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Zhang B, Jia C, Li M, Wang K, Chen J, Zhao J. Multiomics integration for the function of bacterial outer membrane vesicles in the larval settlement of marine sponges. Front Microbiol 2024; 15:1268813. [PMID: 38468855 PMCID: PMC10925772 DOI: 10.3389/fmicb.2024.1268813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Bacterial outer membrane vesicles (OMVs) contain a variety of chemical compounds and play significant roles in maintaining symbiotic relationships in a changing ocean, but little is known about their function, particularly in sponge larval development. During the growth of sponge Tedania sp., OMVs from Bacteroidetes species significantly promoted larval settlement, and Tenacibaculum mesophilum SP-7-OMVs were selected as a representative strain for further investigation. According to OMVs metabolomics, larval settlement might be connected to organic acids and derivatives. The multiomics analysis of the T. mesophilum genome, SP-7-OMVs metabolome, and larval transcriptome revealed 47 shared KEGG pathways. Among the number of candidate metabolites, arginine was chosen for its greater ability to increase the settlement rate and its role as the principal substrate for nitric oxide (NO) synthesis of sponge larvae. In summary, these results demonstrated that sponge-associated bacteria might utilize OMVs and their cargo to support host development and make up for host metabolic pathway deficiencies. This study enhances our fundamental knowledge of OMVs in interactions between metazoan hosts and microorganisms that are crucial in the coevolution of marine ecosystems and the complex marine environment.
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Affiliation(s)
- Beibei Zhang
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Chenzheng Jia
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Mingyu Li
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Kai Wang
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Jun Chen
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Jing Zhao
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
- Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen, Fujian, China
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2
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Han SM, Park JS. Ruegeria spongiae sp. nov., isolated from Callyspongia elongata. Int J Syst Evol Microbiol 2023; 73. [PMID: 37560994 DOI: 10.1099/ijsem.0.006001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] Open
Abstract
A Gram-stain-negative, rod-shaped, polar flagellated, aerobic, light-yellow bacterium, designated as 2012CJ41-6T, was isolated from a sponge sample of Callyspongia elongata from Chuja-myeon, Jeju-si, Jeju-do, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain 2012CJ41-6T clustered with species of the genus Ruegeria and appeared closely related to R. halocynthiae DSM 27839T (96.46 % similarity), R. denitrificans CECT 4357T (96.32 %), R. profundi ZGT108T (96.32 %), R. litorea CECT 7639T (96.32 %) and R. atlantica CECT 4292T (96.16 %). The average nucleotide identity and digital DNA-DNA hybridization between strain 2012CJ41-6T and the most closely related strain was 75.3 % and 19.6 %, indicating that 2012CJ41-6T represents a novel species of the genus Ruegeria. Growth occurred at 15-37 °C on marine medium in the presence of 0.5-10 % (w/v) NaCl and at pH 5.5-8.5. The DNA G+C content of the genomic DNA was 60.80 mol%, and ubiquinone-10 (Q-10) was the major respiratory quinone. The major cellular fatty acids (>5 %) were C18 : 1 ω7c and/or C18:1 ω6c (summed feature 8). The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, one unidentified aminolipid, one unidentified aminophospholipid and five unidentified lipids. Physiological and biochemical characteristics indicated that strain 2012CJ41-6T represents a novel species of the genus Ruegeria, for which the name Ruegeria spongiae sp. nov. is proposed. The type strain is 2012CJ41-6T (=KACC 22645T=LMG 32585T).
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Affiliation(s)
- Seung-Min Han
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon 34430, Republic of Korea
| | - Jin-Sook Park
- Department of Biological Sciences and Biotechnology, Hannam University Jeonmin-dong, Yuseong-gu, Daejeon 34430, Republic of Korea
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3
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Ramírez GA, Bar-Shalom R, Furlan A, Romeo R, Gavagnin M, Calabrese G, Garber AI, Steindler L. Bacterial aerobic methane cycling by the marine sponge-associated microbiome. MICROBIOME 2023; 11:49. [PMID: 36899421 PMCID: PMC9999580 DOI: 10.1186/s40168-023-01467-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane-oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed. RESULTS Here, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methane synthesis occurring in fully oxygenated shallow-water habitats. Specifically, we suggest methane generation occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C1-metabolic loop that involves both the sponge host and specific members of the associated microbial community. CONCLUSION Given the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge-hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methane production and consumption, sponges may serve as marine sources or sinks of this potent greenhouse gas. Video Abstract.
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Affiliation(s)
- Gustavo A Ramírez
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
- Present address: Department of Biological Sciences, California State University, Los Angeles, CA, USA
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Andrea Furlan
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Roberto Romeo
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Trieste, Italy
| | - Michelle Gavagnin
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Gianluca Calabrese
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Arkadiy I Garber
- School of Life Science, Arizona State University, Tempe, AZ, USA
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel.
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4
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Schmittmann L, Rahn T, Busch K, Fraune S, Pita L, Hentschel U. Stability of a dominant sponge-symbiont in spite of antibiotic-induced microbiome disturbance. Environ Microbiol 2022; 24:6392-6410. [PMID: 36250983 DOI: 10.1111/1462-2920.16249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 10/13/2022] [Indexed: 01/12/2023]
Abstract
Marine sponges are known for their complex and stable microbiomes. However, the lack of a gnotobiotic sponge-model and experimental methods to manipulate both the host and the microbial symbionts currently limit our mechanistic understanding of sponge-microbial symbioses. We have used the North Atlantic sponge species Halichondria panicea to evaluate the use of antibiotics to generate gnotobiotic sponges. We further asked whether the microbiome can be reestablished via recolonization with the natural microbiome. Experiments were performed in marine gnotobiotic facilities equipped with a custom-made, sterile, flow-through aquarium system. Bacterial abundance dynamics were monitored qualitatively and quantitatively by 16 S rRNA gene amplicon sequencing and qPCR, respectively. Antibiotics induced dysbiosis by favouring an increase of opportunistic, antibiotic-resistant bacteria, resulting in more complex, but less specific bacteria-bacteria interactions than in untreated sponges. The abundance of the dominant symbiont, Candidatus Halichondribacter symbioticus, remained overall unchanged, reflecting its obligately symbiotic nature. Recolonization with the natural microbiome could not reverse antibiotic-induced dysbiosis. However, single bacterial taxa that were transferred, successfully recolonized the sponge and affected bacteria-bacteria interactions. By experimentally manipulating microbiome composition, we could show the stability of a sponge-symbiont clade despite microbiome dysbiosis. This study contributes to understanding both host-bacteria and bacteria-bacteria interactions in the sponge holobiont.
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Affiliation(s)
- Lara Schmittmann
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - Sebastian Fraune
- Heinrich-Heine-University, Zoology and Organismic Interactions, Düsseldorf, Germany
| | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany.,Institut de Ciències del Mar - CSIC, Marine Biology and Oceanography, Marine Biogeochemistry, Atmosphere and Climate, Barcelona, Spain
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany.,Christian-Albrechts-University Kiel, Kiel, Germany
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5
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Abbas S, Mahmoud H. Identification of Sponge-Associated Bacteria From the Coast of Kuwait and Their Potential Biotechnological Applications. Front Microbiol 2022; 13:896718. [PMID: 35859748 PMCID: PMC9289682 DOI: 10.3389/fmicb.2022.896718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/07/2022] [Indexed: 11/19/2022] Open
Abstract
Sponges are among the most ancient animals harboring complex microbial communities with potential applications in biotechnology. The Arabian Gulf is a thermally stressed enclosed body of water located in an arid region where sponges and their halobionts are understudied. This study combined 16S rRNA next-generation gene amplicon sequencing and cultivation techniques to explore the abundance and diversity of sponge-associated bacteria. Culture-independent techniques showed the associations of more than 25 bacterial phyla with Amphimedon sp., Chondrilla australiensis, Haliclona sp., and Niphates spp. Regarding cultivable bacteria, 315 bacterial isolates associated with the sponge Haliclona sp. were cultivated; these isolates were affiliated with the phyla Proteobacteria and Firmicutes and were distributed among six bacterial genera. Selected strains of Bacillus, Ferrimonas, Pseudovibrio, Shewanella, Spongiobacter, and Vibrio were tested for antimicrobial activity against indicator microorganisms and protease enzyme production. Seven Bacillus strains exhibited weak to moderate growth inhibition against Bacillus subtilis, Staphylococcus aureus, and Candida albicans. Furthermore, 29 different strains of Bacillus, Ferrimonas, Shewanella, and Vibrio exhibited different degrees of positive protease activity. In addition, cultivated strains of Bacillus, Shewanella, Pseudovibrio, and Vibrio were tested for their biomineralization abilities. Herein we report for the first time the isolation of biomineralizing bacteria from sponge tissue where eleven bacterial isolates produced different shapes of calcium carbonate crystals on agar. Our observations shed light on the diversity and biotechnological potentials of sponges-associated bacteria inhabiting one of the world’s hottest seas.
