investigate the effects of the combined use of LMB and CP(LMB + CP)on the sediment P, dissolved organic matter (DOM) and iron (Fe) concentrations through a 90-day incubation experiment. The combined treatment showed strong removal effects on sediment P and DOM. Indeed, the SRP and DOM concentrations in the 0-10 cm sediment layer decreased following the combined application of LMB and CP by 40.67 and 28.95%, respectively, compared to those of the control group (CK). In contrast, the HCl-P in the 0-5 cm sediment layer increased following the combined treatment by 13.28%. In addition, compared with the single application of LMB, the LMB + CP treatment significantly reduced the soluble Fe (Ⅱ) in the sediment pore water and promoted the oxidation of Fe. Therefore, LMB + CP can enhance the removal of internal P from sediments. The DOM removal and Fe oxidation in sediment pore waters are beneficial for enhancing the adsorption of P by LMB. On the other hand, the single and combined applications of LMB and CP increased the richness of the sediment microbial communities while exhibiting slight effects on their diversity. According to the results of this study, the combined use of LMB and oxidizing materials represents a novel method for treating lakes with high internal phosphorus and DOM loads in sediments.
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Affiliation(s)
- Xiang Chen
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Ling Liu
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Yan Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Xiaohui You
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Wenming Yan
- National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Minjuan Li
- National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Qi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Xiangyu He
- College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Lan Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Li Zhou
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Jing Xiao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Dongdong Zhu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Jiabao Yan
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Xiaoshuai Hang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China.
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5
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Díez-Vives C, Riesgo A. High compositional and functional similarity in the microbiome of deep-sea sponges. THE ISME JOURNAL 2024; 18:wrad030. [PMID: 38365260 PMCID: PMC10837836 DOI: 10.1093/ismejo/wrad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/18/2024]
Abstract
Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Systems Biology, Centro Nacional de Biotecnología, c/ Darwin, 3, 28049 Madrid, Spain
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
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6
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. MICROBIAL ECOLOGY 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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7
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Caudal F, Rodrigues S, Dufour A, Artigaud S, Le Blay G, Petek S, Bazire A. Extracts from Wallis Sponges Inhibit Vibrio harveyi Biofilm Formation. Microorganisms 2023; 11:1762. [PMID: 37512934 PMCID: PMC10383632 DOI: 10.3390/microorganisms11071762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Pathogenic bacteria and their biofilms are involved in many human and animal diseases and are a major public health problem with, among other things, the development of antibiotic resistance. These biofilms are known to induce chronic infections for which classical treatments using antibiotic therapy are often ineffective. Sponges are sessile filter-feeding marine organisms known for their dynamic symbiotic partnerships with diverse microorganisms and their production of numerous metabolites of interest. In this study, we investigated the antibiofilm efficacy of different extracts from sponges, isolated in Wallis, without biocidal activity. Out of the 47 tested extracts, from 28 different genera, 11 showed a strong activity against Vibrio harveyi biofilm formation. Moreover, one of these extracts also inhibited two quorum-sensing pathways of V. harveyi.
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Affiliation(s)
- Flore Caudal
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Sophie Rodrigues
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
| | - Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
| | | | | | - Sylvain Petek
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Alexis Bazire
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56100 Lorient, France
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Nguyen VH, Wemheuer B, Song W, Bennett H, Webster N, Thomas T. Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species. Syst Appl Microbiol 2023; 46:126426. [PMID: 37141831 DOI: 10.1016/j.syapm.2023.126426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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9
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Busch K, Slaby BM, Bach W, Boetius A, Clefsen I, Colaço A, Creemers M, Cristobo J, Federwisch L, Franke A, Gavriilidou A, Hethke A, Kenchington E, Mienis F, Mills S, Riesgo A, Ríos P, Roberts EM, Sipkema D, Pita L, Schupp PJ, Xavier J, Rapp HT, Hentschel U. Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome. Nat Commun 2022; 13:5160. [PMID: 36056000 PMCID: PMC9440067 DOI: 10.1038/s41467-022-32684-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 08/11/2022] [Indexed: 11/09/2022] Open
Abstract
In the deep ocean symbioses between microbes and invertebrates are emerging as key drivers of ecosystem health and services. We present a large-scale analysis of microbial diversity in deep-sea sponges (Porifera) from scales of sponge individuals to ocean basins, covering 52 locations, 1077 host individuals translating into 169 sponge species (including understudied glass sponges), and 469 reference samples, collected anew during 21 ship-based expeditions. We demonstrate the impacts of the sponge microbial abundance status, geographic distance, sponge phylogeny, and the physical-biogeochemical environment as drivers of microbiome composition, in descending order of relevance. Our study further discloses that fundamental concepts of sponge microbiology apply robustly to sponges from the deep-sea across distances of >10,000 km. Deep-sea sponge microbiomes are less complex, yet more heterogeneous, than their shallow-water counterparts. Our analysis underscores the uniqueness of each deep-sea sponge ground based on which we provide critical knowledge for conservation of these vulnerable ecosystems. This study presents a large-scale analysis of microbial diversity in deep-sea sponges. They show that sponge microbial abundance status, geographic distance, sponge phylogeny and the physical-biogeochemical environment drive microbiome composition, in descending order of relevance. The uniqueness of each deep-sea sponge ground stresses the need for their strategic preservation.
