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Gong X, Xu L, Langwig MV, Chen Z, Huang S, Zhao D, Su L, Zhang Y, Francis CA, Liu J, Li J, Baker BJ. Globally distributed marine Gemmatimonadota have unique genomic potentials. MICROBIOME 2024; 12:149. [PMID: 39123272 PMCID: PMC11316326 DOI: 10.1186/s40168-024-01871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood. RESULTS Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts. CONCLUSIONS This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong, China.
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA.
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Marguerite V Langwig
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Shujie Huang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Yan Zhang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Christopher A Francis
- Departments of Earth System Science & Oceans, Stanford University, Stanford, CA, 94305, USA
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China.
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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Chavarría-Pizarro L, Núñez-Montero K, Gutiérrez-Araya M, Watson-Guido W, Rivera-Méndez W, Pizarro-Cerdá J. Novel strains of Actinobacteria associated with neotropical social wasps (Vespidae; Polistinae, Epiponini) with antimicrobial potential for natural product discovery. FEMS MICROBES 2024; 5:xtae005. [PMID: 38476864 PMCID: PMC10929769 DOI: 10.1093/femsmc/xtae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Antimicrobial resistance has been considered a public health threat. The World Health Organization has warned about the urgency of detecting new antibiotics from novel sources. Social insects could be crucial in the search for new antibiotic metabolites, as some of them survive in places that favor parasite development. Recent studies have shown the potential of social insects to produce antimicrobial metabolites (e.g. ants, bees, and termites). However, most groups of social wasps remain unstudied. Here, we explored whether Actinobacteria are associated with workers in the Neotropical Social Wasps (Epiponini) of Costa Rica and evaluated their putative inhibitory activity against other bacteria. Most isolated strains (67%) have antagonistic effects, mainly against Bacillus thuringensis and Escherichia coli ATCC 25992. Based on genome analysis, some inhibitory Actinobacteria showed biosynthetic gene clusters (BGCs) related to the production of antimicrobial molecules such as Selvamycin, Piericidin A1, and Nystatin. The Actinobacteria could be associated with social wasps to produce antimicrobial compounds. For these reasons, we speculate that Actinobacteria associated with social wasps could be a novel source of antimicrobial compounds, mainly against Gram-negative bacteria.
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Affiliation(s)
- Laura Chavarría-Pizarro
- Instituto Tecnológico de Costa Rica, Escuela de Biología-Centro de Investigación en Biotecnología, Calle 15, Avenida 14, 159-7050 Cartago, Costa Rica
| | - Kattia Núñez-Montero
- Instituto Tecnológico de Costa Rica, Escuela de Biología-Centro de Investigación en Biotecnología, Calle 15, Avenida 14, 159-7050 Cartago, Costa Rica
- Instituto de Ciencias Aplicadas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Avenida Alemania 1090, 4810101 Temuco, Chile
| | - Mariela Gutiérrez-Araya
- Instituto Tecnológico de Costa Rica, Escuela de Biología-Centro de Investigación en Biotecnología, Calle 15, Avenida 14, 159-7050 Cartago, Costa Rica
| | - William Watson-Guido
- Instituto Tecnológico de Costa Rica, Escuela de Biología-Centro de Investigación en Biotecnología, Calle 15, Avenida 14, 159-7050 Cartago, Costa Rica
| | - William Rivera-Méndez
- Instituto Tecnológico de Costa Rica, Escuela de Biología-Centro de Investigación en Biotecnología, Calle 15, Avenida 14, 159-7050 Cartago, Costa Rica
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit - Institut Pasteur 28, rue du Docteur Roux - 75724 Paris Cedex 15, France
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Lin Q, Li L, De Vrieze J, Li C, Fang X, Li X. Functional conservation of microbial communities determines composition predictability in anaerobic digestion. THE ISME JOURNAL 2023; 17:1920-1930. [PMID: 37666974 PMCID: PMC10579369 DOI: 10.1038/s41396-023-01505-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: 04/30/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Lingjuan Li
- Department of Biology, University of Antwerp, 2610, Wilrijk, Belgium
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoyu Fang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Tiwari A, Kauppinen A, Räsänen P, Salonen J, Wessels L, Juntunen J, Miettinen IT, Pitkänen T. Effects of temperature and light exposure on the decay characteristics of fecal indicators, norovirus, and Legionella in mesocosms simulating subarctic river water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160340. [PMID: 36423850 DOI: 10.1016/j.scitotenv.2022.160340] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Knowledge of the decay characteristics of health-related microbes in surface waters is important for modeling the transportation of waterborne pathogens and for assessing their public health risks. Although water temperature and light exposure are major factors determining the decay characteristics of enteric microbes in surface waters, such effects have not been well studied in subarctic surface waters. This study comprehensively evaluated the effect of temperature and light on the decay characteristics of health-related microbes [Escherichia coli, enterococci, microbial source tracking markers (GenBac3 & HF183 assays), coliphages (F-specific and somatic), noroviruses GII and Legionella spp.] under simulated subarctic river water conditions. The experiments were conducted in four different laboratory settings (4 °C/dark, 15 °C/dark, 15 °C/light, and 22 °C/light). The T90 values (time required for a 90 % reduction in the population of a target) of all targets were higher under cold and dark (2.6-51.3 days depending upon targets) than under warm and light conditions (0.6-3.5 days). Under 4 °C/dark (simulated winter) water conditions, F-specific coliphages had 27.2 times higher, and coliform bacteria had 3.3 times higher T90 value than under 22 °C/light (simulated summer) water conditions. Bacterial molecular markers also displayed high variation in T90 values, with the greatest difference between 4 °C/dark and 22 °C/light recorded for HF183 DNA (20.6 times) and the lowest difference for EC23S857 RNA (6.6 times). E. coli, intestinal enterococci, and somatic coliphages were relatively more sensitive to light than water temperature, but F-specific coliphages, norovirus, and all bacterial rDNA and rRNA markers were relatively more sensitive to temperature than light exposure. Due to the slow microbial decay in winter under subarctic conditions, the microbial quality of river water might remain low for a long time after a sewage spill. This increased risk associated with fecal pollution during winter may deserve more attention, especially when river waters are used for drinking water production.
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Affiliation(s)
- Ananda Tiwari
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland; University of Helsinki, Department of Food Hygiene and Environmental Health, Helsinki, Finland.
| | - Ari Kauppinen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland
| | - Pia Räsänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland
| | - Jenniina Salonen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland; University of Eastern Finland, Department of Environmental and Biological Sciences, Kuopio, Finland
| | - Laura Wessels
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland
| | - Janne Juntunen
- Finnish Environment Institute, Freshwater Center, Jyväskylä, Finland
| | - Ilkka T Miettinen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Kuopio, Finland; University of Helsinki, Department of Food Hygiene and Environmental Health, Helsinki, Finland.