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6
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Vargas S, Leiva L, Wörheide G. Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes. MICROBIAL ECOLOGY 2021; 81:213-222. [PMID: 32767091 PMCID: PMC7794106 DOI: 10.1007/s00248-020-01556-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
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Affiliation(s)
- Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Laura Leiva
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- Biologische Anstalt Helgoland, Shelf Sea System Ecology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, 27498, Helgoland, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, Munich, Germany
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7
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Bell JJ, McGrath E, Kandler NM, Marlow J, Beepat SS, Bachtiar R, Shaffer MR, Mortimer C, Micaroni V, Mobilia V, Rovellini A, Harris B, Farnham E, Strano F, Carballo JL. Interocean patterns in shallow water sponge assemblage structure and function. Biol Rev Camb Philos Soc 2020; 95:1720-1758. [PMID: 32812691 DOI: 10.1111/brv.12637] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 01/04/2023]
Abstract
Sponges are a major component of benthic ecosystems across the world and fulfil a number of important functional roles. However, despite their importance, there have been few attempts to compare sponge assemblage structure and ecological functions across large spatial scales. In this review, we examine commonalities and differences between shallow water (<100 m) sponges at bioregional (15 bioregions) and macroregional (tropical, Mediterranean, temperate, and polar) scales, to provide a more comprehensive understanding of sponge ecology. Patterns of sponge abundance (based on density and area occupied) were highly variable, with an average benthic cover between ~1 and 30%. Sponges were generally found to occupy more space (percentage cover) in the Mediterranean and polar macroregions, compared to temperate and tropical macroregions, although sponge densities (sponges m-2 ) were highest in temperate bioregions. Mean species richness standardised by sampling area was similar across all bioregions, except for a few locations that supported very high small-scale biodiversity concentrations. Encrusting growth forms were generally the dominant sponge morphology, with the exception of the Tropical West Atlantic, where upright forms dominated. Annelids and Arthropods were the most commonly reported macrofauna associated with sponges across bioregions. With respect to reproduction, there were no patterns in gametic development (hermaphroditism versus gonochorism), although temperate, tropical, and polar macroregions had an increasingly higher percentage of viviparous species, respectively, with viviparity being the sole gamete development mechanism reported for polar sponges to date. Seasonal reproductive timing was the most common in all bioregions, but continuous timing was more common in the Mediterranean and tropical bioregions compared to polar and temperate bioregions. We found little variation across bioregions in larval size, and the dominant larval type across the globe was parenchymella. No pattens among bioregions were found in the limited information available for standardised respiration and pumping rates. Many organisms were found to predate sponges, with the abundance of sponge predators being higher in tropical systems. While there is some evidence to support a higher overall proportion of phototrophic species in the Tropical Austalian bioregion compared to the Western Atlantic, both also have large numbers of heterotrophic species. Sponges are important spatial competitors across all bioregions, most commonly being reported to interact with anthozoans and algae. Even though the available information was limited for many bioregions, our analyses demonstrate some differences in sponge traits and functions among bioregions, and among macroregions. However, we also identified similarities in sponge assemblage structure and function at global scales, likely reflecting a combination of regional- and local-scale biological and physical processes affecting sponge assemblages, along with common ancestry. Finally, we used our analyses to highlight geographic bias in past sponge research, and identify gaps in our understanding of sponge ecology globally. By so doing, we identified key areas for future research on sponge ecology. We hope that our study will help sponge researchers to consider bioregion-specific features of sponge assemblages and key sponge-mediated ecological processes from a global perspective.
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Affiliation(s)
- James J Bell
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Emily McGrath
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.,Cawthron Institute, 98 Halifax St E, The Wood, Nelson, 7010, New Zealand
| | - Nora M Kandler
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Joseph Marlow
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Sandeep S Beepat
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Ramadian Bachtiar
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Megan R Shaffer
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Charlotte Mortimer
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Valeria Mobilia
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Alberto Rovellini
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Benjamin Harris
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Elizabeth Farnham
- Ministry of Primary Industries, PO Box 2526, Wellington, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - José Luis Carballo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UNAM), Avenida Joel Montes Camarena, s/n. apartado postal 811, Mazatlán, 82000, Mexico
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8
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García-Hernández JE, Hammerman NM, Cruz-Motta JJ, Schizas NV. Associated organisms inhabiting the calcareous sponge Clathrina lutea in La Parguera, Puerto Rico. CARIBB J SCI 2019. [DOI: 10.18475/cjos.v49i2.a12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Nicholas M. Hammerman
- University of Puerto Rico at Mayagüez, Department of Marine Sciences, Marine Genomic Biodiversity Laboratory, PO Box 9000, Mayagüez, PR 00681
| | - Juan J. Cruz-Motta
- University of Puerto Rico at Mayagüez, Department of Marine Sciences, Marine Genomic Biodiversity Laboratory, PO Box 9000, Mayagüez, PR 00681
| | - Nikolaos V. Schizas
- University of Puerto Rico at Mayagüez, Department of Marine Sciences, Marine Genomic Biodiversity Laboratory, PO Box 9000, Mayagüez, PR 00681
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9
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Gantt SE, McMurray SE, Stubler AD, Finelli CM, Pawlik JR, Erwin PM. Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges. MICROBIOME 2019; 7:124. [PMID: 31466521 PMCID: PMC6716902 DOI: 10.1186/s40168-019-0739-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests that sponges take up dissolved organic carbon (DOC) and, via assimilation and shedding of cells, return carbon to the reef ecosystem as particulate organic carbon (POC). Sponges host complex microbial communities within their tissues that may play a role in carbon and nutrient cycling within the sponge holobiont. To investigate this relationship, we paired microbial community characterization (16S rRNA analysis, Illumina Mi-Seq platform) with carbon (DOC, POC) and nutrient (PO4, NOx, NH4) flux data (specific filtration rate) for 10 common Caribbean sponge species at two distant sites (Florida Keys vs. Belize, ~ 1203 km apart). RESULTS Distance-based linear modeling revealed weak relationships overall between symbiont structure and carbon and nutrient flux, suggesting that the observed differences in POC, DOC, PO4, and NOx flux among sponges are not caused by variations in the composition of symbiont communities. In contrast, significant correlations between symbiont structure and NH4 flux occurred consistently across the dataset. Further, several individual symbiont taxa (OTUs) exhibited relative abundances that correlated with NH4 flux, including one OTU affiliated with the ammonia-oxidizing genus Cenarchaeum. CONCLUSIONS Combined, these results indicate that microbiome structure is uncoupled from sponge carbon cycling and does not explain variation in DOC uptake among Caribbean coral reef sponges. Accordingly, differential DOC assimilation by sponge cells or stable microbiome components may ultimately drive carbon flux in the sponge holobiont.
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Affiliation(s)
- Shelby E Gantt
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Steven E McMurray
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Amber D Stubler
- Biology Department, Occidental College, 1600 Campus Road, Los Angeles, CA, 90041, USA
| | - Christopher M Finelli
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Joseph R Pawlik
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Patrick M Erwin
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA.
