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Wang Y, Hu Y, Liu Y, Chen Q, Xu J, Zhang F, Mao J, Shi Q, He C, Cai R, Lønborg C, Liu L, Guo A, Jiao N, Zheng Q. Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172003. [PMID: 38569948 DOI: 10.1016/j.scitotenv.2024.172003] [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: 02/06/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Heavy metals can impact the structure and function of coastal sediment. The dissolved organic matter (DOM) pool plays an important role in determining both the heavy metal toxicity and microbial community composition in coastal sediments. However, how heavy metals affect the interactions between microbial communities and DOM remains unclear. Here, we investigated the influence of heavy metals on the microbial community structure (including bacteria and archaea) and DOM composition in surface sediments of Beibu Gulf, China. Our results revealed firstly that chromium, zinc, cadmium, and lead were the heavy metals contributing to pollution in our studied area. Furthermore, the DOM chemical composition was distinctly different in the contaminated area from the uncontaminated area, characterized by a higher average O/C ratio and increased prevalence of carboxyl-rich alicyclic molecules (CRAM) and highly unsaturated compounds (HUC). This indicates that DOM in the contaminated area was more recalcitrant compared to the uncontaminated area. Except for differences in archaeal diversity between the two areas, there were no significant variations observed in the structure of archaea and bacteria, as well as the diversity of bacteria, across the two areas. Nevertheless, our co-occurrence network analysis revealed that the B2M28 and Euryarchaeota, dominating bacterial and archaeal groups in the contaminated area were strongly related to CRAM. The network analysis also unveiled correlations between active bacteria and elevated proportions of nitrogen-containing DOM molecules. In contrast, the archaea-DOM network exhibited strong associations with nitrogen- and sulfur-containing molecules. Collectively, these findings suggest that heavy metals indeed influence the interaction between microbial communities and DOM, potentially affecting the accumulation of recalcitrant compounds in coastal sediments.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China; College of Environmental and Ecology, Xiamen University, Xiamen, China
| | - Yuxing Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yanting Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Qi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jinxin Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Fei Zhang
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, China
| | - Jinhua Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Quan Shi
- College of Chemical Engineering and Environment, China University of Petroleum (Beijing), Beijing, China
| | - Chen He
- College of Chemical Engineering and Environment, China University of Petroleum (Beijing), Beijing, China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Christian Lønborg
- Department of Ecoscience, Section for Marine Diversity and Experimental Ecology, University of Aarhus, Roskilde, Denmark
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xiamen, China
| | - Aixing Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
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2
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Wang FQ, Bartosik D, Sidhu C, Siebers R, Lu DC, Trautwein-Schult A, Becher D, Huettel B, Rick J, Kirstein IV, Wiltshire KH, Schweder T, Fuchs BM, Bengtsson MM, Teeling H, Amann RI. Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides. MICROBIOME 2024; 12:32. [PMID: 38374154 PMCID: PMC10877868 DOI: 10.1186/s40168-024-01757-5] [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: 11/07/2023] [Accepted: 01/04/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses. RESULTS Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria. CONCLUSIONS Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.
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Grants
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/10-3 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- BE 3869/4-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/11-3 Deutsche Forschungsgemeinschaft,Germany
- FU 627/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- Max Planck Institute for Marine Microbiology (2)
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Affiliation(s)
- Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Daniel Bartosik
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Robin Siebers
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - De-Chen Lu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Marine College, Shandong University, Weihai, 264209, China
| | - Anke Trautwein-Schult
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné-Weg 10, 50829, Cologne, Germany
| | - Johannes Rick
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Inga V Kirstein
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Karen H Wiltshire
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany.
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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Stuij TM, Cleary DFR, Rocha RJM, Polónia ARM, Silva DAM, Louvado A, de Voogd NJ, Gomes NCM. Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp. FEMS Microbiol Ecol 2024; 100:fiae022. [PMID: 38366951 PMCID: PMC10939426 DOI: 10.1093/femsec/fiae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.
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Affiliation(s)
- Tamara M Stuij
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Rui J M Rocha
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Davide A M Silva
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Antonio Louvado
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Newton C M Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
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4
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Peng S, Ye L, Li Y, Wang F, Sun T, Wang L, Zhao J, Dong Z. Metagenomic insights into jellyfish-associated microbiome dynamics during strobilation. ISME COMMUNICATIONS 2024; 4:ycae036. [PMID: 38571744 PMCID: PMC10988111 DOI: 10.1093/ismeco/ycae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Host-associated microbiomes can play key roles in the metamorphosis of animals. Most scyphozoan jellyfish undergo strobilation in their life cycles, similar to metamorphosis in classic bilaterians. The exploration of jellyfish microbiomes may elucidate the ancestral mechanisms and evolutionary trajectories of metazoan-microbe associations and interactions during metamorphosis. However, current knowledge of the functional features of jellyfish microbiomes remains limited. Here, we performed a genome-centric analysis of associated microbiota across four successive life stages (polyp, early strobila, advanced strobila, and ephyra) during strobilation in the common jellyfish Aurelia coerulea. We observed shifts in taxonomic and functional diversity of microbiomes across distinct stages and proposed that the low microbial diversity in ephyra stage may be correlated with the high expression of the host-derived antimicrobial peptide aurelin. Furthermore, we recovered 43 high-quality metagenome-assembled genomes and determined the nutritional potential of the dominant Vibrio members. Interestingly, we observed increased abundances of genes related to the biosynthesis of amino acids, vitamins, and cofactors, as well as carbon fixation during the loss of host feeding ability, indicating the functional potential of Aurelia-associated microbiota to support the synthesis of essential nutrients. We also identified several potential mechanisms by which jellyfish-associated microbes establish stage-specific community structures and maintain stable colonization in dynamic host environments, including eukaryotic-like protein production, bacterial secretion systems, restriction-modification systems, and clustered regularly interspaced short palindromic repeats-Cas systems. Our study characterizes unique taxonomic and functional changes in jellyfish microbiomes during strobilation and provides foundations for uncovering the ancestral mechanism of host-microbe interactions during metamorphosis.
