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El Samak M, Zakeer S, Hanora A, Solyman SM. Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community. Mar Genomics 2023; 70:101032. [PMID: 37084583 DOI: 10.1016/j.margen.2023.101032] [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: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.
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Affiliation(s)
- Manar El Samak
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt.
| | - Samar M Solyman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt; Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University- Elkantara branch, Egypt
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2
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Engelberts JP, Robbins SJ, Herbold CW, Moeller FU, Jehmlich N, Laffy PW, Wagner M, Webster NS. Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta. Environ Microbiol 2023; 25:646-660. [PMID: 36480164 PMCID: PMC10947273 DOI: 10.1111/1462-2920.16302] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.
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Affiliation(s)
- Joan Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Steven J. Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz‐Centre for Environmental Research – UFZLeipzigGermany
| | - Patrick W. Laffy
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Nicole S. Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Antarctic DivisionKingstonTasmaniaAustralia
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3
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Indraningrat AAG, Steinert G, Becking LE, Mueller B, de Goeij JM, Smidt H, Sipkema D. Sponge holobionts shift their prokaryotic communities and antimicrobial activity from shallow to lower mesophotic depths. Antonie Van Leeuwenhoek 2022; 115:1265-1283. [PMID: 35998007 PMCID: PMC9534810 DOI: 10.1007/s10482-022-01770-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/07/2022] [Indexed: 11/05/2022]
Abstract
In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30–60 m (upper mesophotic), and 60–90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.
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Affiliation(s)
- Anak Agung Gede Indraningrat
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Faculty of Medicine and Health Sciences, Warmadewa University, Jln Terompong 24, 80235, Denpasar, Bali, Indonesia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Leontine E Becking
- Marine Animal Ecology Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Wageningen Marine Research, Wageningen University and Research, Ankerpark 27, 1781 AG, Den Helder, The Netherlands
| | - Benjamin Mueller
- Department of Freshwater and Marine Ecology, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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4
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Chekidhenkuzhiyil J, Anas A, Thomas P, Tharakan B, Nair S. Characterization of archaeal symbionts of sponges from the coral reef ecosystems of the Gulf of Mannar, Southeast coast of India. Saudi J Biol Sci 2021; 28:3783-3788. [PMID: 34220232 PMCID: PMC8241630 DOI: 10.1016/j.sjbs.2021.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/10/2021] [Accepted: 03/21/2021] [Indexed: 10/26/2022] Open
Abstract
Sponges accommodate a diverse group of microorganisms with varied metabolic capabilities. The bacterial associates of sponges are widely studied while our understanding of archaeal counterparts is scanty. In the present study, we report the archaeal associates of two sponges, Pseudoceratina purpurea (NCBI barcode: KX454492) and Cinachyra sp. (NCBI barcode: KX454495), found in the coral reef ecosystems of Gulf of Mannar, India. Archaea in the water column was predominated by members of class Halobacteria of Phylum Euryarchaeota (97%) followed by a minor fraction (3%) of Nitrosopumilus sp. of phylum Thaumarchaeota. Interestingly, Thaumarchaeota was identified as the sole archaeal population associated with the two sponges studied, among which Nitrosopumilus sp. occuppied 80 and 100% of the sequences in the clone library of P. purpurea and Cinachyra sp. respectively. Other archaea found in the P. purpurea were Nitrososphaera (10%) and unclassified ones (10%). The study identified Nitrosopumilus sp. as a unique symbiotic archaeon of sponges, P. purpurea and Cinachyra sp. The existence of host driven factors in selecting specific associates from a diverse group of archaea in the environment may need further investigations.
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Affiliation(s)
| | - Abdulaziz Anas
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
| | - P.A. Thomas
- Panachammoottil, Gandhipuram, Thiruvananthapuram, Kerala 695017, India
| | - Balu Tharakan
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
| | - Shanta Nair
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
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5
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Robbins SJ, Song W, Engelberts JP, Glasl B, Slaby BM, Boyd J, Marangon E, Botté ES, Laffy P, Thomas T, Webster NS. A genomic view of the microbiome of coral reef demosponges. THE ISME JOURNAL 2021; 15:1641-1654. [PMID: 33469166 PMCID: PMC8163846 DOI: 10.1038/s41396-020-00876-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 01/30/2023]
Abstract
Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.
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Affiliation(s)
- S J Robbins
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - W Song
- Centre for Marine Science & Innovation, University of New South Wales, Kensington, NSW, 2052, Australia
| | - J P Engelberts
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - B Glasl
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - B M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - J Boyd
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - E Marangon
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, 4810, Australia
| | - E S Botté
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - P Laffy
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - T Thomas
- Centre for Marine Science & Innovation, University of New South Wales, Kensington, NSW, 2052, Australia
| | - N S Webster
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia.
