Bacterial Community Dynamics in the Marine Sponge Rhopaloeides odorabile Under In Situ and Ex Situ Cultivation

Webster, Nicole S.; Cobb, Rose; Soo, Rochelle M.; Anthony, Shelley L.; Battershill, Christopher N.; Whalan, Steve W; Evans-Illidge, Elizabeth

doi:10.1007/s10126-010-9300-4

Cited by 56 publications

(52 citation statements)

References 33 publications

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“…This is consistent with the previous study of bacterial community by Kim and colleagues (2008), where they found WS3 to be the most abundant candidate phylum in the tidal flat sediment geographically close to our sampling site. The candidate phylum WS3 has been reported to be present in a variety of niches such as mud volcano (Kormas et al, 2008), marine sponge (Webster et al, 2010), sulfur-rich spring (Elshahed et al, 2007), anaerobic sludge digester (Chouari et al, 2005), and rice roots (Derakshani et al, 2001). With pyrosequencing, the percentage of candidate divisions was shown to decrease with depth from 1.7% at the surface to 1.2% at 5 m depth, and to 1.2% at 20 m depth (Fig.…”

Section: (A) (B)mentioning

confidence: 87%

Comparative approach to capture bacterial diversity of coastal waters

Kim

Yoon

et al. 2011

J Microbiol.

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Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1 % of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.

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Section: (A) (B)mentioning

confidence: 87%

Comparative approach to capture bacterial diversity of coastal waters

Kim

Yoon

et al. 2011

J Microbiol.

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“…Marine sponges are ecologically important components of the benthic community due to their wide diversity and high biomass (Ilan et al, 2004; de Goeij et al, 2013). In addition, they play a key functional role linking benthic and pelagic ecosystems, as they efficiently remove particulate organic carbon from the seawater (Díaz and Rützler, 2001; Ilan et al, 2004; Webster et al, 2011). Indeed, these sessile invertebrates are able to filter considerable amounts of seawater; a 1 kg sponge can filter up to 24000 L of water per day (Vogel, 1977).…”

Section: Introductionmentioning

confidence: 99%

Two distinct microbial communities revealed in the sponge Cinachyrella

et al. 2014

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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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“…Other studies have reported higher levels of variability across seasons (74) and when repeatedly sampling the same individuals over time (3), indicating some degree of symbiont fluctuation over time and individual variation among hosts. The prospect of sponge aquaculture for the production of bioactive metabolites has prompted investigations of host-symbiont stability under ex situ aquarium conditions, revealing high symbiont stability over short-term time scales (11 days to 12 weeks [23,67]), while longer-term maintenance (6 months to 2 years) can result in substantial shifts in symbiont composition (39,40,67). Additional studies of temporal variation in sponge-associated bacteria under natural conditions will aid future aquaculture efforts by determining natural variation in the sponge microbiota and its consequences for host-symbiont dynamics.…”

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confidence: 99%

Stability of Sponge-Associated Bacteria over Large Seasonal Shifts in Temperature and Irradiance

Erwin

Pita

López‐Legentil

et al. 2012

Appl Environ Microbiol

165

158

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bComplex microbiomes reside in marine sponges and consist of diverse microbial taxa, including functional guilds that may contribute to host metabolism and coastal marine nutrient cycles. Our understanding of these symbiotic systems is based primarily on static accounts of sponge microbiota, while their temporal dynamics across seasonal cycles remain largely unknown. Here, we investigated temporal variation in bacterial symbionts of three sympatric sponges (Ircinia spp.) over 1.5 years in the northwestern (NW) Mediterranean Sea, using replicated terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of bacterial 16S rRNA gene sequences. Bacterial symbionts in Ircinia spp. exhibited host species-specific structure and remarkable stability throughout the monitoring period, despite large fluctuations in temperature and irradiance. In contrast, seawater bacteria exhibited clear seasonal shifts in community structure, indicating that different ecological constraints act on free-living and on symbiotic marine bacteria. Symbiont profiles were dominated by persistent, sponge-specific bacterial taxa, notably affiliated with phylogenetic lineages capable of photosynthesis, nitrite oxidation, and sulfate reduction. Variability in the sponge microbiota was restricted to rare symbionts and occurred most prominently in warmer seasons, coincident with elevated thermal regimes. Seasonal stability of the sponge microbiota supports the hypothesis of host-specific, stable associations between bacteria and sponges. Further, the core symbiont profiles revealed in this study provide an empirical baseline for diagnosing abnormal shifts in symbiont communities. Considering that these sponges have suffered recent, episodic mass mortalities related to thermal stresses, this study contributes to the development of model sponge-microbe symbioses for assessing the link between symbiont fluctuations and host health. Sponges are sessile invertebrates that form a species-rich phylum at the base of the metazoan tree of life (Ͼ8,500 valid species [65]). Renowned for their efficient filter-feeding capabilities and bioactive secondary metabolite production, sponges have important ecological and biotechnological relevance as major players in marine nutrient cycles (11,12,26) and the most prolific producers of marine natural products (Ͼ6,600 secondary metabolites [16]). The discovery and characterization of diverse microbial symbionts inhabiting the sponge body have prompted the adoption of the holobiont concept, thereby incorporating microbial symbionts in the study of sponge ecology and evolution (55). The resulting field of sponge microbiology has grown rapidly in the past 2 decades (59) and revealed a tight ecological link between host health and symbiont composition. Indeed, sponge-associated microbes have been implicated in host metabolism and growth (20,22,75), chemical defense production (21), and susceptibility to biotic (e.g., disease) and abiotic (e.g., temperature stress) stressors (33,66,72).The remarkable...

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Bacterial Community Dynamics in the Marine Sponge Rhopaloeides odorabile Under In Situ and Ex Situ Cultivation

Cited by 56 publications

References 33 publications

Comparative approach to capture bacterial diversity of coastal waters

Comparative approach to capture bacterial diversity of coastal waters

Two distinct microbial communities revealed in the sponge Cinachyrella

Stability of Sponge-Associated Bacteria over Large Seasonal Shifts in Temperature and Irradiance

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