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Affiliation(s)
- Saijun Peng
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lijing Ye
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Yongxue Li
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanghan Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Sun
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Lei Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Jianmin Zhao
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijun Dong
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Davison HR, Hurst GDD. Hidden from plain sight: Novel Simkaniaceae and Rhabdochlamydiaceae diversity emerging from screening genomic and metagenomic data. Syst Appl Microbiol 2023; 46:126468. [PMID: 37847957 DOI: 10.1016/j.syapm.2023.126468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Chlamydiota are an ancient and hyperdiverse phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic Chlamydiota are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of Chlamydiota diversity and its hosts, in particular the Order Parachlamydiales. We extract one Rhabdochlamydiaceae and three Simkaniaceae Metagenome-Assembled Genomes (MAGs) from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 MAGs respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names "Sacchlamyda saccharinae" (Family Rhabdochlamydiaceae) and "Amphrikana amoebophyrae" (Family Simkaniaceae), as well as a third new clade of environmental MAGs "Acheromyda pituitae" (Family Rhabdochlamydiaceae). The extent of uncharacterized diversity within the Rhabdochlamydiaceae and Simkaniaceae is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, there was great predicted diversity in Parachlamydiales metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade.
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Affiliation(s)
- Helen R Davison
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB UK.
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB UK
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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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Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M. Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta. THE ISME JOURNAL 2023; 17:1208-1223. [PMID: 37188915 PMCID: PMC10356861 DOI: 10.1038/s41396-023-01420-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.
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Affiliation(s)
- Florian U Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cherie Motti
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bettina Glasl
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, St Lucia, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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8
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Roveta C, Calcinai B, Girolametti F, Fernandes Couceiro J, Puce S, Annibaldi A, Costa R. The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection. ZOOLOGY 2023; 158:126091. [PMID: 37003141 DOI: 10.1016/j.zool.2023.126091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Microbial communities inhabiting sponges are known to take part in many metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of 16S rRNA genes to characterize the prokaryotic communities present in the cortex and choanosome, respectively the external and internal body region of Chondrosia reniformis, and in the surrounding seawater. Furthermore, we estimated the total mercury content (THg) in these body regions of the sponge and in the corresponding microbial cell pellets. Fifteen prokaryotic phyla were detected in association with C. reniformis, 13 belonging to the domain Bacteria and two to the Archaea. No significant differences between the prokaryotic community composition of the two regions were found. Three lineages of ammonium-oxidizing organisms (Cenarchaeum symbiosum, Nitrosopumilus maritimus, and Nitrosococcus sp.) co-dominated the prokaryotic community, suggesting ammonium oxidation/nitrification as a key metabolic pathway within the microbiome of C. reniformis. In the sponge fractions, higher THg levels were found in the choanosome compared to the cortex. In contrast, comparable THg levels found in the microbial pellets obtained from both regions were significantly lower than those observed in the corresponding sponge fractions. Our work provides new insights into the prokaryotic communities and TEs distribution in different body parts of a model organism relevant for marine conservation and biotechnology. In this sense, this study paves the way for scientists to deepen the possible application of sponges not only as bioindicators, but also as bioremediation tools of metal polluted environments.
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Affiliation(s)
- Camilla Roveta
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Barbara Calcinai
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Federico Girolametti
- Department of Industrial Engineering and Mathematical Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Joana Fernandes Couceiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Stefania Puce
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna Annibaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Portugal
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9
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Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
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Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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10
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Xiao Y, Chen L, Li C, Ma J, Chen R, Yang B, Liu G, Liu S, Fang J. Role of the rhizosphere bacterial community in assisting phytoremediation in a lead-zinc area. FRONTIERS IN PLANT SCIENCE 2023; 13:1106985. [PMID: 36874912 PMCID: PMC9982732 DOI: 10.3389/fpls.2022.1106985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Heavy metals (HMs) contamination and vegetation destruction in the mining area caused by mining activities are severely increasing. It is urgent to restore vegetation and stabilize HMs. In this study, we compared the ability of HMs phytoextraction/phytostabilization of three dominant plants, including Artemisia argyi (LA), Miscanthus floridulus (LM), and Boehmeria nivea (LZ) in a lead-zinc mining area in Huayuan County (China). We also explored the role of the rhizosphere bacterial community in assisting phytoremediation using 16S rRNA sequencing technology. Bioconcentration factor (BCF) and translocation factor (TF) analysis showed that LA preferred accumulating Cd, LZ preferred accumulating Cr and Sb, and LM preferred accumulating Cr and Ni. Significant (p < 0.05) differences were found among the rhizosphere soil microbial communities of these three plants. The key genera of LA were Truepera and Anderseniella, that of LM were Paracoccus and Erythrobacter, and of LZ was Novosphingobium. Correlation analysis showed some rhizosphere bacterial taxa (e.g., Actinomarinicola, Bacillariophyta and Oscillochloris) affected some soil physicochemical parameters (e.g., organic matter and pH) of the rhizosphere soil and enhanced the TF of metals. Functional prediction analysis of soil bacterial community showed that the relative abundances of genes related to the synthesis of some proteins (e.g., manganese/zinc-transporting P-type ATPase C, nickel transport protein and 1-aminocyclopropane-1-carboxylate deaminase) was positively correlated with the phytoextraction/phytostabilization capacity of plants for heavy metals. This study provided theoretical guidance on selecting appropriate plants for different metal remediation applications. We also found some rhizosphere bacteria might enhance the phytoremediation of multi-metals, which could provide a reference for subsequent research.