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5
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Amelia TSM, Suaberon FAC, Vad J, Fahmi ADM, Saludes JP, Bhubalan K. Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:492-512. [PMID: 35567600 DOI: 10.1007/s10126-022-10130-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.
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Affiliation(s)
- Tan Suet May Amelia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Ferr Angelus C Suaberon
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Johanne Vad
- Changing Oceans Research Group, School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Afiq Durrani Mohd Fahmi
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Jonel P Saludes
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
- Department of Chemistry, University of San Agustin, 5000, Iloilo City, Philippines
- Department of Science and Technology, Balik Scientist Program, Philippine Council for Health Research & Development (PCHRD), Bicutan, 1631, Taguig, Philippines
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
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6
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Micaroni V, Strano F, McAllen R, Woods L, Turner J, Harman L, Bell JJ. Adaptive strategies of sponges to deoxygenated oceans. GLOBAL CHANGE BIOLOGY 2022; 28:1972-1989. [PMID: 34854178 DOI: 10.1111/gcb.16013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/08/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Ocean deoxygenation is one of the major consequences of climate change. In coastal waters, this process can be exacerbated by eutrophication, which is contributing to an alarming increase in the so-called 'dead zones' globally. Despite its severity, the effect of reduced dissolved oxygen has only been studied for a very limited number of organisms, compared to other climate change impacts such as ocean acidification and warming. Here, we experimentally assessed the response of sponges to moderate and severe simulated hypoxic events. We ran three laboratory experiments on four species from two different temperate oceans (NE Atlantic and SW Pacific). Sponges were exposed to a total of five hypoxic treatments, with increasing severity (3.3, 1.6, 0.5, 0.4 and 0.13 mg O2 L-1 , over 7-12-days). We found that sponges are generally very tolerant of hypoxia. All the sponges survived in the experimental conditions, except Polymastia crocea, which showed significant mortality at the lowest oxygen concentration (0.13 mg O2 L-1 , lethal median time: 286 h). In all species except Suberites carnosus, hypoxic conditions do not significantly affect respiration rate down to 0.4 mg O2 L-1 , showing that sponges can uptake oxygen at very low concentrations in the surrounding environment. Importantly, sponges displayed species-specific phenotypic modifications in response to the hypoxic treatments, including physiological, morphological and behavioural changes. This phenotypic plasticity likely represents an adaptive strategy to live in reduced or low oxygen water. Our results also show that a single sponge species (i.e., Suberites australiensis) can display different strategies at different oxygen concentrations. Compared to other sessile organisms, sponges generally showed higher tolerance to hypoxia, suggesting that sponges could be favoured and survive in future deoxygenated oceans.
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Affiliation(s)
- Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Rob McAllen
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Lisa Woods
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington, New Zealand
| | - John Turner
- School of Ocean Sciences, Bangor University, Anglesey, UK
| | - Luke Harman
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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7
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Mujakić I, Piwosz K, Koblížek M. Phylum Gemmatimonadota and Its Role in the Environment. Microorganisms 2022; 10:microorganisms10010151. [PMID: 35056600 PMCID: PMC8779627 DOI: 10.3390/microorganisms10010151] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/06/2023] Open
Abstract
Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.
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Affiliation(s)
- Izabela Mujakić
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- National Marine Fisheries Research Institute, Kołłątaja 1, 81-332 Gdynia, Poland
| | - Michal Koblížek
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
- Correspondence:
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8
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Silva DP, Epstein HE, Vega Thurber RL. Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics. Front Microbiol 2022; 13:1007877. [PMID: 36891260 PMCID: PMC9987214 DOI: 10.3389/fmicb.2022.1007877] [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: 07/31/2022] [Accepted: 12/30/2022] [Indexed: 02/22/2023] Open
Abstract
Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host's responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.
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Affiliation(s)
- Denise P Silva
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Hannah E Epstein
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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9
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Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions. Microbiol Spectr 2021; 9:e0081721. [PMID: 34668732 PMCID: PMC8528121 DOI: 10.1128/spectrum.00817-21] [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] [Indexed: 11/20/2022] Open
Abstract
The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that “naturalized” populations of Enterococcus faecalis exist in the extraenteric environment. The extent to which these naturalized E. faecalis organisms can confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of three E. faecalis isolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and quantitative PCR (qPCR) counts. However, the enteric isolates exhibited a spike in copy number ratios of 16S rRNA gene transcripts to 16S rRNA gene DNA copies (rRNA:rDNA ratios) between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential gene expression between environmental and enteric isolates related to habitat adaptation in the accompanying mesocosm metatranscriptomes. Overall, our results provide novel information on how rRNA levels may vary over different growth conditions (e.g., standard lab versus oligotrophic) for this important indicator bacteria. We also observed some evidence for habitat adaptation in E. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring. IMPORTANCE Enterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, closely related enterococci strains adapted to living in the extraenteric environment may represent a lower public health risk and confound water quality estimates. We developed an rRNA:rDNA viability assay for E. faecalis (a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher-risk) fecal pollution because rRNA levels significantly decreased after 1 week in all isolates.
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10
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Rahlff J, Stolle C, Giebel HA, Mustaffa NIH, Wurl O, P R Herlemann D. Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water. FEMS Microbiol Ecol 2021; 97:6149170. [PMID: 33625484 PMCID: PMC8012113 DOI: 10.1093/femsec/fiab035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
The occurrence of foams at oceans’ surfaces is patchy and generally short-lived, but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here, we investigated how marine foams differ from the sea-surface microlayer (SML), a <1-mm-thick layer at the air–sea interface, and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the North Sea and Timor Sea indicated that foams were often characterized by a high abundance of small eukaryotic phototrophic and prokaryotic cells as well as a high concentration of surface-active substances (SAS). Amplicon sequencing of 16S rRNA (gene) revealed distinctive foam bacterial communities compared with SML and underlying water, with high abundance of Gammaproteobacteria. Typical SML dwellers such as Pseudoalteromonas and Vibrio were highly abundant, active foam inhabitants and thus might enhance foam formation and stability by producing SAS. Despite a clear difference in the overall bacterial community composition between foam and SML, the presence of SML bacteria in foams supports the previous assumption that foam is strongly influenced by the SML. We conclude that active and abundant bacteria from interfacial habitats potentially contribute to foam formation and stability, carbon cycling and air–sea exchange processes in the ocean.