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Affiliation(s)
- Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Wolfgang Bach
- MARUM-Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Antje Boetius
- MARUM-Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359, Bremen, Germany.,MPI-Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany.,AWI-Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Ina Clefsen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Ana Colaço
- OKEANOS-Institute of Marine Research, University of the Açores, Rua Prof Frederico Machado, 9901-862, Horta, Portugal
| | - Marie Creemers
- OKEANOS-Institute of Marine Research, University of the Açores, Rua Prof Frederico Machado, 9901-862, Horta, Portugal.,MARBEC, University of Montpellier, CNRS, IFREMER, IRD, Avenue Jean Monnet, CS 30171 - 34203, Sète, France
| | - Javier Cristobo
- IEO-CSIC-Spanish Oceanographic Institute, Oceanographic Centre Gijón, Avda. Principe de Asturias 70 bis, 33212, Gijón, Spain
| | - Luisa Federwisch
- AWI-Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.,University of Bremen, Faculty 2 Biology/Chemistry, Leobener Str., 28359, Bremen, Germany
| | - Andre Franke
- IKMB-Institute of Clinical Molecular Biology, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Asimenia Gavriilidou
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Andrea Hethke
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Ellen Kenchington
- DFO-Department of Fisheries and Oceans, Bedford Institute of Oceanography, P.O. Box 1006, 1 Challenger Dr., B2Y 4A2, Dartmouth, NS, Canada
| | - Furu Mienis
- NIOZ-Royal Netherlands Institute for Sea Research, 1790 AB, Den Burg, Texel, the Netherlands
| | - Sadie Mills
- NIWA-National Institute of Water and Atmospheric Research, 301 Evans Bay Parade Hataitai, Wellington, New Zealand
| | - Ana Riesgo
- MNCN-National Museum of Natural Sciences, Department of Biodiversity and Evolutionary Biology, c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.,NHM-Natural History Museum of London, Department of Life Sciences, Cromwell Road, SW7 5BD, London, UK
| | - Pilar Ríos
- IEO-CSIC-Spanish Oceanographic Institute, Oceanographic Centre Gijón, Avda. Principe de Asturias 70 bis, 33212, Gijón, Spain
| | - Emyr Martyn Roberts
- University of Bergen, Department of Biological Sciences and K.G. Jebsen Centre for Deep Sea Research, PO Box 7803, 5020, Bergen, Norway.,Bangor University, School of Ocean Sciences, Menai Bridge, LL59 5AB, Anglesey, UK
| | - Detmer Sipkema
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.,ICM-CSIC-Institute of Marine Sciences, Passeig de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Peter J Schupp
- ICBM-Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstraße 1, 26382, Wilhelmshaven, Germany.,HIFMB-Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Ammerländer Heerstraße 231, 26129, Oldenburg, Germany
| | - Joana Xavier
- University of Bergen, Department of Biological Sciences and K.G. Jebsen Centre for Deep Sea Research, PO Box 7803, 5020, Bergen, Norway.,CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
| | - Hans Tore Rapp
- University of Bergen, Department of Biological Sciences and K.G. Jebsen Centre for Deep Sea Research, PO Box 7803, 5020, Bergen, Norway
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany. .,University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany.
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10
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Sánchez-Suárez J, Díaz L, Junca H, Garcia-Bonilla E, Villamil L. Microbiome composition of the marine sponge Cliona varians at the Neotropical Southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae. J Appl Microbiol 2022; 133:2027-2038. [PMID: 35818766 DOI: 10.1111/jam.15714] [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: 11/22/2021] [Revised: 06/10/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022]
Abstract
AIMS This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification. METHODS AND RESULTS We analyzed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral-reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation. CONCLUSION Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen source. SIGNIFICANCE AND IMPACT OF STUDY Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystems units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.
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Affiliation(s)
- Jeysson Sánchez-Suárez
- Doctorate in Biosciences, School of Engineering, Universidad de La Sabana, Campus del Puente del Común, Chía, Cundinamarca, Colombia.,Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Campus del Puente del Común, Chía, Cundinamarca, Colombia
| | - Luis Díaz
- Doctorate in Biosciences, School of Engineering, Universidad de La Sabana, Campus del Puente del Común, Chía, Cundinamarca, Colombia.,Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Campus del Puente del Común, Chía, Cundinamarca, Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, Chía, Cundinamarca, Colombia
| | - Erika Garcia-Bonilla
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, Chía, Cundinamarca, Colombia
| | - Luisa Villamil
- Doctorate in Biosciences, School of Engineering, Universidad de La Sabana, Campus del Puente del Común, Chía, Cundinamarca, Colombia
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11
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Liu J, Su J, Zhang M, Luo Z, Li X, Chai B. Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China. Front Microbiol 2021; 12:669131. [PMID: 34276600 PMCID: PMC8282455 DOI: 10.3389/fmicb.2021.669131] [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: 02/18/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities have been described as early indicators of both regional and global climatic change and play a critical role in the global biogeochemical cycle. Exploring the mechanisms that determine the diversity patterns of bacterial communities and how they share different habitats along environmental gradients are, therefore, a central theme in microbial ecology research. We characterized the diversity patterns of bacterial communities in Pipahai Lake (PPH), Mayinghai Lake (MYH), and Gonghai Lake (GH), three subalpine natural lakes in Ningwu County, Shanxi, China, and analyzed the distribution of their shared and unique taxa (indicator species). Results showed that the species composition and structure of bacterial communities were significantly different among the three lakes. Both the structure of the entire bacterial community and the unique taxa were significantly influenced by the carbon content (TOC and IC) and space distance; however, the structure of the shared taxa was affected by conductivity (EC), pH, and salinity. The structure of the entire bacterial community and unique taxa were mainly affected by the same factors, suggesting that unique taxa may be important in maintaining the spatial distribution diversity of bacterial communities in subalpine natural freshwater lakes. Our results provide new insights into the diversity maintenance patterns of the bacterial communities in subalpine lakes, and suggest dispersal limitation on bacterial communities between adjacent lakes, even in a small local area. We revealed the importance of unique taxa in maintaining bacterial community structure, and our results are important in understanding how bacterial communities in subalpine lakes respond to environmental change in local habitats.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Jiahe Su
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China.,Department of Geography, Xinzhou Teachers University, Xinzhou, China
| | - Xiaoqi Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
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12
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Durán C, Ciucci S, Palladini A, Ijaz UZ, Zippo AG, Sterbini FP, Masucci L, Cammarota G, Ianiro G, Spuul P, Schroeder M, Grill SW, Parsons BN, Pritchard DM, Posteraro B, Sanguinetti M, Gasbarrini G, Gasbarrini A, Cannistraci CV. Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome. Nat Commun 2021; 12:1926. [PMID: 33771992 PMCID: PMC7997970 DOI: 10.1038/s41467-021-22135-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
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Affiliation(s)
- Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Alessandra Palladini
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum Munchen, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Umer Z Ijaz
- Department of Infrastructure and Environment University of Glasgow, School of Engineering, Glasgow, UK
| | - Antonio G Zippo
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche, Milan, Italy
| | | | - Luca Masucci
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Cammarota
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianluca Ianiro
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Pirjo Spuul
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Stephan W Grill
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bryony N Parsons
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - D Mark Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - Brunella Posteraro
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany.