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6
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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7
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Haber M, Burgsdorf I, Handley KM, Rubin-Blum M, Steindler L. Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges. Front Microbiol 2021; 11:622824. [PMID: 33537022 PMCID: PMC7848895 DOI: 10.3389/fmicb.2020.622824] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.
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Affiliation(s)
- Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research Institute, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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8
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Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte. Antonie van Leeuwenhoek 2020; 114:95-112. [DOI: 10.1007/s10482-020-01503-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
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9
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Abstract
The Archaea domain was recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago. It is now known as part of the human microbiome; however, given that its roles in oral sites are still poorly understood, this review aimed to establish the current level of evidence regarding archaea in the oral cavity to guide future research, providing insights on the present knowledge about the human oral archaeome. A scoping review was conducted with the PRISMA Extension for Scoping Reviews checklist. Five electronic databases were searched, as well as gray literature. Two independent reviewers performed the selection and characterization of the studies. Clinical studies were included when the target population consisted of humans of any age who were donors of samples from the oral cavity. A qualitative analysis was performed, based on the type of oral site and by considering the methods employed for archaeal identification and taxonomy, including the DNA extraction protocols, primers, and probes used. Fifty articles were included in the final scoping review, published from 1987 to 2019. Most studies sampled periodontal sites. Methanogens were the most abundant archaea in those sites, and their presence could be associated with other periodontal pathogens. No consistent relationship with different disease conditions was observed in studies that evaluated the microbiota surviving in endodontic sites. Few articles analyzed the presence of archaea in dental caries, saliva, or tongue microbiota, as well as in archaeologic samples, also showing a relationship with healthy microbiota. Archaea have been detected in different oral niches of individuals from diverse geographic locations and clinical conditions, suggesting potential roles in oral diseases. Methodological limitations may hamper our current knowledge about archaeal diversity and prevalence in oral samples, and future research with diversified methodological approaches may lead to a better comprehension of the human oral archaeome.
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Affiliation(s)
- A Belmok
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - J A de Cena
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
| | - C M Kyaw
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - N Damé-Teixeira
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
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10
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Behera P, Mohapatra M, Kim JY, Rastogi G. Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135709. [PMID: 31806293 DOI: 10.1016/j.scitotenv.2019.135709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
Benthic Archaea play a crucial role in the biogeochemical cycles and food webs, however, their spatiotemporal distribution and environmental drivers are not well investigated in brackish sediments. The composition and abundances of benthic archaeal communities were examined from a coastal lagoon; Chilika (India) which is experiencing an intense pressure from anthropogenic and natural factors. High-throughput sequencing of 16S rRNA genes revealed that sediment (n = 96) archaeal communities were largely composed of Crenarchaeota (18.76%), Euryarchaeota (18.34%), Thaumarchaeota (13.45%), Woesearchaeota (10.05%), and Pacearchaeota (4.21%). Archaeal taxa affiliated to methanogens, sulfate-reducers, and ammonia-oxidizers were detected suggesting that carbon, sulfur, and nitrogen cycles might be prominent in benthic sediments. Salinity, total organic carbon, available nitrogen, available phosphorus, macrophyte (Phragmites karka) and inter-taxa relationships between community members and with bacterial communities played steering roles in structuring the archaeal communities. Marine sites with mesohaline-polyhaline regime were dominated by Nitrosopumilus and Thaumarchaeota. In contrast, riverine sites with oligohaline regime demonstrated a higher abundance of Thermoprotei. Macrophyte dominated zones were enriched in Methanomicrobia and Methanobacteria in their rhizosphere sediments, whereas, bulk (un-vegetated) sediments were dominated by Nitrosopumilus. Spatial patterns in archaeal communities demonstrated 'distance-decay' patterns which were correlated with changes in physicochemical factors over geographical distances. Heterotrophic microbial communities showed much higher metabolic diversity and activity in their carbon utilization profiles in rhizosphere sediments than the bulk sediments. This baseline information on benthic archaea and their environmental drivers would be useful to assess the impact of anthropogenic and natural pressures on these communities and associated biogeochemical cycles.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India
| | - Ji Yoon Kim
- Center for Climate Change Adaptation, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India.
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11
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Moreno-Pino M, Cristi A, Gillooly JF, Trefault N. Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach. Sci Rep 2020; 10:645. [PMID: 31959785 PMCID: PMC6971038 DOI: 10.1038/s41598-020-57464-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 12/11/2019] [Indexed: 01/22/2023] Open
Abstract
Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO2 fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.
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Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
| | - Antonia Cristi
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
| | - James F Gillooly
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile.
