Pyrosequencing of Bacterial Symbionts within Axinella corrugata Sponges: Diversity and Seasonal Variability

Abstract

Background Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge “holobiont” system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. Methodology/Principal Findings We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata , from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs). Approximately 65,550 rRNA sequences (24%) could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species ( Amphimedon compressa ), and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata- specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata , comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. Conclusions/Significance Slight shifts in several bacterial taxa were observed between communities sampled during spring and fall seasons. New 16 S rDNA sequences and concomitant identifications greatly expand the microbial community profile for this model reef sponge, and will likely be useful as a baseline for any future comparisons regarding sponge microbial community dynamics.

Draft Genomes Shed Light on the Dual Bacterial Symbiosis that Dominates the Microbiome of the Coral Reef Sponge Amphimedon queenslandica

“…HK1, have been reported in taxonomically distant sponges that live at varying latitudes and depths (Taylor et al, 2007b;Jensen et al, 2008;Kennedy et al, 2008;Giles et al, 2012;Radax et al, 2012;KarlinskaBatres and Wörheide, 2013;Pita et al, 2013;Olson et al, 2014;Della Sala et al, 2014). Furthermore, other studies on sponge symbionts have recorded the presence of both known and novel Chromatiales representatives belonging to either the Ectothiorhodospiraceae or Chromatiaceae family (Imhoff and Trüper, 1976;White et al, 2012), as well as sulfur-oxidizing bacteria from the Alphaproteobacteria class (Rhodospirillaceae, Rhodobacteraceae) and the phylum Chlorobi (Imhoff and Trüper, 1976;Bondarev et al, 2013).…”

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

“…The general consensus is that sponge-microbe associations are largely stable over temporal scales (56), including epibionts (31), cultivatable symbionts (68), and entire bacterial communities (57,60,61,73). 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.…”

Bacterial Diversity of the South Pacific Sponge, Dactylospongia metachromia Based on DGGE Fingerprinting

“…미생물 군집구조의 분석에는 16S rDNA에 기반한 PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis), T-RFLP (terminal-restriction fragment length polymorphism), pyrosequencing 등 다양한 분자적 방법들이 이용되고 있으며, 배 양(culture-dependent)과 비배양(culture-independent)에 근거하여 군집 분석이 이루어지고 있다 (Jackson et al, 2012;White et al, 2012). 해면 공생미생물은 그 수와 종류에 있어 매우 풍부하고 다양하여 29개의 문에 이른다 (Dupont et al, 2013 …”