- Center for Complex Network Intelligence (CCNI) at Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Biomedical Engineering, Tsinghua University, Beijing, China.
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13
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Gong X, Huang D, Liu Y, Zou D, Hu X, Zhou L, Wu Z, Yang Y, Xiao Z. Nanoscale zerovalent iron, carbon nanotubes and biochar facilitated the phytoremediation of cadmium contaminated sediments by changing cadmium fractions, sediments properties and bacterial community structure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111510. [PMID: 33120259 DOI: 10.1016/j.ecoenv.2020.111510] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 05/04/2023]
Abstract
Environment functional materials have been widely used, but whether their effects on the contaminated environment could facilitate phytoremediation is not yet well understood. In this study, starch stabilized nanoscale zerovalent iron (SN), multiwall carbon nanotubes (MW) and tea waste derived biochar (TB) were used to facilitate the phytoremediation of cadmium (Cd) contaminated sediments by Boehmeria nivea (L.) Gaudich. Results showed that 100 mg/kg SN, 500 mg/kg MW and 500 mg/kg TB facilitated phytoremediation, as evidenced by increasing Cd accumulation and/or promoting plant growth. These concentrations of materials increased the reducible fraction of Cd by 9-10% and decreased the oxidizable proportion of Cd by 48-52%, indicating the improvement of Cd bioavailability through converting the oxidizable Cd into reducible form. The activities of urease, phosphatase and catalase, which related to nutrient utilization and oxidative stress alleviation, increased by 20-24%, 25-26%, and 8-9% in the sediments treated with 500 mg/kg MW and 500 mg/kg TB, respectively. In addition, the 16S rRNA gene sequence results showed that these concentrations of materials changed the bacterial diversity. The abundance of Acidobacteria, Actinobacteria, Nitrospirae and Firmicutes were increased by some of the applied materials, which could promote plant growth, change Cd bioavailability and reduce Cd toxicity. These findings indicated that the applied environment functional materials could facilitate the phytoremediation of Cd contaminated environment by changing Cd fractions, sediments properties and bacterial community structure.
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Affiliation(s)
- Xiaomin Gong
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha 410128, China.
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.
| | - Yunguo Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Dongsheng Zou
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha 410128, China
| | - Xi Hu
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lu Zhou
- School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Zhibin Wu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha 410128, China
| | - Yang Yang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha 410128, China
| | - Zhihua Xiao
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha 410128, China
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14
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Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte. Antonie van Leeuwenhoek 2020; 114:95-112. [DOI: 10.1007/s10482-020-01503-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
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15
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Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Dobson ADW, Laport MS. Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea. Microorganisms 2020; 8:E1978. [PMID: 33322780 PMCID: PMC7764410 DOI: 10.3390/microorganisms8121978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 11/25/2020] [Indexed: 01/28/2023] Open
Abstract
Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.
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Affiliation(s)
- Bruno F. R. Oliveira
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
| | - Isabelle R. Lopes
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Anna L. B. Canellas
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Guilherme Muricy
- Laboratório de Biologia de Porifera, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940040, Brazil;
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
- Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Marinella S. Laport
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
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16
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de Oliveira BFR, Freitas-Silva J, Sánchez-Robinet C, Laport MS. Transmission of the sponge microbiome: moving towards a unified model. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:619-638. [PMID: 33048474 DOI: 10.1111/1758-2229.12896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Jéssyca Freitas-Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Claudia Sánchez-Robinet
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
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17
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Bibi F, Azhar EI. Analysis of bacterial communities in sponges and coral inhabiting Red Sea, using barcoded 454 pyrosequencing. Saudi J Biol Sci 2020; 28:847-854. [PMID: 33424375 PMCID: PMC7783839 DOI: 10.1016/j.sjbs.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial communities are linked with marine sponge are diverse in their structure and function. Our understanding of the sponge-associated microbial diversity is limited especially from Red Sea in Saudi Arabia where few species of sponges have been studied. Here we used pyrosequencing to study two marine sponges and coral species sampled from Obhur region from Red sea in Jeddah. A total of 168 operational taxonomic units (OTUs) were identified from Haliclona caerulea, Stylissa carteri and Rhytisma fulvum. Taxonomic identification of tag sequences of 16S ribosomal RNA revealed 6 different bacterial phyla and 9 different classes. A proportion of unclassified reads were was also observed in sponges and coral sample. We found diverse bacterial communities associated with two sponges and a coral sample. Diversity and richness estimates based on OUTs revealed that sponge H. caerulea had significantly high bacterial diversity. The identified OTUs showed unique clustering in three sponge samples as revealed by Principal coordinate analysis (PCoA). Proteobacteria (88-95%) was dominant phyla alonwith Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes and Nitrospirae. Seventeen different genera were identified where genus Pseudoalteromonas was dominant in all three samples. This is first study to assess bacterial communities of sponge and coral sample that have never been studied before to unravel their microbial communities using 454-pyrosequencing method.