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10
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Tang Q, Wan B, Yuan X, Muscente AD, Xiao S. Spiculogenesis and biomineralization in early sponge animals. Nat Commun 2019; 10:3348. [PMID: 31350398 PMCID: PMC6659672 DOI: 10.1038/s41467-019-11297-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/28/2019] [Indexed: 11/08/2022] Open
Abstract
Most sponges have biomineralized spicules. Molecular clocks indicate sponge classes diverged in the Cryogenian, but the oldest spicules are Cambrian in age. Therefore, sponges either evolved spiculogenesis long after their divergences or Precambrian spicules were not amenable to fossilization. The former hypothesis predicts independent origins of spicules among sponge classes and presence of transitional forms with weakly biomineralized spicules, but this prediction has not been tested using paleontological data. Here, we report an early Cambrian sponge that, like several other early Paleozoic sponges, had weakly biomineralized and hexactine-based siliceous spicules with large axial filaments and high organic proportions. This material, along with Ediacaran microfossils containing putative non-biomineralized axial filaments, suggests that Precambrian sponges may have had weakly biomineralized spicules or lacked them altogether, hence their poor record. This work provides a new search image for Precambrian sponge fossils, which are critical to resolving the origin of sponge spiculogenesis and biomineralization.
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Affiliation(s)
- Qing Tang
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bin Wan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, 210008, Nanjing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, 210008, Nanjing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - A D Muscente
- Department of Geological Sciences, University of Texas, Austin, TX, 78712, USA
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, 24061, USA.
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11
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Burgsdorf I, Handley KM, Bar-Shalom R, Erwin PM, Steindler L. Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. mSystems 2019; 4:e00057-19. [PMID: 31086829 PMCID: PMC6506613 DOI: 10.1128/msystems.00057-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023] Open
Abstract
"Candidatus Synechococcus feldmannii" is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont "Candidatus Synechococcus spongiarum." Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of "Ca. Synechococcus feldmannii." By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by "Ca. Synechococcus feldmannii" and free-living cyanobacteria, while they are absent in the obligate symbiont "Ca. Synechococcus spongiarum." These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on "Ca. Synechococcus feldmannii" its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.
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Affiliation(s)
- Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Patrick M. Erwin
- Department of Biology and Marine Biology, Centre for Marine Science, University of North Carolina—Wilmington, Wilmington, North Carolina, USA
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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12
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Villegas-Plazas M, Wos-Oxley ML, Sanchez JA, Pieper DH, Thomas OP, Junca H. Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth. MICROBIAL ECOLOGY 2019; 78:243-256. [PMID: 30413836 DOI: 10.1007/s00248-018-1285-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 10/30/2018] [Indexed: 06/08/2023]
Abstract
Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.
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Affiliation(s)
- Marcela Villegas-Plazas
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, Chía, 250008, Colombia
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Honorary Research Associate, South Australian Museum, Adelaide, Australia
| | - Juan A Sanchez
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, Galway, H91 TK33, Ireland
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, Chía, 250008, Colombia.
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13
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Junk L, Kazmaier U. Total Synthesis and Configurational Revision of Mozamide A, a Hydroxy-Brunsvicamide. J Org Chem 2019; 84:2489-2500. [DOI: 10.1021/acs.joc.8b02836] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lukas Junk
- Organic Chemistry I, Saarland University, Campus Building C4.2, D-66123 Saarbrücken, Germany
| | - Uli Kazmaier
- Organic Chemistry I, Saarland University, Campus Building C4.2, D-66123 Saarbrücken, Germany
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Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade. mSystems 2018; 3:mSystems00150-18. [PMID: 30637337 PMCID: PMC6306507 DOI: 10.1128/msystems.00150-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/29/2018] [Indexed: 01/25/2023] Open
Abstract
Chloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought. Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for “Candidatus Poribacteria” and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.
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15
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Evolution of the main skeleton-forming genes in sponges (phylum Porifera) with special focus on the marine Haplosclerida (class Demospongiae). Mol Phylogenet Evol 2018; 131:245-253. [PMID: 30502904 DOI: 10.1016/j.ympev.2018.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/26/2018] [Accepted: 11/19/2018] [Indexed: 01/14/2023]
Abstract
The skeletons of sponges (Phylum Porifera) are comprised of collagen, often embedded with small siliceous structures (spicules) arranged in various forms to provide strength and flexibility. The main proteins responsible for the formation of the spicules in demosponges are the silicateins, which are related to the cathepsins L of other animals. While the silicatein active site, necessary for the formation of biosilica crystals, is characterized by the amino acids SHN, different variants of the silicatein genes have been found, some that retain SHN at the active site and some that don't. As part of an effort to further understand skeleton formation in marine sponges of the order Haplosclerida, a search for all silicatein variants were made in Irish species representing the main clades of this large sponge group. For this task, transcriptomes were sequenced and de novo assembled from Haliclona oculata, H. simulans and H. indistincta. Silicatein genes were identified from these and all available genomes and transcriptomes from Porifera. These were analysed along with all complete silicateins from GenBank. Silicateins were only found in species belonging to the class Demospongiae but excluding Keratosa and Verongimorpha and there was significant duplication and diversity of these genes. Silicateins showing SHN at the active site were polyphyletic. Indeed silicatein sequences were divided into six major clades (CHNI, CHNII, CHNIII, SHNI, SHNII and C/SQN). In those clades where haplosclerids were well represented the silicatein phylogeny reflected previous ribosomal and mitochondrial topologies. The most basal silicatein clade (CHNI) contained sequences only from marine haplosclerids and freshwater sponges while one silicatein from H. indistincta was more related to cathepsins L (outgroup) than to the overall silicatein clade indicating the presence of an old silicatein or an intermediary form. This data could suggest that marine haplosclerids were one of the first groups of extant demosponges to acquire silicatein genes. Furthermore, we suggest that the paucity of spicule types in this group may be due to their single copy of SHNI variants, and the lack of a silintaphin gene.
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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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Li F, Janussen D, Peifer C, Pérez-Victoria I, Tasdemir D. Targeted Isolation of Tsitsikammamines from the Antarctic Deep-Sea Sponge Latrunculia biformis by Molecular Networking and Anticancer Activity. Mar Drugs 2018; 16:md16080268. [PMID: 30072656 PMCID: PMC6117724 DOI: 10.3390/md16080268] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
The Antarctic deep-sea sponge Latrunculia (Latrunculia) biformis Kirkpatrick, 1908 (Class Demospongiae Sollas, Order Poecilosclerida Topsent, Latrunculiidae Topsent) was selected for chemical analyses due to its potent anticancer activity. Metabolomic analysis of its crude extract by HRMS/MS-based molecular networking showed the presence of several clusters of pyrroloiminoquinone alkaloids, i.e., discorhabdin and epinardin-type brominated pyridopyrroloquinolines and tsitsikammamines, the non-brominated bis-pyrroloiminoquinones. Molecular networking approach combined with a bioactivity-guided isolation led to the targeted isolation of the known pyrroloiminoquinone tsitsikammamine A (1) and its new analog 16,17-dehydrotsitsikammamine A (2). The chemical structures of the compounds 1 and 2 were elucidated by spectroscopic analysis (one-dimensional (1D) and two-dimensional (2D) NMR, HR-ESIMS). Due to minute amounts, molecular modeling and docking was used to assess potential affinities to potential targets of the isolated compounds, including DNA intercalation, topoisomerase I-II, and indoleamine 2,3-dioxygenase enzymes. Tsitsikammamines represent a small class of pyrroloiminoquinone alkaloids that have only previously been reported from the South African sponge genus Tsitsikamma Samaai & Kelly and an Australian species of the sponge genus Zyzzya de Laubenfels. This is the first report of tsitsikammamines from the genus Latrunculia du Bocage and the successful application of molecular networking in the identification of comprehensive chemical inventory of L.biformis followed by targeted isolation of new molecules. This study highlights the high productivity of secondary metabolites of Latrunculia sponges and may shed new light on their biosynthetic origin and chemotaxonomy.
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Affiliation(s)
- Fengjie Li
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Marine Natural Products Research Unit Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany.
| | - Dorte Janussen
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt, Germany.
| | - Christian Peifer
- Pharmaceutical Chemistry, Kiel University, Gutenbergstraße 76, 24118 Kiel, Germany.
| | - Ignacio Pérez-Victoria
- Fundación MEDINA, Parque Tecnológico de la Salud, Av. Conocimiento 18016 Granada, Spain.
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Marine Natural Products Research Unit Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany.
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany.