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Affiliation(s)
- Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Liang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chunxiao Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jingjing Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Rui Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Bo Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Gang Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shuming Liu
- College of Chemical and Environmental Sciences, YiLi Normal University, YiLi, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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11
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Almeida JF, Marques M, Oliveira V, Egas C, Mil-Homens D, Viana R, Cleary DFR, Huang YM, Fialho AM, Teixeira MC, Gomes NCM, Costa R, Keller-Costa T. Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens. Mar Drugs 2022; 21:md21010034. [PMID: 36662207 PMCID: PMC9860996 DOI: 10.3390/md21010034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/15/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Marine microbiomes are prolific sources of bioactive natural products of potential pharmaceutical value. This study inspected two culture collections comprising 919 host-associated marine bacteria belonging to 55 genera and several thus-far unclassified lineages to identify isolates with potentially rich secondary metabolism and antimicrobial activities. Seventy representative isolates had their genomes mined for secondary metabolite biosynthetic gene clusters (SM-BGCs) and were screened for antimicrobial activities against four pathogenic bacteria and five pathogenic Candida strains. In total, 466 SM-BGCs were identified, with antimicrobial peptide- and polyketide synthase-related SM-BGCs being frequently detected. Only 38 SM-BGCs had similarities greater than 70% to SM-BGCs encoding known compounds, highlighting the potential biosynthetic novelty encoded by these genomes. Cross-streak assays showed that 33 of the 70 genome-sequenced isolates were active against at least one Candida species, while 44 isolates showed activity against at least one bacterial pathogen. Taxon-specific differences in antimicrobial activity among isolates suggested distinct molecules involved in antagonism against bacterial versus Candida pathogens. The here reported culture collections and genome-sequenced isolates constitute a valuable resource of understudied marine bacteria displaying antimicrobial activities and potential for the biosynthesis of novel secondary metabolites, holding promise for a future sustainable production of marine drug leads.
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Affiliation(s)
- João F. Almeida
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Matilde Marques
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Vanessa Oliveira
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology (CNC), Rua Larga—Faculdade de Medicina, University of Coimbra, 3004-504 Coimbra, Portugal
- Biocant—Transfer Technology Association, BiocantPark, 3060-197 Cantanhede, Portugal
| | - Dalila Mil-Homens
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Romeu Viana
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Daniel F. R. Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Yusheng M. Huang
- Department of Marine Recreation, National Penghu University of Science and Technology, Magong City 880-011, Taiwan
| | - Arsénio M. Fialho
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Miguel C. Teixeira
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Newton C. M. Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rodrigo Costa
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Centre of Marine Sciences (CCMAR/CIMAR LA), University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- Correspondence: (R.C.); (T.K.-C.); Tel.: +351-21-841-7339 (R.C.); +351-21-841-3167 (T.K.-C.)
| | - Tina Keller-Costa
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Correspondence: (R.C.); (T.K.-C.); Tel.: +351-21-841-7339 (R.C.); +351-21-841-3167 (T.K.-C.)
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12
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Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges. Mar Drugs 2022; 21:md21010029. [PMID: 36662202 PMCID: PMC9864124 DOI: 10.3390/md21010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Recent reviews have reinforced sponge-associated bacteria as a valuable source of structurally diverse secondary metabolites with potent biological properties, which makes these microbial communities promising sources of new drug candidates. However, the overall diversity of secondary metabolite biosynthetic potential present in bacteria is difficult to access due to the fact that the majority of bacteria are not readily cultured in the laboratory. Thus, use of cultivation-independent approaches may allow accessing "silent" and "cryptic" secondary metabolite biosynthetic gene clusters present in bacteria that cannot yet be cultured. In the present study, we investigated the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in metagenomes of bacterial communities associated with three sponge species: Clathria reinwardti, Rhabdastrella globostellata, and Spheciospongia sp. The results reveal that the three metagenomes contain a high number of predicted BGCs, ranging from 282 to 463 BGCs per metagenome. The types of BGCs were diverse and represented 12 different cluster types. Clusters predicted to encode fatty acid synthases and polyketide synthases (PKS) were the most dominant BGC types, followed by clusters encoding synthesis of terpenes and bacteriocins. Based on BGC sequence similarity analysis, 363 gene cluster families (GCFs) were identified. Interestingly, no GCFs were assigned to pathways responsible for the production of known compounds, implying that the clusters detected might be responsible for production of several novel compounds. The KS gene sequences from PKS clusters were used to predict the taxonomic origin of the clusters involved. The KS sequences were related to 12 bacterial phyla with Actinobacteria, Proteobacteria, and Firmicutes as the most predominant. At the genus level, the KSs were most related to those found in the genera Mycolicibacterium, Mycobacterium, Burkholderia, and Streptomyces. Phylogenetic analysis of KS sequences resulted in detection of two known 'sponge-specific' BGCs, i.e., SupA and SwfA, as well as a new 'sponge-specific' cluster related to fatty acid synthesis in the phylum Candidatus Poribacteria and composed only by KS sequences of the three sponge-associated bacterial communities assessed here.
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13
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Sugden S, Holert J, Cardenas E, Mohn WW, Stein LY. Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges. THE ISME JOURNAL 2022; 16:2503-2512. [PMID: 35906397 PMCID: PMC9562138 DOI: 10.1038/s41396-022-01296-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.
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Affiliation(s)
- Scott Sugden
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada.
| | - Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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14
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Kelly JB, Carlson DE, Low JS, Thacker RW. Novel trends of genome evolution in highly complex tropical sponge microbiomes. MICROBIOME 2022; 10:164. [PMID: 36195901 PMCID: PMC9531527 DOI: 10.1186/s40168-022-01359-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism. RESULTS A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes. CONCLUSIONS These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.
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Affiliation(s)
- Joseph B Kelly
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany.