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Affiliation(s)
- Janina Rahlff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Christian Stolle
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany.,Leibniz Institute for Baltic Sea Research (IOW), Seestraße 15, 18119 Rostock, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Nur Ili Hamizah Mustaffa
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Oliver Wurl
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Daniel P R Herlemann
- Leibniz Institute for Baltic Sea Research (IOW), Seestraße 15, 18119 Rostock, Germany.,Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
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11
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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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12
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Astudillo-García C, Bell JJ, Montoya JM, Moitinho-Silva L, Thomas T, Webster NS, Taylor MW. Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef. Environ Microbiol 2020; 22:3985-3999. [PMID: 32827171 DOI: 10.1111/1462-2920.15185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/01/2020] [Indexed: 11/30/2022]
Abstract
Marine sponge reefs usually comprise a complex array of taxonomically different sponge species, many of these hosting highly diverse microbial communities. The number of microbial species known to occupy a given sponge ranges from tens to thousands, bringing numerous challenges to their analysis. One way to deal with such complexity is to use a core microbiota approach, in which only prevalent and abundant microbes are considered. Here we aimed to test the strength and sensitivity of the core microbiota approach by applying different core definitions to 20 host sponge species. Application of increasingly stringent relative abundance and/or percentage occurrence thresholds to qualify as part of the core microbiota decreased the number of 'core' OTUs and phyla and, consequently, changed both alpha- and beta-diversity patterns. Moreover, microbial co-occurrence patterns explored using correlation networks were also affected by the core microbiota definition. The application of stricter thresholds resulted in smaller and less compartmentalized networks, with different keystone species. These results highlight that the application of different core definitions to phylogenetically disparate host species can result in the drawing of markedly different conclusions. Consequently, we recommend to assess the effects of different core community definitions on the specific system of study before considering its application.
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Affiliation(s)
- Carmen Astudillo-García
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Jose M Montoya
- Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS-University Paul Sabatier, Moulis, France
| | - Lucas Moitinho-Silva
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Qld, Australia
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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13
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Britstein M, Cerrano C, Burgsdorf I, Zoccarato L, Kenny NJ, Riesgo A, Lalzar M, Steindler L. Sponge microbiome stability during environmental acquisition of highly specific photosymbionts. Environ Microbiol 2020; 22:3593-3607. [PMID: 32656901 DOI: 10.1111/1462-2920.15165] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/15/2020] [Accepted: 07/10/2020] [Indexed: 01/08/2023]
Abstract
In this study, we used in situ transplantations to provide the first evidence of horizontal acquisition of cyanobacterial symbionts by a marine sponge. The acquisition of the symbionts by the host sponge Petrosia ficiformis, which was observed in distinct visible patches, appeared several months after transplantation and at different times on different sponge specimens. We further used 16S rRNA gene amplicon sequencing of genomic DNA (gDNA) and complementary DNA (cDNA) and metatranscriptomics to investigate how the acquisition of the symbiotic cyanobacterium Candidatus Synechococcus feldmannii perturbed the diverse microbiota associated with the host P. ficiformis. To our surprise, the microbiota remained relatively stable during cyanobacterial symbiont acquisition at both structural (gDNA content) and activity (cDNA expression) levels. At the transcriptomic level, photosynthesis was the primary function gained following the acquisition of cyanobacteria. Genes involved in carotene production and oxidative stress tolerance were among those highly expressed by Ca. S. feldmannii, suggesting that this symbiont may protect itself and its host from damaging light radiation.
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Affiliation(s)
- Maya Britstein
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Carlo Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Luca Zoccarato
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Nathan J Kenny
- Life Sciences Department, The Natural History Museum of London, Cromwell Road, London, SW7 5BD, UK
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum of London, Cromwell Road, London, SW7 5BD, UK
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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14
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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15
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Antibacterial Potential of Secondary Metabolites from Indonesian Marine Bacterial Symbionts. Int J Microbiol 2020; 2020:8898631. [PMID: 32676116 PMCID: PMC7341410 DOI: 10.1155/2020/8898631] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/22/2020] [Indexed: 01/01/2023] Open
Abstract
Indonesian marine environments are known to house diverse organisms. However, the potential for bacteria from these environments as a source of antibacterial agents has not been widely studied. This study aims to explore the antibacterial potential of secondary metabolites produced by bacterial symbionts from sponges and corals collected in the Indonesian waters. Extracts of 12 bacterial isolates from sponges or corals were prepared by cultivating the bacteria under a number of different media conditions and using agar well diffusion assays to test for antibacterial activity. In addition, the morphology, physiology, and biochemical characteristics and 16S rRNA sequence of each isolate were used to determine their taxonomic classification. All tested bacterial isolates were able to produce secondary metabolites with various levels of antibacterial activity depending on medium composition and culture conditions. Two of the bacteria (RS3 and RC4) showed strong antibacterial activities against both Gram-negative and Gram-positive bacteria. A number of isolates (RS1, RS3, and RC2) were co-cultured with mycolic acid-containing bacteria, Mycobacterium smegmatis or Rhodococcus sp. However, no improvements in their antibacterial activity were observed. All of the 12 bacteria tested were identified as Streptomyces spp. LC-MS analysis of EtOAc extracts from the most active strains RS3 and RC4 revealed the presence of a number of dactinomycin analogues and potentially new secondary metabolites. Symbiotic Streptomyces spp. from sponges and corals of the Indonesian marine environments have great potential as a source of broad-spectrum antibacterial agents.
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16
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Meyer KM, Hopple AM, Klein AM, Morris AH, Bridgham SD, Bohannan BJM. Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Mol Ecol 2020; 29:1806-1819. [PMID: 32285532 DOI: 10.1111/mec.15442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 02/28/2020] [Accepted: 04/02/2020] [Indexed: 11/30/2022]
Abstract
Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4 )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
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Affiliation(s)
- Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anya M Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ann M Klein
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Andrew H Morris
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Scott D Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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17
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Meyer KM, Petersen IAB, Tobi E, Korte L, Bohannan BJM. Use of RNA and DNA to Identify Mechanisms of Bacterial Community Homogenization. Front Microbiol 2019; 10:2066. [PMID: 31572314 PMCID: PMC6749020 DOI: 10.3389/fmicb.2019.02066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
Biotic homogenization, i.e., the increase in community similarity through time or space, is a commonly observed response following conversion of native ecosystems to agriculture, but our understanding of the ecological mechanisms underlying this process is limited for bacterial communities. Identifying mechanisms of bacterial community homogenization following rapid environmental change may be complicated by the fact only a minority of taxa is active at any time. Here we used RNA- and DNA-based metabarcoding to distinguish putatively active taxa in the bacterial community from inactive taxa. We asked how soil bacterial communities respond to land use change following a rapid transition from rainforest to agriculture in the Congo Basin using a chronosequence that spans from roughly 1 week following slash-and-burn to an active plantation roughly 1.5 years post-conversion. Our results indicate that the magnitude of community homogenization is larger in the RNA-inferred community than the DNA-inferred perspective. We show that as the soil environment changes, the RNA-inferred community structure tracks environmental variation and loses spatial structure. The DNA-inferred community does not respond to environmental variability to the same degree, and is instead homogenized by a subset of taxa that is shared between forest and conversion sites. Our results suggest that complementing DNA-based surveys with RNA can provide insights into the way bacterial communities respond to environmental change.