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Barra L, Barac P, König GM, Crüsemann M, Dickschat JS. Volatiles from the fungal microbiome of the marine sponge Callyspongia cf. flammea. Org Biomol Chem 2018; 15:7411-7421. [PMID: 28872169 DOI: 10.1039/c7ob01837a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The volatiles emitted by five fungal strains previously isolated from the marine sponge Callyspongia cf. flammea were captured with a closed-loop stripping apparatus (CLSA) and analyzed by GC-MS. Besides several widespread compounds, a series of metabolites with interesting bioactivities were found, including the quorum sensing inhibitor protoanemonin, the fungal phytotoxin 3,4-dimethylpentan-4-olide, and the insect attractant 1,2,4-trimethoxybenzene. In addition, the aromatic polyketides isotorquatone and chartabomone that are both known from Eucalyptus and a new O-desmethyl derivative were identified. The biosynthesis of isotorquatone was studied by feeding experiments with isotopically labeled precursors and its absolute configuration was determined by enantioselective synthesis of a reference compound. Bioactivity testings showed algicidal activity for some of the identified compounds, suggesting a potential ecological function in sponge defence.
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Affiliation(s)
- Lena Barra
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, D-53121 Bonn, Germany.
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Gantt SE, López-Legentil S, Erwin PM. Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor. FEMS Microbiol Lett 2018; 364:3833132. [PMID: 28520957 DOI: 10.1093/femsle/fnx105] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/16/2017] [Indexed: 01/04/2023] Open
Abstract
Marine sponges have been shown to harbor diverse microbial symbiont communities that play key roles in host functioning, yet little is known about how anthropogenic disturbances impact sponge-microbe interactions. The Mediterranean sponge Crambe crambe is known to accumulate heavy metals in polluted harbors. In this study, we investigated whether the microbiome of C. crambe differed between sponges inhabiting a polluted harbor in Blanes (Spain) and a nearby (<1 km) natural environment. Triplicate sponge and ambient seawater samples were collected from each site and the microbial composition of each sample was determined by 16S rRNA gene sequence analysis (Illumina Hi-Seq platform). No significant differences in the diversity or structure of microbial communities in C. crambe were detected between habitats, while a significant difference in community structure was observed in ambient seawater inside and outside of the polluted harbor. The microbiome of C. crambe was clearly differentiated from free-living seawater microbes and dominated by Proteobacteria, specifically a single betaproteobacterium that accounted for >86% of all sequence reads. These results indicate that sponge microbiomes exhibit greater stability and pollution tolerance than their free-living microbial counterparts, potentially mitigating the effects of pollutants on coastal marine communities.
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Affiliation(s)
- Shelby E Gantt
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
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20
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Zhang P, Arceneaux DJ, Khattab A. Mechanical properties of 3D printed polycaprolactone honeycomb structure. J Appl Polym Sci 2017. [DOI: 10.1002/app.46018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pengfei Zhang
- Department of Industrial Technology, College of Engineering; University of Louisiana at Lafayette; Lafayette Louisiana 70504-2972
- Laboratory for Composite Materials; Institute for Materials Research & Innovation, UL Lafayette; Lafayette Louisiana 70504-2972
| | - Donald Joseph Arceneaux
- Department of Industrial Technology, College of Engineering; University of Louisiana at Lafayette; Lafayette Louisiana 70504-2972
| | - Ahmed Khattab
- Department of Industrial Technology, College of Engineering; University of Louisiana at Lafayette; Lafayette Louisiana 70504-2972
- Laboratory for Composite Materials; Institute for Materials Research & Innovation, UL Lafayette; Lafayette Louisiana 70504-2972
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22
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Yang H, Ma M, Flower RJ, Thompson JR, Ge W. Preserve Precambrian fossil heritage from mining. Nat Ecol Evol 2017; 1:1048-1049. [PMID: 29046588 DOI: 10.1038/s41559-017-0266-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hong Yang
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing, 400715, China. .,Department of Geography and Environmental Science, University of Reading, Reading, RG6 6AB, UK.
| | - Mingguo Ma
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing, 400715, China.
| | - Roger J Flower
- UCL Department of Geography, University College London, London, WC1E 6BT, UK
| | - Julian R Thompson
- UCL Department of Geography, University College London, London, WC1E 6BT, UK
| | - Wei Ge
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing, 400715, China
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Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T. The sponge microbiome project. Gigascience 2017; 6:1-7. [PMID: 29020741 PMCID: PMC5632291 DOI: 10.1093/gigascience/gix077] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/28/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022] Open
Abstract
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Amnon Amir
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Gail L Ackermann
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Carlo Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | | | - Cole Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Detmer Sipkema
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Fang Liu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Georg Steinert
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giorgos Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Grace P McCormack
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Guofang Feng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Jan Vicente
- Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346
| | - Johannes R Björk
- Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jose M Montoya
- Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France
| | - Julie B Olson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Julie Reveillaud
- INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Mari-Carmen Pineda
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia
| | - Maria V Marra
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paraskevi Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Patrick M Erwin
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Rachel L Simister
- Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3
| | - Rob Knight
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, and Center for Microbiome Innovation, University of California - San Diego, La Jolla, CA 92093, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Susanna Lopez-Legentil
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Thanos Dailianis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Nicole S Webster
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
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24
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Tatzel M, von Blanckenburg F, Oelze M, Bouchez J, Hippler D. Late Neoproterozoic seawater oxygenation by siliceous sponges. Nat Commun 2017; 8:621. [PMID: 28931817 PMCID: PMC5606986 DOI: 10.1038/s41467-017-00586-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/11/2017] [Indexed: 11/09/2022] Open
Abstract
The Cambrian explosion, the rapid appearance of most animal phyla in the geological record, occurred concurrently with bottom seawater oxygenation. Whether this oxygenation event was triggered through enhanced nutrient supply and organic carbon burial forced by increased continental weathering, or by species engaging in ecosystem engineering, remains a fundamental yet unresolved question. Here we provide evidence for several simultaneous developments that took place over the Ediacaran–Cambrian transition: expansion of siliceous sponges, decrease of the dissolved organic carbon pool, enhanced organic carbon burial, increased phosphorus removal and seawater oxygenation. This evidence is based on silicon and carbon stable isotopes, Ge/Si ratios, REE-geochemistry and redox-sensitive elements in a chert-shale succession from the Yangtze Platform, China. According to this reconstruction, sponges have initiated seawater oxygenation by redistributing organic carbon oxidation through filtering suspended organic matter from seawater. The resulting increase in dissolved oxygen levels potentially triggered the diversification of eumetazoans. The Ediacaran–Cambrian oxygenation of seawater is thought to have been caused by lifeforms engaging in ecosystem engineering. Here, the authors show that siliceous sponges increased seawater dissolved oxygen concentrations by redistributing organic carbon oxidation through filtering suspended organic matter.
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Affiliation(s)
- Michael Tatzel
- Section 3.3: Earth Surface Geochemistry Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Telegrafenberg, Potsdam, 14473, Germany. .,Division 1.1: Inorganic Trace Analysis, BAM, Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, Berlin, 12489, Germany.
| | - Friedhelm von Blanckenburg
- Section 3.3: Earth Surface Geochemistry Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Telegrafenberg, Potsdam, 14473, Germany.,Department of Earth Sciences, Institute of Geological Sciences, Freie Universität Berlin, Malteserstr. 74-100, Berlin, 12249, Germany
| | - Marcus Oelze
- Section 3.3: Earth Surface Geochemistry Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Telegrafenberg, Potsdam, 14473, Germany
| | - Julien Bouchez
- Section 3.3: Earth Surface Geochemistry Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Telegrafenberg, Potsdam, 14473, Germany.,Institut de Physique du Globe de Paris-CNRS, Sorbonne Paris-Cité 1 Rue Jussieu, 75238, Paris 05, France
| | - Dorothee Hippler
- Institute of Applied Geosciences Technische Universität Berlin, Ackerstraβe 76, Berlin, 13355, Germany.,Institute of Applied Geosciences, Technische Universität Graz, Rechbauerstraβe 12, 8010, Graz, Austria
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25
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Slaby BM, Hackl T, Horn H, Bayer K, Hentschel U. Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization. ISME JOURNAL 2017; 11:2465-2478. [PMID: 28696422 PMCID: PMC5649159 DOI: 10.1038/ismej.2017.101] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 05/07/2017] [Accepted: 05/21/2017] [Indexed: 01/29/2023]
Abstract
Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.