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - David E Carlson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Jun Siong Low
- Institute of Microbiology,ETH Zürich, Zürich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Panama City, Republic of Panama
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15
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Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts. Microbiol Res 2022; 265:127183. [PMID: 36108440 DOI: 10.1016/j.micres.2022.127183] [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: 02/10/2022] [Revised: 02/24/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
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16
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Rodriguez Jimenez A, Guiglielmoni N, Goetghebuer L, Dechamps E, George IF, Flot JF. Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains. BMC Genomics 2022; 23:618. [PMID: 36008774 PMCID: PMC9413892 DOI: 10.1186/s12864-022-08842-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome. RESULTS We sequenced and assembled de novo the complete genome sequences of five V. fluvialis isolates recovered from marine sponges. Pangenome analysis of the V. fluvialis species (total of 17 genomes) showed a high intraspecific diversity, with 45.5% of orthologous genes found to be strain specific. Despite this diversity, analyses of gene functions clustered all V. fluvialis species together and separated them from other sequenced Vagococcus species. V. fluvialis strains from different habitats were highly similar in terms of functional diversity but the sponge-isolated strains were enriched in several functions related to the marine environment. Furthermore, sponge-isolated strains carried a significantly higher number of mobile genetic elements (MGEs) compared to previously sequenced V. fluvialis strains from other environments. Sponge-isolated strains carried up to 4 circular plasmids each, including a 48-kb conjugative plasmid. Three of the five strains carried an additional circular extrachromosomal sequence, assumed to be an excised prophage as it contained mainly viral genes and lacked plasmid replication genes. Insertion sequences (ISs) were up to five times more abundant in the genomes of sponge-isolated strains compared to the others, including several IS families found exclusively in these genomes. CONCLUSIONS Our findings highlight the dynamics and plasticity of the V. fluvialis genome. The abundance of mobile genetic elements in the genomes of sponge-isolated V. fluvialis strains suggests that the mobilome might be key to understanding the genomic signatures of symbiosis in bacteria.
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Affiliation(s)
- Ana Rodriguez Jimenez
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium. .,Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, Belgium.
| | - Nadège Guiglielmoni
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lise Goetghebuer
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Etienne Dechamps
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Isabelle F George
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium.,Marine Biology, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)², Brussels, Belgium
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17
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Leal CV, Avelino-Alves D, Salazar V, Omachi C, Thompson C, Berlinck RGS, Hajdu E, Thompson F. Sponges present a core prokaryotic community stable across Tropical Western Atlantic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155145. [PMID: 35429557 DOI: 10.1016/j.scitotenv.2022.155145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/24/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Sponges are among the earliest lineages of metazoans, with first fossil records dated back to 890 million years ago. All sponge species present associations with microorganisms to some extension, which influence sponges' survival and adaptation. Sponge species can be divided into two categories, Low Microbial Abundance and High Microbial Abundance, depending on the abundance of the microbial community that they host. Monanchora arbuscula (a Low Microbial Abundance sponge species) and Xestospongia muta (a High Microbial Abundance sponge species) are sponges with widespread distribution in the Tropical Western Atlantic. Despite previous studies on the major features of these species, little is known whether M. arcuscula and X. muta prokaryotic communities are stable across vast geographic regions. We obtained a total of ~9.26 million 16S rRNA gene Illumina sequences for M. arbuscula samples collected at seven locations and for X. muta samples collected at three locations, corresponding to five ecoregions of the Caribbean and the Southwestern Atlantic (N = 105, 39 from M. arcuscula and 66 from X. muta). These samples reflected different ecological strategies for prokaryotic communities assembly, since the core prokaryotic communities of M. arbuscula are more heterotrophic and shared with different sources (corals, sponges, seawater, sediments), while X. muta has more significant photosynthetic prokaryotic communities, mainly outsourced from other sponges. Results of M. arbuscula and X. muta prokaryotic communities analysis demonstrate that both sponge species have core prokaryotic communities stable across a vast geographic area (> 8000 km), and the world's most notable coastal marine biogeographic filter, the Amazon River Mouth, in spite of the significant differences found among transient prokaryotic communities of both sponge species.
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Affiliation(s)
- Camille V Leal
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Dhara Avelino-Alves
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Vinícius Salazar
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Claudia Omachi
- Laboratório de Indicadores Ambientais, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cristiane Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970 São Carlos, SP, Brazil
| | - Eduardo Hajdu
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fabiano Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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18
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Silva SG, Paula P, da Silva JP, Mil-Homens D, Teixeira MC, Fialho AM, Costa R, Keller-Costa T. Insights into the Antimicrobial Activities and Metabolomes of Aquimarina ( Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere. Mar Drugs 2022; 20:423. [PMID: 35877716 PMCID: PMC9323603 DOI: 10.3390/md20070423] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 12/17/2022] Open
Abstract
Two novel natural products, the polyketide cuniculene and the peptide antibiotic aquimarin, were recently discovered from the marine bacterial genus Aquimarina. However, the diversity of the secondary metabolite biosynthetic gene clusters (SM-BGCs) in Aquimarina genomes indicates a far greater biosynthetic potential. In this study, nine representative Aquimarina strains were tested for antimicrobial activity against diverse human-pathogenic and marine microorganisms and subjected to metabolomic and genomic profiling. We found an inhibitory activity of most Aquimarina strains against Candida glabrata and marine Vibrio and Alphaproteobacteria species. Aquimarina sp. Aq135 and Aquimarina muelleri crude extracts showed particularly promising antimicrobial activities, amongst others against methicillin-resistant Staphylococcus aureus. The metabolomic and functional genomic profiles of Aquimarina spp. followed similar patterns and were shaped by phylogeny. SM-BGC and metabolomics networks suggest the presence of novel polyketides and peptides, including cyclic depsipeptide-related compounds. Moreover, exploration of the ‘Sponge Microbiome Project’ dataset revealed that Aquimarina spp. possess low-abundance distributions worldwide across multiple marine biotopes. Our study emphasizes the relevance of this member of the microbial rare biosphere as a promising source of novel natural products. We predict that future metabologenomics studies of Aquimarina species will expand the spectrum of known secondary metabolites and bioactivities from marine ecosystems.
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Affiliation(s)
- Sandra Godinho Silva
- IBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (S.G.S.); (P.P.); (D.M.-H.); (M.C.T.); (A.M.F.)
- Bioengeneering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Patrícia Paula
- IBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (S.G.S.); (P.P.); (D.M.-H.); (M.C.T.); (A.M.F.)