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12
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Najafi A, Moradinasab M, Seyedabadi M, Haghighi MA, Nabipour I. First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran. Open Microbiol J 2018; 12:323-332. [PMID: 30450139 PMCID: PMC6198412 DOI: 10.2174/1874285801812010323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/21/2018] [Accepted: 09/23/2018] [Indexed: 11/22/2022] Open
Abstract
Background Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran. Methods Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning. Results In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group. Conclusion The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad Seyedabadi
- Department of Pharmacology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad A Haghighi
- Department of Microbiology and Parasitology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
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13
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Batista D, Costa R, Carvalho AP, Batista WR, Rua CPJ, de Oliveira L, Leomil L, Fróes AM, Thompson FL, Coutinho R, Dobretsov S. Environmental conditions affect activity and associated microorganisms of marine sponges. MARINE ENVIRONMENTAL RESEARCH 2018; 142:59-68. [PMID: 30274716 DOI: 10.1016/j.marenvres.2018.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/09/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.
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Affiliation(s)
- Daniela Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil.
| | - Rafaela Costa
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Ana Polycarpa Carvalho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - William Romão Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Cintia P J Rua
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Louisi de Oliveira
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Adriana M Fróes
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Sergey Dobretsov
- Marine Science and Fisheries Department, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123. PO Box 34, Muscat, Oman; Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Al-Khoud 123. PO Box 50, Muscat, Oman.
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14
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Deignan LK, Pawlik JR, Erwin PM. Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata. MICROBIAL ECOLOGY 2018; 76:459-466. [PMID: 29299617 DOI: 10.1007/s00248-017-1135-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
The brown tube sponge Agelas tubulata (cf. Agelas conifera) is an abundant and long-lived sponge on Caribbean reefs. Recently, a disease-like condition, Agelas wasting syndrome (AWS), was described from A. tubulata in the Florida Keys, where prevalence of the syndrome increased from 7 to 35% of the sponge population between 2010 and 2015. In this study, we characterized the prokaryotic symbiont community of A. tubulata for the first time from individuals collected within the same monitoring plots where AWS was described. We also sampled tissue from A. tubulata exhibiting symptoms of AWS to determine its effect on the diversity and structure of prokaryotic symbiont communities. Bacteria from the phyla Chloroflexi and Proteobacteria, particularly the class Gammaproteobacteria, dominated the sponge microbiome in tissue samples of both healthy sponges and those exhibiting AWS. Prokaryotic community structure differed significantly between the diseased and healthy sponge samples, with greater variability among communities in diseased samples compared to healthy samples. These differences in prokaryotic community structure included a shift in relative abundance of the dominant, ammonia-oxidizing (Thaumarchaeota) symbionts present in diseased and healthy sponge samples. Further research is required to determine the functional consequences of this shift in microbial community structure and the causal relationship of dysbiosis and sponge disease in A. tubulata.
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Affiliation(s)
- Lindsey K Deignan
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Joseph R Pawlik
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA.
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15
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Najafi A, Moradinasab M, Nabipour I. First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing. Front Microbiol 2018; 9:1500. [PMID: 30034382 PMCID: PMC6043863 DOI: 10.3389/fmicb.2018.01500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
The Persian Gulf is a special habitat of marine sponges whose bacterial communities are under-investigated. Recently, next-generation sequencing technology has comprehensively improved the knowledge of marine sponge-associated bacteria. For the first time, this study aimed to evaluate the diversity of the Persian Gulf sponge-associated bacteria using tag pyrosequencing in Iran. In this study, 10 sponge samples from 6 different taxonomic orders were collected from the Persian Gulf using SCUBA diving. The diversity of the bacteria associated with the marine sponges was investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. A total of 68,628 high-quality sequences were obtained and clustered at a 97% similarity into 724 unique operational taxonomic units (OTUs), representing 17 bacterial phyla. Cyanobacteria was the most abundant phylum in the sponges, followed by Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria. Other phyla were detected as minor groups of bacteria. Bacterial community richness, Shannon, and Simpson indices revealed the highest diversity in sponge S11 (Dictyoceratida sp.) compared to other sponges. This study showed a diverse structure of bacterial communities associated with the Persian Gulf sponges. The dominance of Cyanobacteria may suggest an ecological importance of this phylum in the Persian Gulf sponges.