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Affiliation(s)
- Beate M Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Department of Botany II, Julius-von-Sachs Institute for Biological Science, University of Würzburg, Würzburg, Germany
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannes Horn
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Department of Botany II, Julius-von-Sachs Institute for Biological Science, University of Würzburg, Würzburg, Germany
| | - Kristina Bayer
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Christian-Albrechts University of Kiel, Kiel, Germany
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26
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Manning-Berg AR, Kah LC. Proterozoic microbial mats and their constraints on environments of silicification. GEOBIOLOGY 2017; 15:469-483. [PMID: 28397335 DOI: 10.1111/gbi.12238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
The occurrence of microfossiliferous, early diagenetic chert in Proterozoic successions is broadly restricted to peritidal marine environments. Such coastal environments are amongst the most environmentally variable of marine environments, experiencing both enhanced evaporation and potential influx of terrestrial freshwaters. To better understand potential conditions under which silicification occurs, we focus on microfossiliferous early diagenetic chert from the Mesoproterozoic Bylot Supergroup, northern Baffin Island. Spectacular preservation of silicified microbial mats, their associated mineral phases, and the petrographic fabrics of the chert itself require that silicification occurred at the sediment-water interface, penecontemporaneously with mat growth. In some cases, silica is the primary precipitated mineral phase and is not associated with replacement of precursor mineral phases. In other cases, silica deposition includes the mimetic replacement of carbonate, gypsum, and halite mineral phases. These petrographic constraints suggest that silicification potentially occurred under a range of fluid chemistries associated with environmental variability in nearshore peritidal environments. Here we provide the first direct thermodynamic modeling of hypothetical Proterozoic seawater solutions, seawater-derived brines, and mixed seawater-freshwater solutions, and demonstrate that peritidal environments are capable of providing a wide range of fluid chemistries under which early diagenetic silica can both precipitate and replace primary mineralogical phases. Despite the thermodynamic potential for silica deposition under a wide range of fluid compositions, chert is not ubiquitous in Proterozoic nearshore environments, suggesting that the kinetics of silica polymerization exert a primary control over deposition.
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Affiliation(s)
- A R Manning-Berg
- Department of Earth and Planetary Science, University of Tennessee, Knoxville, TN, USA
| | - L C Kah
- Department of Earth and Planetary Science, University of Tennessee, Knoxville, TN, USA
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27
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Stolper DA, Love GD, Bates S, Lyons TW, Young E, Sessions AL, Grotzinger JP. Paleoecology and paleoceanography of the Athel silicilyte, Ediacaran-Cambrian boundary, Sultanate of Oman. GEOBIOLOGY 2017; 15:401-426. [PMID: 28387009 DOI: 10.1111/gbi.12236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 02/27/2017] [Indexed: 05/22/2023]
Abstract
The Athel silicilyte is an enigmatic, hundreds of meters thick, finely laminated quartz deposit, in which silica precipitated in deep water (>~100-200 m) at the Ediacaran-Cambrian boundary in the South Oman Salt Basin. In contrast, Meso-Neoproterozoic sinks for marine silica were dominantly restricted to peritidal settings. The silicilyte is known to contain sterane biomarkers for demosponges, which today are benthic, obligately aerobic organisms. However, the basin has previously been described as permanently sulfidic and time-equivalent shallow-water carbonate platform and evaporitic facies lack silica. The Athel silicilyte thus represents a unique and poorly understood depositional system with implications for late Ediacaran marine chemistry and paleoecology. To address these issues, we made petrographic observations, analyzed biomarkers in the solvent-extractable bitumen, and measured whole-rock iron speciation and oxygen and silicon isotopes. These data indicate that the silicilyte is a distinct rock type both in its sedimentology and geochemistry and in the original biology present as compared to other facies from the same time period in Oman. The depositional environment of the silicilyte, as compared to the bounding shales, appears to have been more reducing at depth in sediments and possibly bottom waters with a significantly different biological community contributing to the preserved biomarkers. We propose a conceptual model for this system in which deeper, nutrient-rich waters mixed with surface seawater via episodic mixing, which stimulated primary production. The silica nucleated on this organic matter and then sank to the seafloor, forming the silicilyte in a sediment-starved system. We propose that the silicilyte may represent a type of environment that existed elsewhere during the Neoproterozoic. These environments may have represented an important locus for silica removal from the oceans.
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Affiliation(s)
- D A Stolper
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - G D Love
- Department of Earth Sciences, University of California, Riverside, CA, USA
| | - S Bates
- Department of Earth Sciences, University of California, Riverside, CA, USA
| | - T W Lyons
- Department of Earth Sciences, University of California, Riverside, CA, USA
| | - E Young
- Department of Earth and Space Sciences, University of California, Los Angeles, CA, USA
- Institute of Geophysics and Planetary Physics, University of California, Los Angeles, CA, USA
| | - A L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - J P Grotzinger
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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28
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Cyranoski D. Mining threatens Chinese fossil site that revealed planet's earliest animals. Nature 2017; 544:403. [PMID: 28447656 DOI: 10.1038/nature.2017.21869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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The δ 30Si peak value discovered in middle Proterozoic chert and its implication for environmental variations in the ancient ocean. Sci Rep 2017; 7:44000. [PMID: 28272425 PMCID: PMC5341034 DOI: 10.1038/srep44000] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/02/2017] [Indexed: 12/01/2022] Open
Abstract
The silicon isotope composition of chert has recently been used to study the historic evolution of the global ocean. It has been suggested that Precambrian cherts have much higher δ30Si values than Phanerozoic cherts do and that the former show an increasing trend from 3.5 to 0.85 Ga, reflecting a decrease in ocean temperatures. However, cherts have various origins, and their isotopic compositions might be reset by metamorphic fluid circulation; thus, different types of cherts should be distinguished. Here, we present a new set of δ30Si data for cherts from early and middle Proterozoic carbonate rocks from Northern China. We found that cherts of 1.355–1.325 Ga show a peak range of 2.2–3.9‰. Based on these results, we propose that from the Archean to the middle Proterozoic, there was a drastic decrease in silicon content and an increase in the δ30Si value in ocean water due to a temperature decrease and biological activity increase. After that period, the silicon content of the ocean was limited to a low level by a high degree of biological absorption, and their δ30Si values varied in a small range around a significantly lower value.
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30
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Yang XL, Zhao YL, Babcock LE, Peng J. Siliceous spicules in a vauxiid sponge (Demospongia) from the Kaili Biota(Cambrian Stage 5), Guizhou, South China. Sci Rep 2017; 7:42945. [PMID: 28220860 PMCID: PMC5318851 DOI: 10.1038/srep42945] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/17/2017] [Indexed: 11/25/2022] Open
Abstract
Fossils of the sponge Angulosuspongia sinensis from calcareous mudstones of the middle and upper part of the Kaili Formation (Cambrian Stage 5) in the Jianhe area of Guizhou province, South China, exhibit an apparently reticulate pattern, characteristic of the Vauxiidae. Energy Dispersive X-Ray Spectrometry (EDS) and Raman spectroscopy analysis indicate the presence of silica in the skeletal elements of these fossils, suggesting that this taxon possessed a skeleton comprised of spicules. This is the first confirmation of siliceous skeletal elements in fossils of the family Vauxiidae, and it lends support to the hypothesis that some early demosponges possessed biomineralized siliceous skeletons, which were subsequently lost and replaced by spongin later in the evolutionary history of this lineage. The new materials provide critical insight into the phylogeny and evolution of biomineralization in the Demosopongiae.