- Bioengeneering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - José Paulo da Silva
- Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal;
| | - Dalila Mil-Homens
- IBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (S.G.S.); (P.P.); (D.M.-H.); (M.C.T.); (A.M.F.)
- Bioengeneering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Miguel Cacho Teixeira
- IBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (S.G.S.); (P.P.); (D.M.-H.); (M.C.T.); (A.M.F.)
- Bioengeneering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Arsénio Mendes Fialho
- IBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (S.G.S.); (P.P.); (D.M.-H.); (M.C.T.); (A.M.F.)
- Bioengeneering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Rodrigo Costa
- IBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (S.G.S.); (P.P.); (D.M.-H.); (M.C.T.); (A.M.F.)
- Bioengeneering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal;
| | - Tina Keller-Costa
- IBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (S.G.S.); (P.P.); (D.M.-H.); (M.C.T.); (A.M.F.)
- Bioengeneering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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19
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de Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Jackson SA, Dobson ADW, Laport MS. Genomic and in silico protein structural analyses provide insights into marine polysaccharide-degrading enzymes in the sponge-derived Pseudoalteromonas sp. PA2MD11. Int J Biol Macromol 2021; 191:973-995. [PMID: 34555402 DOI: 10.1016/j.ijbiomac.2021.09.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/01/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Active heterotrophic metabolism is a critical metabolic role performed by sponge-associated microorganisms, but little is known about their capacity to metabolize marine polysaccharides (MPs). Here, we investigated the genome of the sponge-derived Pseudoalteromonas sp. strain PA2MD11 focusing on its macroalgal carbohydrate-degrading potential. Carbohydrate-active enzymes (CAZymes) for the depolymerization of agar and alginate were found in PA2MD11's genome, including glycoside hydrolases (GHs) and polysaccharide lyases (PLs) belonging to families GH16, GH50 and GH117, and PL6 and PL17, respectively. A gene potentially encoding a sulfatase was also identified, which may play a role in the strain's ability to consume carrageenans. The complete metabolism of agar and alginate by PA2MD11 could also be predicted and was consistent with the results obtained in physiological assays. The polysaccharide utilization locus (PUL) potentially involved in the metabolism of agarose contained mobile genetic elements from other marine Gammaproteobacteria and its unusual larger size might be due to gene duplication events. Homology modelling and structural protein analyses of the agarases, alginate lyases and sulfatase depicted clear conservation of catalytic machinery and protein folding together with suitable industrially-relevant features. Pseudoalteromonas sp. PA2MD11 is therefore a source of potential MP-degrading biocatalysts for biorefinery applications and in the preparation of pharmacologically-active oligosaccharides.
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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; School of Microbiology, University College Cork, T12 Y960 Cork, Ireland
| | - Isabelle Rodrigues Lopes
- 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
| | - Anna Luiza Bauer Canellas
- 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
| | - Guilherme Muricy
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n°, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Stephen Anthony Jackson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland; Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - 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 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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20
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Waterworth SC, Parker-Nance S, Kwan JC, Dorrington RA. Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts. mBio 2021; 12:e0157721. [PMID: 34519538 PMCID: PMC8546597 DOI: 10.1128/mbio.01577-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.
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Affiliation(s)
- Samantha C. Waterworth
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Shirley Parker-Nance
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Environmental Observation Network, Elwandle Coastal Node, Gqeberha (Port Elizabeth), South Africa
| | - Jason C. Kwan
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Rosemary A. Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa
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21
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The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos. Microbiol Resour Announc 2021; 10:e0032021. [PMID: 34435855 PMCID: PMC8388533 DOI: 10.1128/mra.00320-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba) strains that were obtained from the octocoral Eunicella labiata. Genome annotation revealed multiple symbiosis factors common to all genomes, such as eukaryotic-like repeat protein- and multidrug resistance-encoding genes, which likely underpin symbiotic relationships with marine invertebrate hosts.
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22
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Sweet M, Villela H, Keller-Costa T, Costa R, Romano S, Bourne DG, Cárdenas A, Huggett MJ, Kerwin AH, Kuek F, Medina M, Meyer JL, Müller M, Pollock FJ, Rappé MS, Sere M, Sharp KH, Voolstra CR, Zaccardi N, Ziegler M, Peixoto R. Insights into the Cultured Bacterial Fraction of Corals. mSystems 2021; 6:e0124920. [PMID: 34156291 PMCID: PMC8269258 DOI: 10.1128/msystems.01249-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features-not previously described for coral-bacterium symbioses-potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts. IMPORTANCE Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world. This equated to 1,045 individual isolates which had full-length 16S rRNA gene sequences, after filtering of the original 3,055. We also explored which of these had genomes available. Originally, only 36 were available, and as part of this study, we added a further 38-equating to 74 in total. From this, we investigated potential genetic signatures that may facilitate a host-associated lifestyle. Further, such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and potentially applied as a novel strategy in reef restoration and rehabilitation efforts. In the spirit of open access, we have ensured this collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope many scientists across the globe will ask for access to these cultures for future studies.