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Affiliation(s)
- Kyle M. Meyer
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Ian A. B. Petersen
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Elie Tobi
- Smithsonian Institute, Gabon Biodiversity Program, Gamba, Gabon
| | - Lisa Korte
- Smithsonian Institute, Gabon Biodiversity Program, Gamba, Gabon
| | - Brendan J. M. Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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18
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Gutleben J, Koehorst JJ, McPherson K, Pomponi S, Wijffels RH, Smidt H, Sipkema D. Diversity of tryptophan halogenases in sponges of the genus Aplysina. FEMS Microbiol Ecol 2019; 95:fiz108. [PMID: 31276591 PMCID: PMC6644159 DOI: 10.1093/femsec/fiz108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/04/2019] [Indexed: 12/21/2022] Open
Abstract
Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas. At the phylum level, bacterial community composition was similar amongst all investigated species and predominated by Actinobacteria, Chloroflexi, Cyanobacteria, Gemmatimonadetes, and Proteobacteria. We detected four phylogenetically diverse clades of putative tryptophan halogenase protein sequences, which were only distantly related to previously reported halogenases. The Mediterranean species Aplysina aerophoba harbored unique halogenase sequences, of which the most predominant was related to a sponge-associated Psychrobacter-derived sequence. In contrast, the Caribbean species shared numerous novel halogenase sequence variants and exhibited a highly similar bacterial community composition at the operational taxonomic unit (OTU) level. Correlations of relative abundances of halogenases with those of bacterial taxa suggest that prominent sponge symbiotic bacteria, including Chloroflexi and Actinobacteria, are putative producers of the detected enzymes and may thus contribute to the chemical defense of their host.
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Affiliation(s)
- Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Kyle McPherson
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Shirley Pomponi
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Florida Atlantic University – Harbor Branch, 5600 U.S. 1, Fort Pierce, FL 34946, the United States
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - 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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19
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Bibi F, Alvi SA, Al-Sofyani A, Naseer MI, Yasir M, Azhar EI. Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea, Saudi Arabia. Saudi J Biol Sci 2019; 27:67-73. [PMID: 31889819 PMCID: PMC6933160 DOI: 10.1016/j.sjbs.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 11/16/2022] Open
Abstract
Bacterial communities of marine sponges are believed to be an important partner for host survival but remain poorly studied. Sponges show difference in richness and abundance of microbial population inhabiting them. Three marine sponges belonging to the species of Pione vastifica, Siphonochalina siphonella and Suberea mollis were collected from Red sea in Jeddah and were investigated using high throughput sequencing. Highly diverse communities containing 105 OTUs were identified in S. mollis host. Only 61 and 43 OTUs were found in P. vastifica and S. siphonella respectively. We identified 10 different bacterial phyla and 31 genera using 27,356 sequences. Most of the OTUs belong to phylum Proteobacteria (29%–99%) comprising of Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria where later two were only detected in HMA sponge, S. mollis. A number of 16S rRNA sequences (25%) were not identified to phylum level and may be novel taxa. Richness of bacterial community and Shannon, Simpson diversity revealed that sponge S. mollis harbors high diversity compared to other two LMA sponges. Dominance of Proteobacteria in sponges may indicate an ecological significance of this phylum in the Red sea sponges. These differences in bacterial composition may be due to difference in location site or host responses to environmental conditions. To the best of our knowledge, the microbial communities of these sponges have never been studied before and this is first attempt to unravel bacterial diversity using PCR-based 454-pyrosequencing method.
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Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Sana Akhtar Alvi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Abdulmohsin Al-Sofyani
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
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20
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Cleary DFR, Swierts T, Coelho FJRC, Polónia ARM, Huang YM, Ferreira MRS, Putchakarn S, Carvalheiro L, van der Ent E, Ueng JP, Gomes NCM, de Voogd NJ. The sponge microbiome within the greater coral reef microbial metacommunity. Nat Commun 2019; 10:1644. [PMID: 30967538 PMCID: PMC6456735 DOI: 10.1038/s41467-019-09537-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 03/18/2019] [Indexed: 02/03/2023] Open
Abstract
Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan.
| | - Thomas Swierts
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
| | - Francisco J R C Coelho
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Marine Recreation, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Marina R S Ferreira
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Sumaitt Putchakarn
- Institute of Marine Science, Burapha University, Chon Buri, 20131, Thailand
| | - Luis Carvalheiro
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Esther van der Ent
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
| | - Jinn-Pyng Ueng
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Aquaculture, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Newton C M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
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21
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Rua CPJ, de Oliveira LS, Froes A, Tschoeke DA, Soares AC, Leomil L, Gregoracci GB, Coutinho R, Hajdu E, Thompson CC, Berlinck RGS, Thompson FL. Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes. MICROBIAL ECOLOGY 2018; 76:825-838. [PMID: 29546438 DOI: 10.1007/s00248-018-1172-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.
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Affiliation(s)
- Cintia P J Rua
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Caixa Postal 780 - CEP13560-970, São Carlos, SP, CEP 13566-590, Brazil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Louisi S de Oliveira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Adriana Froes
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Diogo A Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
- Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Av. São José Barreto, 764 - São José do Barreto, Macaé - RJ, Macaé, RJ, CEP 27965-045, Brazil
| | - Ana Carolina Soares
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Gustavo B Gregoracci
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Av. Alm. Saldanha da Gama, 89, Santos, CEP 11030-400, Brazil
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto, 253, Praia dos Anjos, Arraial do Cabo, RJ, CEP 28930-000, Brazil
| | - Eduardo Hajdu
- Museu Nacional - UFRJ, Departamento de Invertebrados. Laboratório de Porifera, Quinta da Boa Vista, s/n. São Cristóvão, Rio de Janeiro, CEP 20940-040, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, s/ n° - CCS, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Caixa Postal 780 - CEP13560-970, São Carlos, SP, CEP 13566-590, Brazil.
| | - Fabiano L Thompson
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Caixa Postal 780 - CEP13560-970, São Carlos, SP, CEP 13566-590, Brazil.
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22
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Kiran GS, Sekar S, Ramasamy P, Thinesh T, Hassan S, Lipton AN, Ninawe AS, Selvin J. Marine sponge microbial association: Towards disclosing unique symbiotic interactions. MARINE ENVIRONMENTAL RESEARCH 2018; 140:169-179. [PMID: 29935729 DOI: 10.1016/j.marenvres.2018.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/01/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Sponges are sessile benthic filter-feeding animals, which harbor numerous microorganisms. The enormous diversity and abundance of sponge associated bacteria envisages sponges as hot spots of microbial diversity and dynamics. Many theories were proposed on the ecological implications and mechanism of sponge-microbial association, among these, the biosynthesis of sponge derived bioactive molecules by the symbiotic bacteria is now well-indicated. This phenomenon however, is not exhibited by all marine sponges. Based on the available reports, it has been well established that the sponge associated microbial assemblages keep on changing continuously in response to environmental pressure and/or acquisition of microbes from surrounding seawater or associated macroorganisms. In this review, we have discussed nutritional association of sponges with its symbionts, interaction of sponges with other eukaryotic organisms, dynamics of sponge microbiome and sponge-specific microbial symbionts, sponge-coral association etc.