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Affiliation(s)
- X-L Yang
- College of Resource and Environment Engineering, Guizhou University, Guiyang 550025, China.,State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, CAS, Nanjing 210008, China
| | - Y-L Zhao
- College of Resource and Environment Engineering, Guizhou University, Guiyang 550025, China
| | - L E Babcock
- School of Earth Sciences, The Ohio State University, Columbus 43210, USA
| | - J Peng
- College of Resource and Environment Engineering, Guizhou University, Guiyang 550025, China
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31
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Determination of the Halogenated Skeleton Constituents of the Marine Demosponge Ianthella basta. Mar Drugs 2017; 15:md15020034. [PMID: 28208597 PMCID: PMC5334614 DOI: 10.3390/md15020034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/19/2017] [Accepted: 02/03/2017] [Indexed: 11/17/2022] Open
Abstract
Demosponges of the order Verongida such as Ianthella basta exhibit skeletons containing spongin, a collagenous protein, and chitin. Moreover, Verongida sponges are well known to produce bioactive brominated tyrosine derivatives. We recently demonstrated that brominated compounds do not only occur in the cellular matrix but also in the skeletons of the marine sponges Aplysina cavernicola and I. basta. Further investigations revealed the amino acid composition of the skeletons of A. cavernicola including the presence of several halogenated amino acids. In the present work, we investigated the skeletal amino acid composition of the demosponge I. basta, which belongs to the Ianthellidae family, and compared it with that of A. cavernicola from the Aplysinidae family. Seventeen proteinogenic and five non-proteinogenic amino acids were detected in I. basta. Abundantly occurring amino acids like glycine and hydroxyproline show the similarity of I. basta and A. cavernicola and confirm the collagenous nature of their sponging fibers. We also detected nine halogenated tyrosines as an integral part of I. basta skeletons. Since both sponges contain a broad variety of halogenated amino acids, this seems to be characteristic for Verongida sponges. The observed differences of the amino acid composition confirm that spongin exhibits a certain degree of variability even among the members of the order Verongida.
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32
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Pita L, Fraune S, Hentschel U. Emerging Sponge Models of Animal-Microbe Symbioses. Front Microbiol 2016; 7:2102. [PMID: 28066403 PMCID: PMC5179597 DOI: 10.3389/fmicb.2016.02102] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/12/2016] [Indexed: 12/30/2022] Open
Abstract
Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host–microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota.
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Affiliation(s)
- Lucia Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Sebastian Fraune
- Zoological Institute, Christian-Albrechts-University of Kiel (CAU), Kiel Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Christian-Albrechts-University of Kiel (CAU), KielGermany
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33
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Horn H, Slaby BM, Jahn MT, Bayer K, Moitinho-Silva L, Förster F, Abdelmohsen UR, Hentschel U. An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes. Front Microbiol 2016; 7:1751. [PMID: 27877161 PMCID: PMC5099237 DOI: 10.3389/fmicb.2016.01751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/19/2016] [Indexed: 11/18/2022] Open
Abstract
Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defense is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. This study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.
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Affiliation(s)
- Hannes Horn
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany
| | - Beate M Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany
| | - Martin T Jahn
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany
| | - Kristina Bayer
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - 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, Australia
| | - Frank Förster
- Department of Bioinformatics, University of WürzburgWürzburg, Germany; Center for Computational and Theoretical Biology, University of WürzburgWürzburg, Germany
| | - Usama R Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Minia UniversityMinia, Egypt
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Christian-Albrechts-Universität zu KielKiel, Germany
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Wray GA. Molecular clocks and the early evolution of metazoan nervous systems. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0046. [PMID: 26554040 DOI: 10.1098/rstb.2015.0046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation.
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Affiliation(s)
- Gregory A Wray
- Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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35
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Cunningham JA, Vargas K, Pengju L, Belivanova V, Marone F, Martínez-Pérez C, Guizar-Sicairos M, Holler M, Bengtson S, Donoghue PCJ. Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng'an Doushantuo biota. Proc Biol Sci 2016; 282:20151169. [PMID: 26180072 PMCID: PMC4528530 DOI: 10.1098/rspb.2015.1169] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular clock analyses estimate that crown-group animals began diversifying hundreds of millions of years before the start of the Cambrian period. However, the fossil record has not yielded unequivocal evidence for animals during this interval. Some of the most promising candidates for Precambrian animals occur in the Weng'an biota of South China, including a suite of tubular fossils assigned to Sinocyclocyclicus, Ramitubus, Crassitubus and Quadratitubus, that have been interpreted as soft-bodied eumetazoans comparable to tabulate corals. Here, we present new insights into the anatomy, original composition and phylogenetic affinities of these taxa based on data from synchrotron radiation X-ray tomographic microscopy, ptychographic nanotomography, scanning electron microscopy and electron probe microanalysis. The patterns of deformation observed suggest that the cross walls of Sinocyclocyclicus and Quadratitubus were more rigid than those of Ramitubus and Crassitubus. Ramitubus and Crassitubus specimens preserve enigmatic cellular clusters at terminal positions in the tubes. Specimens of Sinocyclocyclicus and Ramitubus have biological features that might be cellular tissue or subcellular structures filling the spaces between the cross walls. These observations are incompatible with a cnidarian interpretation, in which the spaces between cross walls are abandoned parts of the former living positions of the polyp. The affinity of the Weng'an tubular fossils may lie within the algae.
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Affiliation(s)
- John A Cunningham
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Kelly Vargas
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Liu Pengju
- Institute of Geology, Chinese Academy of Geological Sciences, 26 Baiwanzhuang Road, Beijing 100037, People's Republic of China
| | - Veneta Belivanova
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Carlos Martínez-Pérez
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK Department of Geology, University of Valencia, C/Dr. Moliner 50, Burjassot, Valencia 46100, Spain
| | | | - Mirko Holler
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Stefan Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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36
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Affiliation(s)
- David J Bottjer
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089-0740, United States
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37
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Fernandez-Valverde SL, Degnan BM. Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome. Sci Rep 2016; 6:22496. [PMID: 26931148 PMCID: PMC4773876 DOI: 10.1038/srep22496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/15/2016] [Indexed: 12/13/2022] Open
Abstract
The regulatory systems underlying animal development must have evolved prior to the emergence of eumetazoans (cnidarians and bilaterians). Although representatives of earlier-branching animals - sponges ctenophores and placozoans - possess most of the developmental transcription factor families present in eumetazoans, the DNA regulatory elements that these transcription factors target remain uncharted. Here we characterise the core promoter sequences, U1 snRNP-binding sites (5' splice sites; 5'SSs) and polyadenylation sites (PASs) in the sponge Amphimedon queenslandica. Similar to unicellular opisthokonts, Amphimedon's genes are tightly packed in the genome and have small introns. In contrast, its genes possess metazoan-like core promoters populated with binding motifs previously deemed to be specific to vertebrates, including Nrf-1 and Krüppel-like elements. Also as in vertebrates, Amphimedon's PASs and 5'SSs are depleted downstream and upstream of transcription start sites, respectively, consistent with non-elongating transcripts being short-lived; PASs and 5'SSs are more evenly distributed in bidirectional promoters in Amphimedon. The presence of bilaterian-like regulatory DNAs in sponges is consistent with these being early and essential innovations of the metazoan gene regulatory repertoire.
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Affiliation(s)
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia
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Hologenome analysis of two marine sponges with different microbiomes. BMC Genomics 2016; 17:158. [PMID: 26926518 PMCID: PMC4772301 DOI: 10.1186/s12864-016-2501-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 02/18/2016] [Indexed: 01/09/2023] Open
Abstract
Background Sponges (Porifera) harbor distinct microbial consortia within their mesohyl interior. We herein analysed the hologenomes of Stylissa carteri and Xestospongia testudinaria, which notably differ in their microbiome content. Results Our analysis revealed that S. carteri has an expanded repertoire of immunological domains, specifically Scavenger Receptor Cysteine-Rich (SRCR)-like domains, compared to X. testudinaria. On the microbial side, metatranscriptome analyses revealed an overrepresentation of potential symbiosis-related domains in X. testudinaria. Conclusions Our findings provide genomic insights into the molecular mechanisms underlying host-symbiont coevolution and may serve as a roadmap for future hologenome analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2501-0) contains supplementary material, which is available to authorized users.
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Aschenbrenner IA, Cernava T, Berg G, Grube M. Understanding Microbial Multi-Species Symbioses. Front Microbiol 2016; 7:180. [PMID: 26925047 PMCID: PMC4757690 DOI: 10.3389/fmicb.2016.00180] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/02/2016] [Indexed: 11/13/2022] Open
Abstract
Lichens are commonly recognized as a symbiotic association of a fungus and a chlorophyll containing partner, either green algae or cyanobacteria, or both. The fungus provides a suitable habitat for the partner, which provides photosynthetically fixed carbon as energy source for the system. The evolutionary result of the self-sustaining partnership is a unique joint structure, the lichen thallus, which is indispensable for fungal sexual reproduction. The classical view of a dual symbiosis has been challenged by recent microbiome research, which revealed host-specific bacterial microbiomes. The recent results about bacterial associations with lichens symbioses corroborate their notion as a multi-species symbiosis. Multi-omics approaches have provided evidence for functional contribution by the bacterial microbiome to the entire lichen meta-organism while various abiotic and biotic factors can additionally influence the bacterial community structure. Results of current research also suggest that neighboring ecological niches influence the composition of the lichen bacterial microbiome. Specificity and functions are here reviewed based on these recent findings, converging to a holistic view of bacterial roles in lichens. Finally we propose that the lichen thallus has also evolved to function as a smart harvester of bacterial symbionts. We suggest that lichens represent an ideal model to study multi-species symbiosis, using the recently available omics tools and other cutting edge methods.