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Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
- Corresponding author at: Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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18
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Astudillo-García C, Bell JJ, Montoya JM, Moitinho-Silva L, Thomas T, Webster NS, Taylor MW. Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef. Environ Microbiol 2020; 22:3985-3999. [PMID: 32827171 DOI: 10.1111/1462-2920.15185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/01/2020] [Indexed: 11/30/2022]
Abstract
Marine sponge reefs usually comprise a complex array of taxonomically different sponge species, many of these hosting highly diverse microbial communities. The number of microbial species known to occupy a given sponge ranges from tens to thousands, bringing numerous challenges to their analysis. One way to deal with such complexity is to use a core microbiota approach, in which only prevalent and abundant microbes are considered. Here we aimed to test the strength and sensitivity of the core microbiota approach by applying different core definitions to 20 host sponge species. Application of increasingly stringent relative abundance and/or percentage occurrence thresholds to qualify as part of the core microbiota decreased the number of 'core' OTUs and phyla and, consequently, changed both alpha- and beta-diversity patterns. Moreover, microbial co-occurrence patterns explored using correlation networks were also affected by the core microbiota definition. The application of stricter thresholds resulted in smaller and less compartmentalized networks, with different keystone species. These results highlight that the application of different core definitions to phylogenetically disparate host species can result in the drawing of markedly different conclusions. Consequently, we recommend to assess the effects of different core community definitions on the specific system of study before considering its application.
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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
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Jose M Montoya
- Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS-University Paul Sabatier, Moulis, France
| | - Lucas Moitinho-Silva
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Qld, Australia
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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19
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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20
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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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21
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Steinert G, Busch K, Bayer K, Kodami S, Arbizu PM, Kelly M, Mills S, Erpenbeck D, Dohrmann M, Wörheide G, Hentschel U, Schupp PJ. Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida). Front Microbiol 2020; 11:716. [PMID: 32390977 PMCID: PMC7193145 DOI: 10.3389/fmicb.2020.00716] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/27/2020] [Indexed: 12/01/2022] Open
Abstract
In the present study, we profiled bacterial and archaeal communities from 13 phylogenetically diverse deep-sea sponge species (Demospongiae and Hexactinellida) from the South Pacific by 16S rRNA-gene amplicon sequencing. Additionally, the associated bacteria and archaea were quantified by real-time qPCR. Our results show that bacterial communities from the deep-sea sponges are mostly host-species specific similar to what has been observed for shallow-water demosponges. The archaeal deep-sea sponge community structures are different from the bacterial community structures in that they are almost completely dominated by a single family, which are the ammonia-oxidizing genera within the Nitrosopumilaceae. Remarkably, the archaeal communities are mostly specific to individual sponges (rather than sponge-species), and this observation applies to both hexactinellids and demosponges. Finally, archaeal 16s gene numbers, as detected by quantitative real-time PCR, were up to three orders of magnitude higher than in shallow-water sponges, highlighting the importance of the archaea for deep-sea sponges in general.
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Affiliation(s)
- Georg Steinert
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Kathrin Busch
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Kristina Bayer
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sahar Kodami
- German Center for Marine Biodiversity Research, Senckenberg Research Institute, Wilhelmshaven, Germany
| | - Pedro Martinez Arbizu
- German Center for Marine Biodiversity Research, Senckenberg Research Institute, Wilhelmshaven, Germany
| | - Michelle Kelly
- National Institute of Water and Atmospheric Research, Ltd., Auckland, New Zealand
| | - Sadie Mills
- National Institute of Water and Atmospheric Research, Ltd., Wellington, New Zealand
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Dohrmann
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrecht University of Kiel, Kiel, Germany
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
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22
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Fiore CL, Jarett JK, Steinert G, Lesser MP. Trait-Based Comparison of Coral and Sponge Microbiomes. Sci Rep 2020; 10:2340. [PMID: 32047192 PMCID: PMC7012828 DOI: 10.1038/s41598-020-59320-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral, Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge, Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed in M. cavernosa, while in X. muta there was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation between the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host.
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Affiliation(s)
- Cara L Fiore
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA.
- Appalachian State University, Biology Department, Boone, NC, USA.
| | - Jessica K Jarett
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA
- AnimalBiome, Oakland, CA, USA
| | - Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Wilhelmshaven, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Symbioses, Kiel, Germany
| | - Michael P Lesser
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA
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23
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Zhang F, Jonas L, Lin H, Hill RT. Microbially mediated nutrient cycles in marine sponges. FEMS Microbiol Ecol 2019; 95:5582607. [DOI: 10.1093/femsec/fiz155] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023] Open
Abstract
ABSTRACTEfficient nutrient cycles mediated by symbiotic microorganisms with their hosts are vital to support the high productivity of coral reef ecosystems. In these ecosystems, marine sponges are important habitat-forming organisms in the benthic community and harbor abundant microbial symbionts. However, few studies have reviewed the critical microbially mediated nutrient cycling processes in marine sponges. To bridge this gap, in this review article, we summarize existing knowledge and recent advances in understanding microbially mediated carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles in sponges, propose a conceptual model that describes potential interactions and constraints in the major nutrient cycles, and suggest that shifting redox state induced by animal behavior like sponge pumping can exert great influence on the activities of symbiotic microbial communities. Constraints include the lack of knowledge on spatial and temporal variations and host behavior; more studies are needed in these areas. Sponge microbiomes may have a significant impact on the nutrient cycles in the world’s coral reef ecosystems.
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Affiliation(s)
- Fan Zhang
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Lauren Jonas
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Hanzhi Lin
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
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24
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Swierts T, Cleary DFR, de Voogd NJ. Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny. FEMS Microbiol Ecol 2019; 94:5115559. [PMID: 30289448 PMCID: PMC6196991 DOI: 10.1093/femsec/fiy194] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/04/2018] [Indexed: 12/19/2022] Open
Abstract
Sponges harbor complex communities of microorganisms that carry out essential roles for the functioning and survival of their hosts. In some cases, genetically related sponges from different geographic regions share microbes, while in other cases microbial communities are more similar in unrelated sponges collected from the same location. To better understand how geography and host phylogeny cause variation in the prokaryotic community of sponges, we compared the prokaryotic community of 44 giant barrel sponges (Xestospongia spp.). These sponges belonged to six reproductively isolated genetic groups from eight areas throughout the Indo-Pacific region. Using Illumina sequencing, we obtained 440 000 sequences of the 16S rRNA gene V3V4 variable region that were assigned to 3795 operational taxonomic units (OTUs). The prokaryotic community of giant barrel sponges was characterized by 71 core OTUs (i.e. OTUs present in each specimen) that represented 57.5% of the total number of sequences. The relative abundance of these core OTUs varied significantly among samples, and this variation was predominantly related to the geographic origin of the sample. These results show that in giant barrel sponges, the variation in the prokaryotic community is primarily associated with geography as opposed to phylogenetic relatedness.