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Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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16
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Dat TTH, Steinert G, Thi Kim Cuc N, Smidt H, Sipkema D. Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam. PeerJ 2018; 6:e4970. [PMID: 29900079 PMCID: PMC5995103 DOI: 10.7717/peerj.4970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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17
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Feng G, Sun W, Zhang F, Orlić S, Li Z. Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:131-143. [PMID: 29423641 DOI: 10.1007/s10126-018-9797-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/19/2017] [Indexed: 05/06/2023]
Abstract
Symbiotic ammonia scavengers contribute to effective removal of ammonia in sponges. However, the phylogenetic diversity and in situ activity of ammonia-scavenging microbiota between different sponge species are poorly addressed. Here, transcribed ammonia monooxygenase genes (amoA), hydrazine synthase genes (hzsA), and glutamine synthetase genes (glnA) were analyzed to reveal the active ammonia-scavenging microbiota in the sympatric sponges Theonella swinhoei, Plakortis simplex, and Phakellia fusca, and seawater. Archaeal amoA and bacterial glnA transcripts rather than bacterial amoA, hzsA, and archaeal glnA transcripts were detected in the investigated sponges and seawater. The transcribed amoA genes were ascribed to two Thaumarchaeota ecotypes, while the transcribed glnA genes were interspersed among the lineages of Cyanobacteria, Tectomicrobia, Poribacteria, Alpha-, Beta-, Gamma-, and Epsilonproteobacteria. In addition, transcribed abundances of archaeal amoA and bacterial glnA genes in these sponges have been quantified, showing significant variation among the investigated sponges and seawater. The transcriptome-based qualitative and quantitative analyses clarified the different phylogenetic diversity and transcription expression of functional genes related to microbially mediated ammonia scavenging in different sympatric sponges, contributing to the understanding of in situ active ecological functions of sponge microbial symbionts in holobiont nitrogen cycling.
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Affiliation(s)
- Guofang Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Wei Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Fengli Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Sandi Orlić
- Ruđer Bošković Institute, Bijeničkacesta 54, 10000, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean region-STIM, Bijeničkacesta 54, 10000, Zagreb, Croatia
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China.
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18
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Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila. Sci Rep 2017; 7:43247. [PMID: 28233813 PMCID: PMC5324122 DOI: 10.1038/srep43247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/20/2017] [Indexed: 11/08/2022] Open
Abstract
Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.
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19
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Tian RM, Sun J, Cai L, Zhang WP, Zhou GW, Qiu JW, Qian PY. The deep-sea glass sponge Lophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur. Environ Microbiol 2016; 18:2481-94. [PMID: 26637128 DOI: 10.1111/1462-2920.13161] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/27/2015] [Indexed: 11/30/2022]
Abstract
Glass sponge (Hexactinellida, Porifera) is a special lineage because of its unique tissue organization and skeleton material. Structure and physiology of glass sponge have been extensively studied. However, our knowledge of the glass sponge-associated microbial community and of the interaction with the host is rather limited. Here, we performed genomic studies on the microbial community in the glass sponge Lophophysema eversa in seamount. The microbial community was dominated by an ammonia-oxidizing archaeum (AOA), a nitrite-oxidizing bacterium (NOB) and a sulfur-oxidizing bacterium (SOB), all of which were autotrophs. Genomic analysis on the AOA, NOB and SOB in the sponge revealed specific functional features of sponge-associated microorganisms in comparison with the closely related free-living relatives, including chemotaxis, phage defence, vitamin biosynthesis and nutrient uptake among others, which are related to ecological functions. The three autotrophs play essential roles in the cycles of carbon, nitrogen and sulfur in the microenvironment inside the sponge body, and they are considered to play symbiotic roles in the host as scavengers of toxic ammonia, nitrite and sulfide. Our study extends knowledge regarding the metabolism and the evolution of chemolithotrophs inside the invertebrate body.
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Affiliation(s)
- Ren-Mao Tian
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jin Sun
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Lin Cai
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Wei-Peng Zhang
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Guo-Wei Zhou
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Pei-Yuan Qian
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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20
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Blackall LL, Wilson B, van Oppen MJH. Coral-the world's most diverse symbiotic ecosystem. Mol Ecol 2015; 24:5330-47. [DOI: 10.1111/mec.13400] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 09/21/2015] [Accepted: 09/24/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Linda L. Blackall
- Department of Chemistry and Biotechnology; Faculty of Science, Engineering & Technology; Swinburne University of Technology; Melbourne Vic. 3122 Australia
| | - Bryan Wilson
- Marine Microbiology Research Group; Department of Biology; University of Bergen; Thormøhlensgate 53B 5020 Bergen Norway
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science; PMB No. 3 Townsville MC Qld. 4810 Australia
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
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21
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Archaeal communities associated with roots of the common reed (Phragmites australis) in Beijing Cuihu Wetland. World J Microbiol Biotechnol 2015; 31:823-32. [DOI: 10.1007/s11274-015-1836-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 02/28/2015] [Indexed: 11/26/2022]
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22
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Bayer K, Moitinho-Silva L, Brümmer F, Cannistraci CV, Ravasi T, Hentschel U. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater. FEMS Microbiol Ecol 2014; 90:832-43. [PMID: 25318900 DOI: 10.1111/1574-6941.12441] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/30/2014] [Accepted: 10/06/2014] [Indexed: 12/12/2022] Open
Abstract
The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.
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Affiliation(s)
- Kristina Bayer
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany
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