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Affiliation(s)
- G Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Sivasankari Sekar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Pasiyappazham Ramasamy
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | | | - Saqib Hassan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Anuj Nishanth Lipton
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - A S Ninawe
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
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23
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Grahl N, Dolben EL, Filkins LM, Crocker AW, Willger SD, Morrison HG, Sogin ML, Ashare A, Gifford AH, Jacobs NJ, Schwartzman JD, Hogan DA. Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA. mSphere 2018; 3:e00292-18. [PMID: 30089648 PMCID: PMC6083091 DOI: 10.1128/msphere.00292-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes, as well as a linear response over more than 3 logs of input RNA. Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString, and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. Compared at the genus level, the relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. We propose that this method may complement other methods designed to understand dynamic microbial communities, may provide information on bacteria and fungi in the same sample with a single assay, and with further development, may provide quick and easily interpreted diagnostic information on diverse bacteria and fungi at the genus or species level.IMPORTANCE Here we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host response to changes in microbial communities.
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Affiliation(s)
- Nora Grahl
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Emily L Dolben
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Laura M Filkins
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Alex W Crocker
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Sven D Willger
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Alix Ashare
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Alex H Gifford
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Nicholas J Jacobs
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joseph D Schwartzman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Deborah A Hogan
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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24
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Chaib De Mares M, Sipkema D, Huang S, Bunk B, Overmann J, van Elsas JD. Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera. Front Microbiol 2017; 8:2560. [PMID: 29326681 PMCID: PMC5742488 DOI: 10.3389/fmicb.2017.02560] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/11/2017] [Indexed: 02/01/2023] Open
Abstract
Sponges are engaged in intimate symbioses with a diversity of microorganisms from all three domains of life, namely Bacteria, Archaea and Eukarya. Sponges have been well studied and categorized for their bacterial communities, some displaying a high microbial abundance (HMA), while others show low microbial abundance (LMA). However, the associated Archaea and Eukarya have remained relatively understudied. We assessed the bacterial, archaeal and eukaryotic diversities in the LMA sponge species Dysidea avara and Dysidea etheria by deep amplicon sequencing, and compared the results to those in the HMA sponges Aplysina aerophoba and Aplysina cauliformis. D. avara and A. aerophoba are sympatric in the Mediterranean Sea, while D. etheria and A. cauliformis are sympatric in the Caribbean Sea. The bacterial communities followed a host-specific pattern, with host species identity explaining most of the variation among samples. We identified OTUs shared by the Aplysina species that support a more ancient association of these microbes, before the split of the two species studied here. These shared OTUs are suitable targets for future studies of the microbial traits that mediate interactions with their hosts. Even though the archaeal communities were not as rich as the bacterial ones, we found a remarkable diversification and specificity of OTUs of the family Cenarchaeaceae and the genus Nitrosopumilus in all four sponge species studied. Similarly, the differences in fungal communities were driven by sponge identity. The structures of the communities of small eukaryotes such as dinophytes and ciliophores (alveolates), and stramenopiles, could not be explained by either sponge host, sponge genus or geographic location. Our analyses suggest that the host specificity that was previously described for sponge bacterial communities also extends to the archaeal and fungal communities, but not to other microbial eukaryotes.
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Affiliation(s)
- Maryam Chaib De Mares
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Sixing Huang
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,German Centre of Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,German Centre of Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Jan Dirk van Elsas
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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25
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Araújo FVDE, Netto MCM, Azevedo GP, Jayme MMA, Nunes-Carvalho MC, Silva MM, Carmo FLDO. Ecology and biotechnological potential of bacterial community from three marine sponges of the coast of Rio de Janeiro, Brazil. AN ACAD BRAS CIENC 2017; 89:2785-2792. [PMID: 29236862 DOI: 10.1590/0001-3765201720170462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/11/2017] [Indexed: 11/22/2022] Open
Abstract
Marine sponges has been a large reservoir of microbial diversity, with the presence of many species specific populations as well as producing biologically active compounds, which has attracted great biotechnological interest. In order to verify the influence of the environment in the composition of the bacterial community present in marine sponges and biotechnological potential of bacteria isolated from these organisms, three species of sponges and the waters surrounding them were collected in different beaches of Rio de Janeiro, Brazil. The profile of the bacterial community present in sponges and water was obtained by PCR-DGGE technique and the biotechnological potential of the strains isolated by producing amylase, cellulase, protease and biosurfactants. The results showed that despite the influence of the environment in the composition of the microbial community, studied marine sponges shown to have specific bacterial populations, with some, showing potential in the production of substances of biotechnological applications.
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Affiliation(s)
- Fábio V DE Araújo
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Marcelle C M Netto
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Gustavo P Azevedo
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Marcelly M A Jayme
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier, 524, 3° andar , Maracanã, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Monica C Nunes-Carvalho
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Av. Athos da Silveira Ramos, 149, 21044-020 Rio de Janeiro, RJ, Brazil
| | - Mariana M Silva
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Flávia L DO Carmo
- Departamento de Microbiologia Geral, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brazil
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26
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Karimi E, Ramos M, Gonçalves JMS, Xavier JR, Reis MP, Costa R. Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium. Front Microbiol 2017; 8:2499. [PMID: 29312205 PMCID: PMC5735121 DOI: 10.3389/fmicb.2017.02499] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis “endosymbiome” as a distinct consortium of uncultured prokaryotes displaying a likely “sit-and-wait” strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe–microbe and host–microbe gene transfer amenability.