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Affiliation(s)
- T Swierts
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.,Institute of Environmental Sciences, Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - D F R Cleary
- Departamento de Biologia CESAM, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.,Institute of Environmental Sciences, Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
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25
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Dubé CE, Ky CL, Planes S. Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling. Front Microbiol 2019; 10:1548. [PMID: 31333634 PMCID: PMC6624473 DOI: 10.3389/fmicb.2019.01548] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/20/2019] [Indexed: 12/21/2022] Open
Abstract
Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of P. margaritifera, including Alpha- and Gammaproteobacteria, Flavobacteriia, and Spirochaetes. We also found a high representation of Endozoicimonaceae symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in P. margaritifera, providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.
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Affiliation(s)
- Caroline Eve Dubé
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence "CORAIL", Mo'orea, French Polynesia
| | - Chin-Long Ky
- Laboratoire d'Excellence "CORAIL", Mo'orea, French Polynesia.,Ifremer, UMR 241, Centre du Pacifique, Tahiti, French Polynesia.,Ifremer, UMR 5244 Interactions Hôtes Pathogènes Environnements, Université de Montpellier, Montpellier, France
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence "CORAIL", Mo'orea, French Polynesia
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26
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Wu S, Ou H, Liu T, Wang D, Zhao J. Structure and dynamics of microbiomes associated with the marine sponge Tedania sp. during its life cycle. FEMS Microbiol Ecol 2019; 94:4956761. [PMID: 29617990 DOI: 10.1093/femsec/fiy055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Tedania sp. is a dominant sponge that is ubiquitous along the southeast coast of China. High-throughput sequencing and transmission electron microscopy were used to describe a detailed profile of sponge-associated microbiomes at seven life stages: adult, embryo-containing spawning adult, embryo, pre-competent larva at 2 h and 4 h, competent larva at 8 h and post-larva within 1-2h after settlement, as well as the surrounding seawater. Among a total of 15098 operational taxonomic units (OTUs), 13 were present exclusively in all stages of the sponge life cycle and could thus be identified as sponge-specific bacteria. Many OTUs were shared between the sponge and seawater, though abundance differed. The relative abundance of β-Proteobacteria associated with sponges was much higher than found in seawater. The microbiomes from each life stage also exhibited a characteristic distribution. Synechococcales dominated in adults, and Enterobacteriaceae was prominent in larvae. The competent larva was notable, with sharp increases in the total OTUs, diversity indices, richness estimates and unique OTUs. Some bacterial groups that were rare in other sponge stages and seawater, such as Clostridia (5.6%), were markedly more abundant in competent larvae. In conclusion, this work greatly advances our understanding of the dynamics and persistence of the sponge-microbe association.
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Affiliation(s)
- Shufei Wu
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Huilong Ou
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Tan Liu
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Dexiang Wang
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Jing Zhao
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
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27
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Wooster MK, Voigt O, Erpenbeck D, Wörheide G, Berumen ML. Sponges of the Red Sea. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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28
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Neave MJ, Apprill A, Aeby G, Miyake S, Voolstra CR. Microbial Communities of Red Sea Coral Reefs. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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García-Bonilla E, Brandão PFB, Pérez T, Junca H. Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida). MICROBIAL ECOLOGY 2019; 77:25-36. [PMID: 29766224 DOI: 10.1007/s00248-018-1201-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.
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Affiliation(s)
- Erika García-Bonilla
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia
| | - Pedro F B Brandão
- Laboratorio de Microbiología Ambiental y Aplicada, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Avenida Carrera 30 No. 45-03, Bogotá, Colombia
| | - Thierry Pérez
- Station Marine d'Endoume SME - IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, UMR 7263 CNRS, Aix-Marseille Université, IRD, Avignon Université, Rue Batterie des Lions, 13007, Marseille, France
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia.
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Najafi A, Moradinasab M, Seyedabadi M, Haghighi MA, Nabipour I. First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran. Open Microbiol J 2018; 12:323-332. [PMID: 30450139 PMCID: PMC6198412 DOI: 10.2174/1874285801812010323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/21/2018] [Accepted: 09/23/2018] [Indexed: 11/22/2022] Open
Abstract
Background Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran. Methods Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning. Results In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group. Conclusion The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad Seyedabadi
- Department of Pharmacology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad A Haghighi
- Department of Microbiology and Parasitology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
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Batista D, Costa R, Carvalho AP, Batista WR, Rua CPJ, de Oliveira L, Leomil L, Fróes AM, Thompson FL, Coutinho R, Dobretsov S. Environmental conditions affect activity and associated microorganisms of marine sponges. MARINE ENVIRONMENTAL RESEARCH 2018; 142:59-68. [PMID: 30274716 DOI: 10.1016/j.marenvres.2018.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/09/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.
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Affiliation(s)
- Daniela Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil.
| | - Rafaela Costa
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Ana Polycarpa Carvalho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - William Romão Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Cintia P J Rua
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Louisi de Oliveira
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Adriana M Fróes
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Sergey Dobretsov
- Marine Science and Fisheries Department, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123. PO Box 34, Muscat, Oman; Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Al-Khoud 123. PO Box 50, Muscat, Oman.