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Affiliation(s)
- Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Helena Villela
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
- Department of Energy, Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefano Romano
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, Australia
- Australian Institute of Marine Science, Townsville, Australia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Megan J. Huggett
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW, Australia
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | | | - Felicity Kuek
- Australian Institute of Marine Science, Townsville, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Julie L. Meyer
- Soil and Water Sciences Department, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Moritz Müller
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Kuching, Sarawak, Malaysia
| | - F. Joseph Pollock
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Hawaii and Palmyra Programs, The Nature Conservancy, Honolulu, Hawaii, USA
| | - Michael S. Rappé
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
| | - Mathieu Sere
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Koty H. Sharp
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | | | - Nathan Zaccardi
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Raquel Peixoto
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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23
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Ho XY, Katermeran NP, Deignan LK, Phyo MY, Ong JFM, Goh JX, Ng JY, Tun K, Tan LT. Assessing the Diversity and Biomedical Potential of Microbes Associated With the Neptune's Cup Sponge, Cliona patera. Front Microbiol 2021; 12:631445. [PMID: 34267732 PMCID: PMC8277423 DOI: 10.3389/fmicb.2021.631445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sponges are known to host a complex microbial consortium that is essential to the health and resilience of these benthic invertebrates. These sponge-associated microbes are also an important source of therapeutic agents. The Neptune's Cup sponge, Cliona patera, once believed to be extinct, was rediscovered off the southern coast of Singapore in 2011. The chance discovery of this sponge presented an opportunity to characterize the prokaryotic community of C. patera. Sponge tissue samples were collected from the inner cup, outer cup and stem of C. patera for 16S rRNA amplicon sequencing. C. patera hosted 5,222 distinct OTUs, spanning 26 bacterial phyla, and 74 bacterial classes. The bacterial phylum Proteobacteria, particularly classes Gammaproteobacteria and Alphaproteobacteria, dominated the sponge microbiome. Interestingly, the prokaryotic community structure differed significantly between the cup and stem of C. patera, suggesting that within C. patera there are distinct microenvironments. Moreover, the cup of C. patera had lower diversity and evenness as compared to the stem. Quorum sensing inhibitory (QSI) activities of selected sponge-associated marine bacteria were evaluated and their organic extracts profiled using the MS-based molecular networking platform. Of the 110 distinct marine bacterial strains isolated from sponge samples using culture-dependent methods, about 30% showed quorum sensing inhibitory activity. Preliminary identification of selected QSI active bacterial strains revealed that they belong mostly to classes Alphaproteobacteria and Bacilli. Annotation of the MS/MS molecular networkings of these QSI active organic extracts revealed diverse classes of natural products, including aromatic polyketides, siderophores, pyrrolidine derivatives, indole alkaloids, diketopiperazines, and pyrone derivatives. Moreover, potential novel compounds were detected in several strains as revealed by unique molecular families present in the molecular networks. Further research is required to determine the temporal stability of the microbiome of the host sponge, as well as mining of associated bacteria for novel QS inhibitors.
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Affiliation(s)
- Xin Yi Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nursheena Parveen Katermeran
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Lindsey Kane Deignan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ma Yadanar Phyo
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Ji Fa Marshall Ong
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Jun Xian Goh
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Juat Ying Ng
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Karenne Tun
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
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24
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Leinberger J, Holste J, Bunk B, Freese HM, Spröer C, Dlugosch L, Kück AC, Schulz S, Brinkhoff T. High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus. Front Microbiol 2021; 12:688754. [PMID: 34262548 PMCID: PMC8273931 DOI: 10.3389/fmicb.2021.688754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain Paracoccus marcusii CP157, which originates from the biofilm on the carapace of a shell disease-affected Cancer pagurus specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 Paracoccus spp. revealed that antimicrobial activity, hemolysis and production of N-acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of Paracoccus spp. in their natural environments.
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Affiliation(s)
- Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jonas Holste
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Heike M. Freese
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Anna-Carlotta Kück
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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25
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Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe. Mar Drugs 2021; 19:md19060298. [PMID: 34073758 PMCID: PMC8225149 DOI: 10.3390/md19060298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.
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26
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Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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Keller-Costa T, Lago-Lestón A, Saraiva JP, Toscan R, Silva SG, Gonçalves J, Cox CJ, Kyrpides N, Nunes da Rocha U, Costa R. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. MICROBIOME 2021; 9:72. [PMID: 33766108 PMCID: PMC7993494 DOI: 10.1186/s40168-021-01031-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/08/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. RESULTS Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system. CONCLUSIONS This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.
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Affiliation(s)
- T. Keller-Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- División de Biología Experimental y Aplicada (DBEA), Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carr. Ensenada-Tijuana 3918, Zona Playitas, C.P 22860 Ensenada, Baja California Mexico
| | - J. P. Saraiva
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Toscan
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - S. G. Silva
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - J. Gonçalves
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - C. J. Cox
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - N. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - U. Nunes da Rocha
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
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Raimundo I, Silva R, Meunier L, Valente SM, Lago-Lestón A, Keller-Costa T, Costa R. Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes. MICROBIOME 2021; 9:43. [PMID: 33583433 PMCID: PMC7883442 DOI: 10.1186/s40168-020-00970-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/18/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater. RESULTS We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates. CONCLUSIONS Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.
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Affiliation(s)
- I. Raimundo
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Silva
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - L. Meunier
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Laboratory of Aquatic Systems Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - S. M. Valente
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- Department of Medical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - T. Keller-Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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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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Steiner PA, Geijo J, Fadeev E, Obiol A, Sintes E, Rattei T, Herndl GJ. Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea. Front Microbiol 2020; 11:584222. [PMID: 33304331 PMCID: PMC7701263 DOI: 10.3389/fmicb.2020.584222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/23/2020] [Indexed: 01/04/2023] Open
Abstract
Marine snow is an important habitat for microbes, characterized by chemical and physical properties contrasting those of the ambient water. The higher nutrient concentrations in marine snow lead to compositional differences between the ambient water and the marine snow-associated prokaryotic community. Whether these compositional differences vary due to seasonal environmental changes, however, remains unclear. Thus, we investigated the seasonal patterns of the free-living and marine snow-associated microbial community composition and their functional potential in the northern Adriatic Sea. Our data revealed seasonal patterns in both, the free-living and marine snow-associated prokaryotes. The two assemblages were more similar to each other in spring and fall than in winter and summer. The taxonomic distinctness resulted in a contrasting functional potential. Motility and adaptations to low temperature in winter and partly anaerobic metabolism in summer characterized the marine snow-associated prokaryotes. Free-living prokaryotes were enriched in genes indicative for functions related to phosphorus limitation in winter and in genes tentatively supplementing heterotrophic growth with proteorhodopsins and CO-oxidation in summer. Taken together, the results suggest a strong influence of environmental parameters on both free-living and marine snow-associated prokaryotic communities in spring and fall leading to higher similarity between the communities, while the marine snow habitat in winter and summer leads to a specific prokaryotic community in marine snow in these two seasons.