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Affiliation(s)
- Ines A. Aschenbrenner
- Institute of Environmental Biotechnology, Graz University of TechnologyPetersgasse, Graz, Austria
- Institute of Plant Sciences, University of GrazGraz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of TechnologyPetersgasse, Graz, Austria
- Austrian Centre of Industrial Biotechnology – Gesellschaft mit beschränkter HaftungGraz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyPetersgasse, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of GrazGraz, Austria
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40
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Tian RM, Sun J, Cai L, Zhang WP, Zhou GW, Qiu JW, Qian PY. The deep-sea glass sponge Lophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur. Environ Microbiol 2016; 18:2481-94. [PMID: 26637128 DOI: 10.1111/1462-2920.13161] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/27/2015] [Indexed: 11/30/2022]
Abstract
Glass sponge (Hexactinellida, Porifera) is a special lineage because of its unique tissue organization and skeleton material. Structure and physiology of glass sponge have been extensively studied. However, our knowledge of the glass sponge-associated microbial community and of the interaction with the host is rather limited. Here, we performed genomic studies on the microbial community in the glass sponge Lophophysema eversa in seamount. The microbial community was dominated by an ammonia-oxidizing archaeum (AOA), a nitrite-oxidizing bacterium (NOB) and a sulfur-oxidizing bacterium (SOB), all of which were autotrophs. Genomic analysis on the AOA, NOB and SOB in the sponge revealed specific functional features of sponge-associated microorganisms in comparison with the closely related free-living relatives, including chemotaxis, phage defence, vitamin biosynthesis and nutrient uptake among others, which are related to ecological functions. The three autotrophs play essential roles in the cycles of carbon, nitrogen and sulfur in the microenvironment inside the sponge body, and they are considered to play symbiotic roles in the host as scavengers of toxic ammonia, nitrite and sulfide. Our study extends knowledge regarding the metabolism and the evolution of chemolithotrophs inside the invertebrate body.
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Affiliation(s)
- Ren-Mao Tian
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jin Sun
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Lin Cai
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Wei-Peng Zhang
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Guo-Wei Zhou
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Pei-Yuan Qian
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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41
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Guzman C, Conaco C. Comparative transcriptome analysis reveals insights into the streamlined genomes of haplosclerid demosponges. Sci Rep 2016; 6:18774. [PMID: 26738846 PMCID: PMC4704026 DOI: 10.1038/srep18774] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/26/2015] [Indexed: 11/23/2022] Open
Abstract
Sponges (Porifera) are one of the most ancestral metazoan groups. They are characterized by a simple body plan lacking the true tissues and organ systems found in other animals. Members of this phylum display a remarkable diversity of form and function and yet little is known about the composition and complexity of their genomes. In this study, we sequenced the transcriptomes of two marine haplosclerid sponges belonging to Demospongiae, the largest and most diverse class within phylum Porifera, and compared their gene content with members of other sponge classes. We recovered 44,693 and 50,067 transcripts expressed in adult tissues of Haliclona amboinensis and Haliclona tubifera, respectively. These transcripts translate into 20,280 peptides in H. amboinensis and 18,000 peptides in H. tubifera. Genes associated with important signaling and metabolic pathways, regulatory networks, as well as genes that may be important in the organismal stress response, were identified in the transcriptomes. Futhermore, lineage-specific innovations were identified that may be correlated with observed sponge characters and ecological adaptations. The core gene complement expressed within the tissues of adult haplosclerid demosponges may represent a streamlined and flexible genetic toolkit that underlies the ecological success and resilience of sponges to environmental stress.
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Affiliation(s)
- Christine Guzman
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, Philippines 1101
| | - Cecilia Conaco
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, Philippines 1101
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42
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Giles EC, Saenz-Agudelo P, Hussey NE, Ravasi T, Berumen ML. Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea. Ecol Evol 2015; 5:2487-502. [PMID: 26257865 PMCID: PMC4523348 DOI: 10.1002/ece3.1511] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 01/21/2023] Open
Abstract
A main goal of population geneticists is to study patterns of gene flow to gain a better understanding of the population structure in a given organism. To date most efforts have been focused on studying gene flow at either broad scales to identify barriers to gene flow and isolation by distance or at fine spatial scales in order to gain inferences regarding reproduction and local dispersal. Few studies have measured connectivity at multiple spatial scales and have utilized novel tools to test the influence of both environment and geography on shaping gene flow in an organism. Here a seascape genetics approach was used to gain insight regarding geographic and ecological barriers to gene flow of a common reef sponge, Stylissa carteri in the Red Sea. Furthermore, a small-scale (<1 km) analysis was also conducted to infer reproductive potential in this organism. At the broad scale, we found that sponge connectivity is not structured by geography alone, but rather, genetic isolation in the southern Red Sea correlates strongly with environmental heterogeneity. At the scale of a 50-m transect, spatial autocorrelation analyses and estimates of full-siblings revealed that there is no deviation from random mating. However, at slightly larger scales (100–200 m) encompassing multiple transects at a given site, a greater proportion of full-siblings was found within sites versus among sites in a given location suggesting that mating and/or dispersal are constrained to some extent at this spatial scale. This study adds to the growing body of literature suggesting that environmental and ecological variables play a major role in the genetic structure of marine invertebrate populations.
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Affiliation(s)
- Emily C Giles
- Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia
| | - Pablo Saenz-Agudelo
- Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia ; Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile Valdivia, Chile
| | | | - Timothy Ravasi
- Division of Biological and Environmental Sciences and Engineering, Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, 23599-6900, Saudi Arabia
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43
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Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges. Proc Natl Acad Sci U S A 2015; 112:4381-6. [PMID: 25713351 DOI: 10.1073/pnas.1423768112] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine sponges are major habitat-forming organisms in coastal benthic communities and have an ancient origin in evolution history. Here, we report significant accumulation of polyphosphate (polyP) granules in three common sponge species of the Caribbean coral reef. The identity of the polyP granules was confirmed by energy-dispersive spectroscopy (EDS) and by the fluorescence properties of the granules. Microscopy images revealed that a large proportion of microbial cells associated with sponge hosts contained intracellular polyP granules. Cyanobacterial symbionts cultured from sponges were shown to accumulate polyP. We also amplified polyphosphate kinase (ppk) genes from sponge DNA and confirmed that the gene was expressed. Based on these findings, we propose here a potentially important phosphorus (P) sequestration pathway through symbiotic microorganisms of marine sponges. Considering the widespread sponge population and abundant microbial cells associated with them, this pathway is likely to have a significant impact on the P cycle in benthic ecosystems.
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44
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Degnan SM. The surprisingly complex immune gene repertoire of a simple sponge, exemplified by the NLR genes: a capacity for specificity? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 48:269-74. [PMID: 25058852 DOI: 10.1016/j.dci.2014.07.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/08/2014] [Accepted: 07/14/2014] [Indexed: 05/20/2023]
Abstract
Most bacteria are not pathogenic to animals, and may instead serve beneficial functions. The requisite need for animals to differentiate between microbial friend and foe is likely borne from a deep evolutionary imperative to recognise self from non-self, a service ably provided by the innate immune system. Recent findings from an ancient lineage of simple animals - marine sponges - have revealed an unexpectedly large and diverse suite of genes belonging to one family of pattern recognition receptors, namely the NLR genes. Because NLRs can recognise a broad spectrum of microbial ligands, they may play a critical role in mediating the animal-bacterial crosstalk needed for sophisticated discrimination between microbes of various relationships. The building blocks for an advanced NLR-based immune specificity encoded in the genome of the coral reef sponge Amphimedon queenslandica may provide a specialisation and diversity of responses that equals, or even exceeds, that of vertebrate NLRs.
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Affiliation(s)
- Sandie M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Qld., Australia.