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Turon M, Cáliz J, Garate L, Casamayor EO, Uriz MJ. Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges. Sci Rep 2018; 8:15201. [PMID: 30315194 PMCID: PMC6185911 DOI: 10.1038/s41598-018-33545-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/25/2018] [Indexed: 02/08/2023] Open
Abstract
We studied the core bacterial communities of 19 sponge species from Nha Trang Bay (Central Vietnam), with particular emphasis on the contribution of planktonic seawater bacteria to the sponge core microbiomes. To ensure consistent sponge-microbe associations and accurate identification of planktonic bacteria transmitted from seawater, we were very restrictive with the definition of the sponge core microbiomes (present in all the replicates), and with the identification of valid biological 16S rRNA gene sequences (100% sequence identity) that belonged to potentially different bacterial taxa. We found a high overlap (>50% relative abundance) between the sponge species core microbiome and the seawater bacterial core in ca. a half of the studied species, including representatives of both, HMA and LMA sponges. From our restrictive analysis, we point to horizontal transmission as a relevant way of symbiont acquisition in sponges. Some species-specific recognition mechanisms may act in sponges to enrich specific seawater bacteria in their tissues. These mechanisms would allow the maintenance of bacterial communities in a species across geographical ranges. Moreover, besides contrasting preferences in bacteria selection from seawater, divergent physiological traits may also account for the different microbiomes in species of HMA and LMA sponges.
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Affiliation(s)
- Marta Turon
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain.
| | - Joan Cáliz
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain
| | - Leire Garate
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain
| | - Emilio O Casamayor
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain
| | - Maria J Uriz
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain.
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Podell S, Blanton JM, Neu A, Agarwal V, Biggs JS, Moore BS, Allen EE. Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. ISME JOURNAL 2018; 13:468-481. [PMID: 30291328 DOI: 10.1038/s41396-018-0292-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/10/2023]
Abstract
Candidatus Poribacteria is a little-known bacterial phylum, previously characterized by partial genomes from a single sponge host, but never isolated in culture. We have reconstructed multiple genome sequences from four different sponge genera and compared them to recently reported, uncharacterized Poribacteria genomes from the open ocean, discovering shared and unique functional characteristics. Two distinct, habitat-linked taxonomic lineages were identified, designated Entoporibacteria (sponge-associated) and Pelagiporibacteria (free-living). These lineages differed in flagellar motility and chemotaxis genes unique to Pelagiporibacteria, and highly expanded families of restriction endonucleases, DNA methylases, transposases, CRISPR repeats, and toxin-antitoxin gene pairs in Entoporibacteria. Both lineages shared pathways for facultative anaerobic metabolism, denitrification, fermentation, organosulfur compound utilization, type IV pili, cellulosomes, and bacterial proteosomes. Unexpectedly, many features characteristic of eukaryotic host association were also shared, including genes encoding the synthesis of eukaryotic-like cell adhesion molecules, extracellular matrix digestive enzymes, phosphoinositol-linked membrane glycolipids, and exopolysaccharide capsules. Complete Poribacteria 16S rRNA gene sequences were found to contain multiple mismatches to "universal" 16S rRNA gene primer sets, substantiating concerns about potential amplification failures in previous studies. A newly designed primer set corrects these mismatches, enabling more accurate assessment of Poribacteria abundance in diverse marine habitats where it may have previously been overlooked.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Alexander Neu
- Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, Guam, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA. .,Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA. .,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.
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Rua CPJ, de Oliveira LS, Froes A, Tschoeke DA, Soares AC, Leomil L, Gregoracci GB, Coutinho R, Hajdu E, Thompson CC, Berlinck RGS, Thompson FL. Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes. MICROBIAL ECOLOGY 2018; 76:825-838. [PMID: 29546438 DOI: 10.1007/s00248-018-1172-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.
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Affiliation(s)
- Cintia P J Rua
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Caixa Postal 780 - CEP13560-970, São Carlos, SP, CEP 13566-590, Brazil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Louisi S de Oliveira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Adriana Froes
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Diogo A Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
- Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Av. São José Barreto, 764 - São José do Barreto, Macaé - RJ, Macaé, RJ, CEP 27965-045, Brazil
| | - Ana Carolina Soares
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Gustavo B Gregoracci
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Av. Alm. Saldanha da Gama, 89, Santos, CEP 11030-400, Brazil
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto, 253, Praia dos Anjos, Arraial do Cabo, RJ, CEP 28930-000, Brazil
| | - Eduardo Hajdu
- Museu Nacional - UFRJ, Departamento de Invertebrados. Laboratório de Porifera, Quinta da Boa Vista, s/n. São Cristóvão, Rio de Janeiro, CEP 20940-040, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Caixa Postal 780 - CEP13560-970, São Carlos, SP, CEP 13566-590, Brazil.
| | - Fabiano L Thompson
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Caixa Postal 780 - CEP13560-970, São Carlos, SP, CEP 13566-590, Brazil.
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Najafi A, Moradinasab M, Nabipour I. First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing. Front Microbiol 2018; 9:1500. [PMID: 30034382 PMCID: PMC6043863 DOI: 10.3389/fmicb.2018.01500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
The Persian Gulf is a special habitat of marine sponges whose bacterial communities are under-investigated. Recently, next-generation sequencing technology has comprehensively improved the knowledge of marine sponge-associated bacteria. For the first time, this study aimed to evaluate the diversity of the Persian Gulf sponge-associated bacteria using tag pyrosequencing in Iran. In this study, 10 sponge samples from 6 different taxonomic orders were collected from the Persian Gulf using SCUBA diving. The diversity of the bacteria associated with the marine sponges was investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. A total of 68,628 high-quality sequences were obtained and clustered at a 97% similarity into 724 unique operational taxonomic units (OTUs), representing 17 bacterial phyla. Cyanobacteria was the most abundant phylum in the sponges, followed by Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria. Other phyla were detected as minor groups of bacteria. Bacterial community richness, Shannon, and Simpson indices revealed the highest diversity in sponge S11 (Dictyoceratida sp.) compared to other sponges. This study showed a diverse structure of bacterial communities associated with the Persian Gulf sponges. The dominance of Cyanobacteria may suggest an ecological importance of this phylum in the Persian Gulf sponges.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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Dat TTH, Steinert G, Thi Kim Cuc N, Smidt H, Sipkema D. Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam. PeerJ 2018; 6:e4970. [PMID: 29900079 PMCID: PMC5995103 DOI: 10.7717/peerj.4970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Cárdenas CA, González-Aravena M, Font A, Hestetun JT, Hajdu E, Trefault N, Malmberg M, Bongcam-Rudloff E. High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas. PeerJ 2018; 6:e4935. [PMID: 29892508 PMCID: PMC5994334 DOI: 10.7717/peerj.4935] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/19/2018] [Indexed: 01/07/2023] Open
Abstract
Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities associated with Mycale species inhabiting different geographical areas have not been previously compared. Here, we provide the first detailed description of the microbiota of two Mycale species inhabiting the sub-Antarctic Magellan region (53°S) and the Western Antarctic Peninsula (62-64°S), two geographically distant areas (>1,300 km) with contrasting environmental conditions. The sponges Mycale (Aegogropila) magellanica and Mycale (Oxymycale) acerata are both abundant members of benthic communities in the Magellan region and in Antarctica, respectively. High throughput sequencing revealed a remarkable similarity in the microbiota of both sponge species, dominated by Proteobacteria and Bacteroidetes, with both species sharing more than 74% of the OTUs. In contrast, 16% and 10% of the OTUs were found only in either M. magellanica or M. acerata, respectively. Interestingly, despite slight differences in the relative abundance, the most dominant OTUs were present in both species, whereas the unique OTUs had very low abundances (less than 1% of the total abundance). These results show a significant overlap among the microbiota of both Mycale species and also suggest the existence of a low level of specificity of the most dominant symbiont groups.