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Affiliation(s)
- Elham Karimi
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Miguel Ramos
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Jorge M S Gonçalves
- Fisheries, Biodiversity and Conservation Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Joana R Xavier
- Department of Biology and K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Margarida P Reis
- Faculty of Science and Technology, University of Algarve, Faro, Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal.,Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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27
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Tout J, Astudillo-García C, Taylor MW, Tyson GW, Stocker R, Ralph PJ, Seymour JR, Webster NS. Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:750-755. [PMID: 28892304 DOI: 10.1111/1758-2229.12591] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Marine sponges host stable and species-specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile. Flow cytometry analysis revealed significant levels of microbial chemotaxis towards R. odorabile extracts and 16S rRNA gene amplicon sequencing showed enrichment of 'sponge-specific' microbial phylotypes, including a cluster within the Gemmatimonadetes and another within the Actinobacteria. These findings infer a potential mechanism for how sponges can acquire bacterial symbionts from the surrounding environment and suggest an active role of the symbionts in finding their host.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology & Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | | | - Michael W Taylor
- School of Biological Sciences, University of Auckland, New Zealand
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter J Ralph
- Plant Functional Biology & Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Justin R Seymour
- Plant Functional Biology & Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
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28
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Astudillo-García C, Slaby BM, Waite DW, Bayer K, Hentschel U, Taylor MW. Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges. Environ Microbiol 2017; 20:561-576. [DOI: 10.1111/1462-2920.13965] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/20/2017] [Accepted: 10/19/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Carmen Astudillo-García
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Institute of Marine Science, University of Auckland; Auckland New Zealand
| | - Beate M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences, University of Würzburg; Würzburg Germany
| | - David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences; The University of Queensland; QLD, St Lucia Australia
| | - Kristina Bayer
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Christian-Albrechts-Universität zu Kiel; Kiel Germany
| | - Michael W. Taylor
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland; New Zealand
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29
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Moitinho-Silva L, Steinert G, Nielsen S, Hardoim CCP, Wu YC, McCormack GP, López-Legentil S, Marchant R, Webster N, Thomas T, Hentschel U. Predicting the HMA-LMA Status in Marine Sponges by Machine Learning. Front Microbiol 2017; 8:752. [PMID: 28533766 PMCID: PMC5421222 DOI: 10.3389/fmicb.2017.00752] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered “HMA indicators” and “LMA indicators.” Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Cristiane C P Hardoim
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Yu-Chen Wu
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
| | - Grace P McCormack
- Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, and Center for Marine Science, University of North CarolinaWilmington, NC, USA
| | - Roman Marchant
- Centre for Translational Data Science, School of Information Technologies, University of SydneySydney, NSW, Australia
| | - Nicole Webster
- Australian Institute of Marine ScienceTownsville, QLD, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of QueenslandSt. Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
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30
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Matcher GF, Waterworth SC, Walmsley TA, Matsatsa T, Parker‐Nance S, Davies‐Coleman MT, Dorrington RA. Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts. Microbiologyopen 2017; 6:e00417. [PMID: 27781403 PMCID: PMC5387304 DOI: 10.1002/mbo3.417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 01/13/2023] Open
Abstract
The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids. Previously it was shown that the bacterial community associated with a Tsitsikamma sponge species comprises unusual bacterial taxa and is dominated by a novel Betaproteobacterium. Here, we have characterized the bacterial communities associated with six latrunculid species representing three genera (Tsitsikamma, Cyclacanthia, and Latrunculia) as well as a Mycale species, collected from Algoa Bay on the South African southeast coast. The bacterial communities of all seven sponge species were dominated by a single Betaproteobacterium operational taxonomic unit (OTU0.03 ), while a second OTU0.03 was dominant in the Mycale sp. The Betaproteobacteria OTUs from the different latrunculid sponges are closely related and their phylogenetic relationship follows that of their hosts. We propose that the latrunculid Betaproteobacteria OTUs are members of a specialized group of sponge symbionts that may have coevolved with their hosts. A single dominant Spirochaetae OTU0.03 was present in the Tsitsikamma and Cyclacanthia sponge species, but absent from the Latrunculia and Mycale sponges. This study sheds new light on the interactions between latrunculid sponges and their bacterial communities and may point to the potential involvement of dominant symbionts in the biosynthesis of the bioactive secondary metabolites.
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Affiliation(s)
- Gwynneth F. Matcher
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | | | - Tara A. Walmsley
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
- Department of BiotechnologyVaal University of TechnologyVanderbijlparkSouth Africa
| | - Tendayi Matsatsa
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Shirley Parker‐Nance
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Michael T. Davies‐Coleman
- Department of ChemistryRhodes UniversityGrahamstownSouth Africa
- Faculty of Natural ScienceUniversity of the Western CapeCape TownSouth Africa
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Jensen S, Fortunato SAV, Hoffmann F, Hoem S, Rapp HT, Øvreås L, Torsvik VL. The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle. MICROBIAL ECOLOGY 2017; 73:668-676. [PMID: 27664049 DOI: 10.1007/s00248-016-0836-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.
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Affiliation(s)
- Sigmund Jensen
- Department of Biology, University of Bergen, Bergen, Norway
| | - Sofia A V Fortunato
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Friederike Hoffmann
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway
| | - Solveig Hoem
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway
| | - Hans Tore Rapp
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway
| | - Lise Øvreås
- Department of Biology, University of Bergen, Bergen, Norway
| | - Vigdis L Torsvik
- Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, Bergen, 5020, Norway.
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Culturable bacterial communities associated to Brazilian Oscarella species (Porifera: Homoscleromorpha) and their antagonistic interactions. Antonie van Leeuwenhoek 2016; 110:489-499. [DOI: 10.1007/s10482-016-0818-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 12/08/2016] [Indexed: 01/08/2023]
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Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment. Mar Genomics 2016; 29:69-80. [DOI: 10.1016/j.margen.2016.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/17/2022]
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Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon. Sci Rep 2016; 6:32165. [PMID: 27577787 PMCID: PMC5006002 DOI: 10.1038/srep32165] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/28/2016] [Indexed: 12/04/2022] Open
Abstract
The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies.
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Lin Q, He G, Rui J, Fang X, Tao Y, Li J, Li X. Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion. Microb Cell Fact 2016; 15:96. [PMID: 27260194 PMCID: PMC4893225 DOI: 10.1186/s12934-016-0491-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/23/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Temperature is an important factor determining the performance and stability of the anaerobic digestion process. However, the microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion systems remain further elusive. To address this issue, we investigated the changes in composition, diversity and activities of microbial communities under temperature gradient from 25 to 55 °C using 16S rRNA gene amplicon sequencing approach based on genomic DNA (refer to as "16S rDNA") and total RNA (refer to as "16S rRNA"). RESULTS Microbial community structure and activities changed dramatically along the temperature gradient, which corresponded to the variations in digestion performance (e.g., daily CH4 production, total biogas production and volatile fatty acids concentration). The ratios of 16S rRNA to 16S rDNA of microbial taxa, as an indicator of the potentially relative activities in situ, and whole activities of microbial community assessed by the similarity between microbial community based on 16S rDNA and rRNA, varied strongly along the temperature gradient, reflecting different metabolic activities. The daily CH4 production increased with temperature from 25 to 50 °C and declined at 55 °C. Among all the examined microbial properties, the whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities showed highest correlations to the performance. CONCLUSIONS The whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities were sensitive indicators for the performance of anaerobic digestion systems under temperature gradient, while beta-diversity could predict functional differences. Microorganism-regulated mechanisms of temperature effects on anaerobic digestion performance were likely realized through increasing alpha-diversity of both microbial communities and potentially relative activities to supply more functional pathways and activities for metabolic network, and increasing the whole activities of microbial community, especially methanogenesis, to improve the strength and efficiency in anaerobic digestion process.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Guihua He
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junpeng Rui
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoyu Fang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yong Tao
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Klein AM, Bohannan BJM, Jaffe DA, Levin DA, Green JL. Molecular Evidence for Metabolically Active Bacteria in the Atmosphere. Front Microbiol 2016; 7:772. [PMID: 27252689 PMCID: PMC4878314 DOI: 10.3389/fmicb.2016.00772] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/09/2016] [Indexed: 01/02/2023] Open
Abstract
Bacterial metabolisms are responsible for critical chemical transformations in nearly all environments, including oceans, freshwater, and soil. Despite the ubiquity of bacteria in the atmosphere, little is known about the metabolic functioning of atmospheric bacterial communities. To gain a better understanding of the metabolism of bacterial communities in the atmosphere, we used a combined empirical and model-based approach to investigate the structure and composition of potentially active bacterial communities in air sampled at a high elevation research station. We found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from the total bacterial community (assayed via rDNA). Rare taxa in the total (rDNA) community were disproportionately active relative to abundant taxa, and members of the order Rhodospirillales had the highest potential for activity. We developed theory to explore the effects of random sampling from the rRNA and rDNA communities on observed differences between the communities. We found that random sampling, particularly in cases where active taxa are rare in the rDNA community, will give rise to observed differences in community composition including the occurrence of “phantom taxa”, taxa which are detected in the rRNA community but not the rDNA community. We show that the use of comparative rRNA/rDNA techniques can reveal the structure and composition of the metabolically active portion of bacterial communities. Our observations suggest that metabolically active bacteria exist in the atmosphere and that these communities may be involved in the cycling of organic compounds in the atmosphere.