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45
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Tian RM, Lee OO, Wang Y, Cai L, Bougouffa S, Chiu JMY, Wu RSS, Qian PY. Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis. Front Microbiol 2015; 5:799. [PMID: 25642227 PMCID: PMC4294214 DOI: 10.3389/fmicb.2014.00799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/27/2014] [Indexed: 11/13/2022] Open
Abstract
Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2′,4,4′-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge.
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Affiliation(s)
- Ren-Mao Tian
- Divison of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - On On Lee
- Divison of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Yong Wang
- Divison of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Lin Cai
- Divison of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | - Salim Bougouffa
- Divison of Life Science, The Hong Kong University of Science and Technology Hong Kong, China
| | | | - Rudolf Shiu Sun Wu
- School of Biological Sciences, The University of Hong Kong Hong Kong, China ; State Key Laboratory of Marine Pollution, The City University of Hong Kong Hong Kong, China
| | - Pei-Yuan Qian
- Divison of Life Science, The Hong Kong University of Science and Technology Hong Kong, China ; State Key Laboratory of Marine Pollution, The City University of Hong Kong Hong Kong, China
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46
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Matzke-Karasz R, Neil JV, Smith RJ, Symonová R, Mořkovský L, Archer M, Hand SJ, Cloetens P, Tafforeau P. Subcellular preservation in giant ostracod sperm from an early Miocene cave deposit in Australia. Proc Biol Sci 2015; 281:rspb.2014.0394. [PMID: 24827442 DOI: 10.1098/rspb.2014.0394] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cypridoidean ostracods are one of a number of animal taxa that reproduce with giant sperm, up to 10 000 µm in length, but they are the only group to have aflagellate, filamentous giant sperm. The evolution and function of this highly unusual feature of reproduction with giant sperm are currently unknown. The hypothesis of long-term evolutionary persistence of this kind of reproduction has never been tested. We here report giant sperm discovered by propagation phase contrast X-ray synchrotron micro- and nanotomography, preserved in five Miocene ostracod specimens from Queensland, Australia. The specimens belong to the species Heterocypris collaris Matzke-Karasz et al. 2013 (one male and three females) and Newnhamia mckenziana Matzke-Karasz et al. 2013 (one female). The sperm are not only the oldest petrified gametes on record, but include three-dimensional subcellular preservation. We provide direct evidence that giant sperm have been a feature of this taxon for at least 16 Myr and provide an additional criterion (i.e. longevity) to test hypotheses relating to origin and function of giant sperm in the animal kingdom. We further argue that the highly resistant, most probably chitinous coats of giant ostracod sperm may play a role in delaying decay processes, favouring early mineralization of soft tissue.
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Affiliation(s)
- Renate Matzke-Karasz
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilian-University and GeoBio-Center, Richard-Wagner-Strasse 10, 80333 Munich, Germany
| | - John V Neil
- School of Civil Engineering and Physical Sciences, La Trobe University, PO Box 199, Bendigo, Victoria 3552, Australia
| | - Robin J Smith
- Lake Biwa Museum, Oroshimo 1091, Kusatsu, Shiga 525-0001, Japan
| | - Radka Symonová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Praha, Czech Republic
| | - Libor Mořkovský
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Praha, Czech Republic
| | - Michael Archer
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Suzanne J Hand
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Peter Cloetens
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
| | - Paul Tafforeau
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
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47
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Xiao S, Muscente AD, Chen L, Zhou C, Schiffbauer JD, Wood AD, Polys NF, Yuan X. The Weng'an biota and the Ediacaran radiation of multicellular eukaryotes. Natl Sci Rev 2014. [DOI: 10.1093/nsr/nwu061] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The rise of multicellularity represents a major evolutionary transition and it occurred independently in multiple eukaryote clades. Although simple multicellular organisms may have evolved in the Mesoproterozoic Era or even earlier, complex multicellular eukaryotes began to diversify only in the Ediacaran Period, just before the Cambrian explosion. Thus, the Ediacaran fossil record can provide key paleontological evidence about the early radiation of multicellular eukaryotes that ultimately culminated in the Cambrian explosion. The Ediacaran Weng'an biota in South China hosts exceptionally preserved eukaryote fossils, including various acanthomorphic acritarchs, pseudoparenchymatous thalli, tubular microfossils, and spheroidal fossils such as Megasphaera, Helicoforamina, Spiralicellula, and Caveasphaera. Many of these fossils have been interpreted as multicellular eukaryotes, although alternative interpretations have also been proposed. In this review, we critically examine these various interpretations, focusing particularly on Megasphaera, which has been variously interpreted as a sulfur-oxidizing bacterium, a unicellular protist, a mesomycetozoean-like holozoan, a volvocine green alga, a stem-group animal, or a crown-group animal. We conclude that Megasphaera is a multicellular eukaryote with evidence for cell-to-cell adhesion, a flexible membrane unconstrained by a rigid cell wall, spatial cellular differentiation, germ–soma separation, and programmed cell death. These features are inconsistent with the bacterium, unicellular protist, and mesomycetozoean-like holozoan interpretations. Thus, the surviving hypotheses, particularly the stem-group animal and algal interpretations, should be further tested with additional evidence. The Weng'an biota also hosts cellularly differentiated pseudoparenchymatous thalli with specialized reproductive structures indicative of an affinity with florideophyte red algae. The other Weng'an fossils reviewed here may also be multicellular eukaryotes, although direct cellular evidence is lacking in some and phylogenetic affinities are poorly constrained in others. The Weng'an biota offers many research opportunities to resolve the life histories and phylogenetic diversity of early multicellular eukaryotes and to illuminate the evolutionary prelude to the Cambrian explosion.
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Affiliation(s)
- Shuhai Xiao
- Department of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - A. D. Muscente
- Department of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lei Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanming Zhou
- Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - James D. Schiffbauer
- Department of Geological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Andrew D. Wood
- Advanced Research Computing, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Nicholas F. Polys
- Advanced Research Computing, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
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48
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Cuvelier ML, Blake E, Mulheron R, McCarthy PJ, Blackwelder P, Thurber RLV, Lopez JV. Two distinct microbial communities revealed in the sponge Cinachyrella. Front Microbiol 2014; 5:581. [PMID: 25408689 PMCID: PMC4219487 DOI: 10.3389/fmicb.2014.00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022] Open
Abstract
Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.
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Affiliation(s)
- Marie L. Cuvelier
- Biological Sciences Department, Florida International UniversityMiami, FL, USA
| | - Emily Blake
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
| | - Rebecca Mulheron
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
| | - Peter J. McCarthy
- Marine Biomedical and Biotechnology Research, Harbor Branch Oceanographic Institute, Florida Atlantic UniversityFort Pierce, FL, USA
| | - Patricia Blackwelder
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
- Marine Geosciences, Rosenstiel School of Marine and Atmospheric Science, University of MiamiMiami, FL, USA
| | | | - Jose V. Lopez
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
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Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review. Mar Drugs 2014; 12:5089-122. [PMID: 25272328 PMCID: PMC4210886 DOI: 10.3390/md12105089] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/16/2022] Open
Abstract
Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.
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50
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Tian RM, Wang Y, Bougouffa S, Gao ZM, Cai L, Bajic V, Qian PY. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge. Environ Microbiol 2014; 16:3548-61. [DOI: 10.1111/1462-2920.12586] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Ren-Mao Tian
- Divison of Life Science; Hong Kong University of Science and Technology; Hong Kong
| | - Yong Wang
- Divison of Life Science; Hong Kong University of Science and Technology; Hong Kong
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; San Ya Hai Nan China
| | - Salim Bougouffa
- Computational Bioscience Research Center (CBRC); King Abdullah University of Science and Technology (KAUST); Thuwal Saudi Arabia
| | - Zhao-Ming Gao
- Divison of Life Science; Hong Kong University of Science and Technology; Hong Kong
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; San Ya Hai Nan China
| | - Lin Cai
- Divison of Life Science; Hong Kong University of Science and Technology; Hong Kong
| | - Vladimir Bajic
- Computational Bioscience Research Center (CBRC); King Abdullah University of Science and Technology (KAUST); Thuwal Saudi Arabia
| | - Pei-Yuan Qian
- Divison of Life Science; Hong Kong University of Science and Technology; Hong Kong
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