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Affiliation(s)
- César A. Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | | | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Jon T. Hestetun
- Marine Biodiversity Group, Department of Biology, University of Bergen, Bergen, Norway
| | - Eduardo Hajdu
- Museu Nacional, Departamento de Invertebrados, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Maja Malmberg
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Miendlarzewska EA, Ciucci S, Cannistraci CV, Bavelier D, Schwartz S. Reward-enhanced encoding improves relearning of forgotten associations. Sci Rep 2018; 8:8557. [PMID: 29867116 PMCID: PMC5986818 DOI: 10.1038/s41598-018-26929-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/18/2018] [Indexed: 12/16/2022] Open
Abstract
Research on human memory has shown that monetary incentives can enhance hippocampal memory consolidation and thereby protect memory traces from forgetting. However, it is not known whether initial reward may facilitate the recovery of already forgotten memories weeks after learning. Here, we investigated the influence of monetary reward on later relearning. Nineteen healthy human participants learned object-location associations, for half of which we offered money. Six weeks later, most of these associations had been forgotten as measured by a test of declarative memory. Yet, relearning in the absence of any reward was faster for the originally rewarded associations. Thus, associative memories encoded in a state of monetary reward motivation may persist in a latent form despite the failure to retrieve them explicitly. Alternatively, such facilitation could be analogous to the renewal effect observed in animal conditioning, whereby a reward-associated cue can reinstate anticipatory arousal, which would in turn modulate relearning. This finding has important implications for learning and education, suggesting that even when learned information is no longer accessible via explicit retrieval, the enduring effects of a past prospect of reward could facilitate its recovery.
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Affiliation(s)
- Ewa A Miendlarzewska
- Department of Neuroscience, University of Geneva, Geneva, Switzerland. .,Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland. .,Geneva Finance Research Institute, University of Geneva, Geneva, Switzerland.
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.,Lipotype GmbH, Tatzberg 47, 01307, Dresden, Germany
| | - Carlo V Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, 98124, Italy
| | - Daphne Bavelier
- Psychology Section, FPSE, University of Geneva, Geneva, Switzerland.,Brain & Cognitive Sciences, University of Rochester, Rochester, NY, United States
| | - Sophie Schwartz
- Department of Neuroscience, University of Geneva, Geneva, Switzerland. .,Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland. .,Geneva Neuroscience Center, University of Geneva, Geneva, Switzerland.
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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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40
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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41
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Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T. The sponge microbiome project. Gigascience 2017; 6:1-7. [PMID: 29020741 PMCID: PMC5632291 DOI: 10.1093/gigascience/gix077] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/28/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022] Open
Abstract
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Amnon Amir
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Gail L Ackermann
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Carlo Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | | | - Cole Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Detmer Sipkema
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Fang Liu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Georg Steinert
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giorgos Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Grace P McCormack
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Guofang Feng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Jan Vicente
- Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346
| | - Johannes R Björk
- Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jose M Montoya
- Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France
| | - Julie B Olson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Julie Reveillaud
- INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Mari-Carmen Pineda
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia
| | - Maria V Marra
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paraskevi Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Patrick M Erwin
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Rachel L Simister
- Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3
| | - Rob Knight
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, and Center for Microbiome Innovation, University of California - San Diego, La Jolla, CA 92093, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Susanna Lopez-Legentil
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Thanos Dailianis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Nicole S Webster
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
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42
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Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks. Sci Rep 2017; 7:2542. [PMID: 28566699 PMCID: PMC5451456 DOI: 10.1038/s41598-017-02656-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 04/18/2017] [Indexed: 12/24/2022] Open
Abstract
Sponges (Porifera) are abundant and diverse members of benthic filter feeding communities in most marine ecosystems, from the deep sea to tropical reefs. A characteristic feature is the associated dense and diverse prokaryotic community present within the sponge mesohyl. Previous molecular genetic studies revealed the importance of host identity for the community composition of the sponge-associated microbiota. However, little is known whether sponge host-specific prokaryotic community patterns observed at 97% 16S rRNA gene sequence similarity are consistent at high taxonomic ranks (from genus to phylum level). In the present study, we investigated the prokaryotic community structure and variation of 24 sponge specimens (seven taxa) and three seawater samples from Sweden. Results show that the resemblance of prokaryotic communities at different taxonomic ranks is consistent with patterns present at 97% operational taxonomic unit level.