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Affiliation(s)
- Ann M Klein
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR USA
| | - Daniel A Jaffe
- Department of Atmospheric Sciences, University of Washington Bothell, Bothell, WA USA
| | - David A Levin
- Department of Mathematics, University of Oregon, Eugene, OR USA
| | - Jessica L Green
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, ORUSA; Santa Fe Institute, Santa Fe, NMUSA
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Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei. Sci Rep 2016; 6:24966. [PMID: 27113140 PMCID: PMC4844951 DOI: 10.1038/srep24966] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei.
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Abstract
A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host’s phenotype and evolution. In the process, an era of “holobiont” research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge’s phenotype in fact act on the genomic interplay between the different components of the holobiont.
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Cleary DFR, de Voogd NJ, Polónia ARM, Freitas R, Gomes NCM. Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia. MICROBIAL ECOLOGY 2015; 70:889-903. [PMID: 26072397 DOI: 10.1007/s00248-015-0632-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/21/2015] [Indexed: 05/23/2023]
Abstract
In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus were predicted to be enriched for KOs related to the toxin-antitoxin (TA) system, nutrient starvation and heavy metal export.
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Affiliation(s)
- Daniel F R Cleary
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Ana R M Polónia
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Rossana Freitas
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Newton C M Gomes
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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Stauffert M, Cravo-Laureau C, Duran R. Dynamic of sulphate-reducing microorganisms in petroleum-contaminated marine sediments inhabited by the polychaete Hediste diversicolor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15273-15284. [PMID: 25256587 DOI: 10.1007/s11356-014-3624-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
The behaviour of sulphate-reducing microbial community was investigated at the oxic-anoxic interface (0-2 cm) of marine sediments when submitted to oil and enhanced bioturbation activities by the addition of Hediste diversicolor. Although total hydrocarbon removal was not improved by the addition of H. diversicolor, terminal restriction fragment length polymorphism (T-RFLP) analyses based on dsrAB (dissimilatory sulphite reductase) genes and transcripts showed different patterns according to the presence of H. diversicolor which favoured the abundance of dsrB genes during the early stages of incubation. Complementary DNA (cDNA) dsrAB libraries revealed that in presence of H. diversicolor, most dsrAB sequences belonged to hydrocarbonoclastic Desulfobacteraceae, suggesting that sulphate-reducing microorganisms (SRMs) may play an active role in hydrocarbon biodegradation in sediments where the reworking activity is enhanced. Furthermore, the presence of dsrAB sequences related to sequences found associated to environments with high dinitrogen fixation activity suggested potential N2 fixation by SRMs in bioturbated-polluted sediments.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
| | - Robert Duran
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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Telke AA, Rolain JM. Functional genomics to discover antibiotic resistance genes: The paradigm of resistance to colistin mediated by ethanolamine phosphotransferase in Shewanella algae MARS 14. Int J Antimicrob Agents 2015; 46:648-52. [PMID: 26498987 DOI: 10.1016/j.ijantimicag.2015.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/01/2015] [Accepted: 09/03/2015] [Indexed: 02/06/2023]
Abstract
Shewanella algae MARS 14 is a colistin-resistant clinical isolate retrieved from bronchoalveolar lavage of a hospitalised patient. A functional genomics strategy was employed to discover the molecular support for colistin resistance in S. algae MARS 14. A pZE21 MCS-1 plasmid-based genomic expression library was constructed in Escherichia coli TOP10. The estimated library size was 1.30×10(8) bp. Functional screening of colistin-resistant clones was carried out on Luria-Bertani agar containing 8 mg/L colistin. Five colistin-resistant clones were obtained after complete screening of the genomic expression library. Analysis of DNA sequencing results found a unique gene in all selected clones. Amino acid sequence analysis of this unique gene using the Integrated Microbial Genomes (IMG) and KEGG databases revealed that this gene encodes ethanolamine phosphotransferase (EptA, or so-called PmrC). Reverse transcription PCR analysis indicated that resistance to colistin in S. algae MARS 14 was associated with overexpression of EptA (27-fold increase), which plays a crucial role in the arrangement of outer membrane lipopolysaccharide.
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Affiliation(s)
- Amar A Telke
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Jean-Marc Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France.
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Erwin PM, Coma R, López-Sendino P, Serrano E, Ribes M. Stable symbionts across the HMA-LMA dichotomy: low seasonal and interannual variation in sponge-associated bacteria from taxonomically diverse hosts. FEMS Microbiol Ecol 2015; 91:fiv115. [DOI: 10.1093/femsec/fiv115] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2015] [Indexed: 12/13/2022] Open
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Kormas KA, Pachiadaki MG, Karayanni H, Leadbetter ER, Bernhard JM, Edgcomb VP. Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins. Extremophiles 2015; 19:949-60. [DOI: 10.1007/s00792-015-0770-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/28/2015] [Indexed: 11/29/2022]
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44
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Zeng Q, Sukumaran J, Wu S, Rodrigo A. Neutral Models of Microbiome Evolution. PLoS Comput Biol 2015; 11:e1004365. [PMID: 26200800 PMCID: PMC4511668 DOI: 10.1371/journal.pcbi.1004365] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/18/2015] [Indexed: 12/11/2022] Open
Abstract
There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.