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Affiliation(s)
- Paul A. Steiner
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Javier Geijo
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Aleix Obiol
- Institut de Ciències del Mar, Institut de Ci ncies del Mar – Consejo Superior de Investigaciones Cient ficas (ICM-CSIC), Barcelona, Spain
| | - Eva Sintes
- Instituto Español de Oceanografia, Centre Oceanogràfic de les Balears, Palma, Spain
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Utrecht, Netherlands
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Konstantinou D, Voultsiadou E, Panteris E, Gkelis S. Revealing new sponge-associated cyanobacterial diversity: Novel genera and species. Mol Phylogenet Evol 2020; 155:106991. [PMID: 33098986 DOI: 10.1016/j.ympev.2020.106991] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022]
Abstract
Cyanobacteria are often reported as abundant components of the sponge microbiome; however their diversity below the phylum level is still underestimated. Aiming to broaden our knowledge of sponge-cyanobacteria association, we isolated cyanobacterial strains from Aegean Sea sponges in previous research, which revealed high degree of novel cyanobacterial diversity. Herein, we aim to further characterize sponge-associated cyanobacteria and re-evaluate their classification based on an extensive polyphasic approach, i.e. a combination of molecular, morphological and ecological data. This approach resulted in the description of five new genera (Rhodoploca, Cymatolege, Metis, Aegeococcus, and Thalassoporum) and seven new species (R. sivonenia, C. spiroidea, C. isodiametrica, M. fasciculata, A. anagnostidisi, A. thureti, T. komareki) inside the order Synechococcales, and a new pleurocapsalean species (Xenococcus spongiosum). X. spongiosum is a baeocyte-producing species that shares some morphological features with other Xenococcus species, but has distinct phylogenetic and ecological identity. Rhodoploca, Cymatolege, Metis and Thalassoporum are novel well supported linages of filamentous cyanobacteria that possess distinct characters compared to their sister taxa. Aegeococcus is a novel monophyletic linage of Synechococcus-like cyanobacteria exhibiting a unique ecology, as sponge-dweller. The considerable number of novel taxa characterized in this study highlights the importance of employing polyphasic culture-dependent approaches in order to reveal the true cyanobacterial diversity associated with sponges.
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Affiliation(s)
- Despoina Konstantinou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki GR-541 24, Greece; Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki GR-541 124, Greece
| | - Eleni Voultsiadou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki GR-541 124, Greece
| | - Emmanuel Panteris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki GR-541 24, Greece
| | - Spyros Gkelis
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki GR-541 24, Greece.
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Gavriilidou A, Gutleben J, Versluis D, Forgiarini F, van Passel MWJ, Ingham CJ, Smidt H, Sipkema D. Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genomics 2020; 21:569. [PMID: 32819293 PMCID: PMC7440613 DOI: 10.1186/s12864-020-06971-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/05/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. RESULTS Comparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains. CONCLUSIONS Our study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Francesca Forgiarini
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Mark W. J. van Passel
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Present address: Ministry of Health, Welfare and Sport, Parnassusplein 5, 2511 VX, The Hague, The Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Modolon F, Barno AR, Villela HDM, Peixoto RS. Ecological and biotechnological importance of secondary metabolites produced by coral-associated bacteria. J Appl Microbiol 2020; 129:1441-1457. [PMID: 32627318 DOI: 10.1111/jam.14766] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/20/2020] [Accepted: 06/28/2020] [Indexed: 12/16/2022]
Abstract
Symbiotic relationships between corals and their associated micro-organisms are essential to maintain host homeostasis. Coral-associated bacteria (CAB) can have different beneficial roles in the coral metaorganism, such as metabolizing essential nutrients for the coral host and protecting the coral from pathogens. Many CAB exert these functions via secondary metabolites, which include antibacterial, antifouling, antitumour, antiparasitic and antiviral compounds. This review describes how analysis of CAB has led to the discovery of secondary metabolites with potential biotechnological applications. The most commonly found types of secondary metabolites, antimicrobial and antibiofilm compounds, are emphasized and described. Recently developed methods that can be applied to enhance the culturing of CAB from shallow-water reefs and the less-studied deep-sea coral reefs are also discussed. Last, we suggest how the combined use of meta-omics and innovative growth-diffusion techniques can vastly improve the discovery of novel compounds in coral environments.
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Affiliation(s)
- F Modolon
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - A R Barno
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - H D M Villela
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - R S Peixoto
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, RJ, Brazil
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35
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Yang Q, Franco CMM, Lin HW, Zhang W. Untapped sponge microbiomes: structure specificity at host order and family levels. FEMS Microbiol Ecol 2020; 95:5554005. [PMID: 31494678 DOI: 10.1093/femsec/fiz136] [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: 02/27/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022] Open
Abstract
Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their 'signature identity'. 70%-87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia
| | - Hou-Wen Lin
- Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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36
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Engelberts JP, Robbins SJ, de Goeij JM, Aranda M, Bell SC, Webster NS. Characterization of a sponge microbiome using an integrative genome-centric approach. THE ISME JOURNAL 2020; 14:1100-1110. [PMID: 31992859 PMCID: PMC7174397 DOI: 10.1038/s41396-020-0591-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
Marine sponges often host diverse and species-specific communities of microorganisms that are critical for host health. Previous functional genomic investigations of the sponge microbiome have focused primarily on specific symbiont lineages, which frequently make up only a small fraction of the overall community. Here, we undertook genome-centric analysis of the symbiont community in the model species Ircinia ramosa and analyzed 259 unique, high-quality metagenome-assembled genomes (MAGs) that comprised 74% of the I. ramosa microbiome. Addition of these MAGs to genome trees containing all publicly available microbial sponge symbionts increased phylogenetic diversity by 32% within the archaea and 41% within the bacteria. Metabolic reconstruction of the MAGs showed extensive redundancy across taxa for pathways involved in carbon fixation, B-vitamin synthesis, taurine metabolism, sulfite oxidation, and most steps of nitrogen metabolism. Through the acquisition of all major taxa present within the I. ramosa microbiome, we were able to analyze the functional potential of a sponge-associated microbial community in unprecedented detail. Critical functions, such as carbon fixation, which had previously only been assigned to a restricted set of sponge-associated organisms, were actually spread across diverse symbiont taxa, whereas other essential pathways, such as ammonia oxidation, were confined to specific keystone taxa.