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43
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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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44
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Reverter M, Sasal P, Tapissier-Bontemps N, Lecchini D, Suzuki M. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems. FEMS Microbiol Ecol 2017; 93:3738480. [DOI: 10.1093/femsec/fix051] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/17/2017] [Indexed: 12/26/2022] Open
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45
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Matcher GF, Waterworth SC, Walmsley TA, Matsatsa T, Parker‐Nance S, Davies‐Coleman MT, Dorrington RA. Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts. Microbiologyopen 2017; 6:e00417. [PMID: 27781403 PMCID: PMC5387304 DOI: 10.1002/mbo3.417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 01/13/2023] Open
Abstract
The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids. Previously it was shown that the bacterial community associated with a Tsitsikamma sponge species comprises unusual bacterial taxa and is dominated by a novel Betaproteobacterium. Here, we have characterized the bacterial communities associated with six latrunculid species representing three genera (Tsitsikamma, Cyclacanthia, and Latrunculia) as well as a Mycale species, collected from Algoa Bay on the South African southeast coast. The bacterial communities of all seven sponge species were dominated by a single Betaproteobacterium operational taxonomic unit (OTU0.03 ), while a second OTU0.03 was dominant in the Mycale sp. The Betaproteobacteria OTUs from the different latrunculid sponges are closely related and their phylogenetic relationship follows that of their hosts. We propose that the latrunculid Betaproteobacteria OTUs are members of a specialized group of sponge symbionts that may have coevolved with their hosts. A single dominant Spirochaetae OTU0.03 was present in the Tsitsikamma and Cyclacanthia sponge species, but absent from the Latrunculia and Mycale sponges. This study sheds new light on the interactions between latrunculid sponges and their bacterial communities and may point to the potential involvement of dominant symbionts in the biosynthesis of the bioactive secondary metabolites.
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Affiliation(s)
- Gwynneth F. Matcher
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | | | - Tara A. Walmsley
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
- Department of BiotechnologyVaal University of TechnologyVanderbijlparkSouth Africa
| | - Tendayi Matsatsa
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Shirley Parker‐Nance
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Michael T. Davies‐Coleman
- Department of ChemistryRhodes UniversityGrahamstownSouth Africa
- Faculty of Natural ScienceUniversity of the Western CapeCape TownSouth Africa
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46
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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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47
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Pita L, Fraune S, Hentschel U. Emerging Sponge Models of Animal-Microbe Symbioses. Front Microbiol 2016; 7:2102. [PMID: 28066403 PMCID: PMC5179597 DOI: 10.3389/fmicb.2016.02102] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/12/2016] [Indexed: 12/30/2022] Open
Abstract
Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host–microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota.
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Affiliation(s)
- Lucia Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Sebastian Fraune
- Zoological Institute, Christian-Albrechts-University of Kiel (CAU), Kiel Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Christian-Albrechts-University of Kiel (CAU), KielGermany
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48
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Li Z, Wang Y, Li J, Liu F, He L, He Y, Wang S. Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:659-671. [PMID: 27819120 DOI: 10.1007/s10126-016-9725-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/14/2016] [Indexed: 05/20/2023]
Abstract
Sponges host complex symbiotic communities, but to date, the whole picture of the metabolic potential of sponge microbiota remains unclear, particularly the difference between the shallow-water and deep-sea sponge holobionts. In this study, two completely different sponges, shallow-water sponge Theonella swinhoei from the South China Sea and deep-sea sponge Neamphius huxleyi from the Indian Ocean, were selected to compare their whole symbiotic communities and metabolic potential, particularly in element transformation. Phylogenetically diverse bacteria, archaea, fungi, and algae were detected in both shallow-water sponge T. swinhoei and deep-sea sponge N. huxleyi, and different microbial community structures were indicated between these two sponges. Metagenome-based gene abundance analysis indicated that, though the two sponge microbiota have similar core functions, they showed different potential strategies in detailed metabolic processes, e.g., in the transformation and utilization of carbon, nitrogen, phosphorus, and sulfur by corresponding microbial symbionts. This study provides insight into the putative metabolic potentials of the microbiota associated with the shallow-water and deep-sea sponges at the whole community level, extending our knowledge of the sponge microbiota's functions, the association of sponge- microbes, as well as the adaption of sponge microbiota to the marine environment.
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Affiliation(s)
- Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
| | - Jinlong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Fang Liu
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Liming He
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Ying He
- Laboratory of Marine Oceanography, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Shenyue Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
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Souza DT, Genuário DB, Silva FSP, Pansa CC, Kavamura VN, Moraes FC, Taketani RG, Melo IS. Analysis of bacterial composition in marine sponges reveals the influence of host phylogeny and environment. FEMS Microbiol Ecol 2016; 93:fiw204. [PMID: 27702764 DOI: 10.1093/femsec/fiw204] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/14/2016] [Accepted: 10/02/2016] [Indexed: 01/10/2023] Open
Abstract
Bacterial communities associated with sponges are influenced by environmental factors; however, some degree of genetic influence of the host on the microbiome is also expected. In this work, 16S rRNA gene amplicon sequencing revealed diverse bacterial phylotypes based on the phylogenies of three tropical sponges (Aplysina fulva, Aiolochroia crassa and Chondrosia collectrix). Despite their sympatric occurrence, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were observed within sponges from the same phylogenetic group. The relationships between operational taxonomic units (OTUs) recovered from the sponges and database sequences revealed associations among sequences from unrelated sponge species and sequences retrieved from diverse environmental samples. In addition, one Proteobacteria OTU retrieved from A. fulva was identical to sequences previously reported from A. fulva specimens collected along the Brazilian coast. Based on these results, we conclude that bacterial communities associated with marine sponges are shaped by host identity, while environmental conditions seem to be less important in shaping symbiont communities. This is the first study to assess bacterial communities associated with marine sponges in the remote St. Peter and St. Paul Archipelago using amplicon sequencing of the 16S rRNA gene.
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Affiliation(s)
- Danilo T Souza
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Diego B Genuário
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Fabio Sérgio P Silva
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Camila C Pansa
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Vanessa N Kavamura
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Fernando C Moraes
- Rio de Janeiro Botanical Garden Research Institute, 22460-030, Rio de Janeiro, RJ, Brazil
- National Museum, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, RJ, Brazil
| | - Rodrigo G Taketani
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Itamar S Melo
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
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50
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Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment. Mar Genomics 2016; 29:69-80. [DOI: 10.1016/j.margen.2016.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/17/2022]
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