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Affiliation(s)
- Qinglong Zeng
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Jeet Sukumaran
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Steven Wu
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Allen Rodrigo
- Biology Department, Duke University, Durham, North Carolina, United States of America
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Graça AP, Viana F, Bondoso J, Correia MI, Gomes L, Humanes M, Reis A, Xavier JR, Gaspar H, Lage OM. The antimicrobial activity of heterotrophic bacteria isolated from the marine sponge Erylus deficiens (Astrophorida, Geodiidae). Front Microbiol 2015; 6:389. [PMID: 25999928 PMCID: PMC4423441 DOI: 10.3389/fmicb.2015.00389] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/15/2015] [Indexed: 11/22/2022] Open
Abstract
Interest in the study of marine sponges and their associated microbiome has increased both for ecological reasons and for their great biotechnological potential. In this work, heterotrophic bacteria associated with three specimens of the marine sponge Erylus deficiens, were isolated in pure culture, phylogenetically identified and screened for antimicrobial activity. The isolation of bacteria after an enrichment treatment in heterotrophic medium revealed diversity in bacterial composition with only Pseudoalteromonas being shared by two specimens. Of the 83 selected isolates, 58% belong to Proteobacteria, 23% to Actinobacteria and 19% to Firmicutes. Diffusion agar assays for bioactivity screening against four bacterial strains and one yeast, revealed that a high number of the isolated bacteria (68.7%) were active, particularly against Candida albicans and Vibrio anguillarum. Pseudoalteromonas, Microbacterium, and Proteus were the most bioactive genera. After this preliminary screening, the bioactive strains were further evaluated in liquid assays against C. albicans, Bacillus subtilis and Escherichia coli. Filtered culture medium and acetone extracts from three and 5 days-old cultures were assayed. High antifungal activity against C. albicans in both aqueous and acetone extracts as well as absence of activity against B. subtilis were confirmed. Higher levels of activity were obtained with the aqueous extracts when compared to the acetone extracts and differences were also observed between the 3 and 5 day-old extracts. Furthermore, a low number of active strains was observed against E. coli. Potential presence of type-I polyketide synthases (PKS-I) and non-ribosomal peptide synthetases (NRPSs) genes were detected in 17 and 30 isolates, respectively. The high levels of bioactivity and the likely presence of associated genes suggest that Erylus deficiens bacteria are potential sources of novel marine bioactive compounds.
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Affiliation(s)
- Ana Patrícia Graça
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; Centre of Marine and Environmental Research (CIIMAR) Porto, Portugal
| | - Flávia Viana
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa Lisboa, Portugal
| | - Joana Bondoso
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; Centre of Marine and Environmental Research (CIIMAR) Porto, Portugal
| | - Maria Inês Correia
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal
| | - Luis Gomes
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal
| | - Madalena Humanes
- Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa Lisboa, Portugal
| | - Alberto Reis
- Bioenergy Unit, National Laboratory for Energy and Geology I.P. Lisboa, Portugal
| | - Joana R Xavier
- Department of Biology and Centre for Geobiology, University of Bergen Bergen, Norway
| | - Helena Gaspar
- Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa Lisboa, Portugal
| | - Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; Centre of Marine and Environmental Research (CIIMAR) Porto, Portugal
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Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India. PLoS One 2015; 10:e0123222. [PMID: 25938436 PMCID: PMC4418615 DOI: 10.1371/journal.pone.0123222] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/02/2015] [Indexed: 11/22/2022] Open
Abstract
Sponges are abundant, diverse and functionally important organisms of coral reef ecosystems. Sponge-associated microorganisms have been receiving greater attention because of their significant contribution to sponge biomass, biogeochemical cycles and biotechnological potentials. However, our understanding of the sponge microbiome is limited to a few species of sponges from restricted geographical locations. Here, we report for the first time the bacterial diversity of two cohabiting sponges, viz. Cinachyra cavernosa and Haliclona pigmentifera, as well as that in the ambient water from the coral reef ecosystems of the Gulf of Mannar, located along the southeast coast of India. Two hundred and fifty two clones in the 16S rRNA gene library of these sponges were grouped into eight distinct phyla, of which four belonged to the core group that are associated only with sponges. Phylogenetic analysis of the core bacteria showed close affinity to other sponge-associated bacteria from different geographical locations. γ-Proteobacteria, Chloroflexi, Planctomycetes and Deferribacter were the core groups in C. cavernosa while β and δ-Proteobacteria performed this role in H. pigmentifera. We observed greater OTU diversity for C. cavernosa (Hǀ 2.07) compared to H. pigmentifera (Hǀ 1.97). UniFrac analysis confirmed the difference in bacterial diversity of the two sponge species and also between the sponges and the reef water (p<0.001). The results of our study restate the existence of a host driven force in shaping the sponge microbiome.
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Fiore CL, Labrie M, Jarett JK, Lesser MP. Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange. Front Microbiol 2015; 6:364. [PMID: 25972851 PMCID: PMC4412061 DOI: 10.3389/fmicb.2015.00364] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/10/2015] [Indexed: 11/13/2022] Open
Abstract
Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. Furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. In this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, Xestospongia muta, from the Caribbean. In combination with a gene-specific approach, our goals were to (1) characterize genetic evidence for nitrogen cycling in X. muta, an important limiting nutrient on coral reefs (2) identify which prokaryotic symbiont lineages are metabolically active and, (3) characterize the metabolic potential of the prokaryotic community. Xestospongia muta expresses genes from multiple nitrogen transformation pathways that when combined with the abundance of this sponge, and previous data on dissolved inorganic nitrogen fluxes, shows that this sponge is an important contributor to nitrogen cycling biogeochemistry on coral reefs. Additionally, we observed significant differences in gene expression of the archaeal amoA gene, which is involved in ammonia oxidation, between coral reef locations consistent with differences in the fluxes of dissolved inorganic nitrogen previously reported. In regards to symbiont metabolic potential, the genes in the biosynthetic pathways of several amino acids were present in the prokaryotic metatranscriptome dataset but in the host-derived transcripts only the catabolic reactions for these amino acids were present. A similar pattern was observed for the B vitamins (riboflavin, biotin, thiamin, cobalamin). These results expand our understanding of biogeochemical cycling in sponges, and the metabolic interchange highlighted here advances the field of symbiont physiology by elucidating specific metabolic pathways where there is high potential for host-prokaryote interactions.
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Affiliation(s)
- Cara L. Fiore
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Micheline Labrie
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Jessica K. Jarett
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Michael P. Lesser
- School of Marine Science and Ocean Engineering, University of New HampshireDurham, NH, USA
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de Voogd NJ, Cleary DFR, Polónia ARM, Gomes NCM. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia. FEMS Microbiol Ecol 2015; 91:fiv019. [PMID: 25764467 DOI: 10.1093/femsec/fiv019] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2015] [Indexed: 11/12/2022] Open
Abstract
In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.
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Affiliation(s)
- Nicole J de Voogd
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands Institute for Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, the Netherlands
| | - Daniel F R Cleary
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Ana R M Polónia
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Polónia ARM, Cleary DFR, Freitas R, de Voogd NJ, Gomes NCM. The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment. Mol Ecol 2015; 24:409-23. [DOI: 10.1111/mec.13024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 11/23/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Ana R. M. Polónia
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Daniel F. R. Cleary
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Rossana Freitas
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Nicole J. de Voogd
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden The Netherlands
| | - Newton C. M. Gomes
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
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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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