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Affiliation(s)
- J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Institute of Marine Science, Townsville, QLD, Australia.
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37
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Ferreira MRS, Cleary DFR, Coelho FJRC, Gomes NCM, Huang YM, Polónia ARM, de Voogd NJ. Geographical location and habitat predict variation in prokaryotic community composition of Suberites diversicolor. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01546-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Marine lakes are unique habitats that house diverse assemblages of benthic and planktonic organisms including endemic species. In this study, we aimed to assess to what extent geographical location (Berau versus Papua) and the degree of marine lake connectivity (relatively open versus closed) to the surrounding marine environment structures the prokaryotic community composition of the sponge species Suberites diversicolor.
Methods
Sponge specimens were sampled in five marine lakes in Borneo and Papua and one open sea habitat in Taiwan.
Result
Prokaryotic communities of S. diversicolor were dominated by members assigned to the Proteobacteria (particularly Alphaproteobacteria and Gammaproteobacteria) and Cyanobacteria, which together made up from 78 to 87% of sequences in all samples. The dominant operational taxonomic units (OTUs) in most samples, OTUs 1 and 3, were both assigned to the alphaproteobacterial order Rhodospirillales with OTU-1 dominant in the marine lakes of Berau and Papua and OTU-3 in Taiwan. OTU-3 was also largely absent from Papuan samples but present in all Berau samples. Compositionally, S. diversicolor samples clustered according to geographical location with the main axis of variation separating marine lake samples collected in Berau from those collected in Papua and the second axis of variation separating open sea samples collected in Taiwan from all marine lake samples. In addition, our results suggest that the degree of lake connectivity to the open sea also influences prokaryotic composition.
Conclusion
Although previous studies have shown that sponge-associated microbial communities tend to be stable across different geographical and environmental gradients, in the present study, both geography and local environmental conditions were significant predictors of variation in prokaryotic community composition of S. diversicolor.
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38
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Pascoal F, Magalhães C, Costa R. The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential. Front Microbiol 2020; 11:231. [PMID: 32140148 PMCID: PMC7042395 DOI: 10.3389/fmicb.2020.00231] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022] Open
Abstract
Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.
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Affiliation(s)
- Francisco Pascoal
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,School of Science & Engineering, University of Waikato, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Halitax, NS, Canada
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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39
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Panahi L, Gholizadeh M, Hajimohammadi R. Investigating the degradability of polyethylene using starch, oxo‐material, and polylactic acid under the different environmental conditions. ASIA-PAC J CHEM ENG 2020. [DOI: 10.1002/apj.2402] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lotfollah Panahi
- Department of Chemical EngineeringAhar Branch, Islamic Azad University Ahar Iran
| | - Mortaza Gholizadeh
- Faculty of Chemical and Petroleum EngineeringUniversity of Tabriz Tabriz Iran
| | - Reza Hajimohammadi
- Department of Chemical EngineeringAhar Branch, Islamic Azad University Ahar Iran
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40
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Knobloch S, Jóhannsson R, Marteinsson VÞ. Genome analysis of sponge symbiont 'Candidatus Halichondribacter symbioticus' shows genomic adaptation to a host-dependent lifestyle. Environ Microbiol 2019; 22:483-498. [PMID: 31747724 DOI: 10.1111/1462-2920.14869] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 10/03/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022]
Abstract
The marine sponge Halichondria panicea inhabits coastal areas around the globe and is a widely studied sponge species in terms of its biology, yet the ecological functions of its dominant bacterial symbiont 'Candidatus Halichondribacter symbioticus' remain unknown. Here, we present the draft genome of 'Ca. H. symbioticus' HS1 (2.8 Mbp, ca. 87.6% genome coverage) recovered from the sponge metagenome of H. panicea in order to study functions and symbiotic interactions at the genome level. Functional genome comparison of HS1 against closely related free-living seawater bacteria revealed a reduction of genes associated with carbohydrate transport and transcription regulation, pointing towards a limited carbohydrate metabolism, and static transcriptional dynamics reminiscent of other bacterial symbionts. In addition, HS1 was enriched in sponge symbiont specific gene families related to host-symbiont interactions and defence. Similarity in the functional gene repertoire between HS1 and a phylogenetically more distant symbiont in the marine sponge Aplysina aerophoba, based on COG category distribution, suggest a convergent evolution of symbiont specific traits and general metabolic features. This warrants further investigation into convergent genomic evolution of symbionts across different sponge species and habitats.
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Affiliation(s)
- Stephen Knobloch
- Microbiology Group, Department of Research and Innovation, Matís ohf, 113, Reykjavik, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, 101, Reykjavík, Iceland
| | - Ragnar Jóhannsson
- Marine and Freshwater Research Institute, Hafrannsóknastofnun, 101, Reykjavik, Iceland
| | - Viggó Þór Marteinsson
- Microbiology Group, Department of Research and Innovation, Matís ohf, 113, Reykjavik, Iceland.,Faculty of Food Science and Nutrition, University of Iceland, 101, Reykjavik, Iceland
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41
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Silva SG, Blom J, Keller‐Costa T, Costa R. Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host‐associated and free‐living
Aquimarina
(
Bacteroidetes, Flavobacteriaceae
) species. Environ Microbiol 2019; 21:4002-4019. [DOI: 10.1111/1462-2920.14747] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 07/12/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Sandra G. Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology Justus‐Liebig‐University Giessen 35392 Giessen Germany
| | - Tina Keller‐Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
- Centre of Marine Sciences (CCMAR) Algarve University 8005‐139 Faro Portugal
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