Symbiosis insights through metagenomic analysis of a microbial consortium

Abstract

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here, we used a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut, and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulfur-oxidizing and sulfate-reducing bacteria, all of which are capable of carbon fixation, providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model which describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments which it inhabits. 3 Symbiosis plays a major role in shaping the evolution and diversity of eukaryotic organisms 1 . Remarkably, only recently has there been an emerging recognition that most eukaryotic organisms are intimately associated with a complex community of beneficial microbes that are essential for their development, health, and interactions with the environment 2 . This renaissance in symbiosis research stems from advances in molecular approaches that have enabled the study of natural microbial consortia using cultivationindependent methods [3][4][5] . Metagenomic analyses have provided a new dimension in the study of community organization and metabolism in natural microbial communities [6][7][8][9][10] .To date, however, genomic analyses of symbiotic microbes from eukaryotes have been confined to individual strains (for the only exception see Wu et al. 11), limiting our ability to understand the intricate interactions involving communication, competition, and resource partitioning that shape symbiotic microbial communities.Here, we used random shotgun sequencing and nucleotide-signature based binning to study the symbiotic community in Olavius algarvensis. This marine worm belongs to a group of oligochaetes (phylum Annelida) that lack a mouth, gut, and anus, and are unique among annelid worms in having reduced their nephridial excretory system 12 . They live in obligate and species-specific associations with multiple extracellular bacterial endosymbionts located just below the worm cuticle 12 . Since the symbionts have yet to be grown in culture, their phylogeny has only been accessible through 16S rRNA analysis and fluorescence in situ hybridization (FISH) 13,14 . O. algarvensis lives in coastalMediterranean sediments and harbors a chemoautotrophic sulfur-oxidizing Gammaproteobacterium ( 1 symbiont) and a deltaproteobacterial sulfate reducer ( 1 symbiont), recently shown to be engaged in an endosymbiotic sulfur cycle 14. An additional gamma-and deltaproteobacterial symbiont ( 3 and 4 symbionts) of ...

Molecular eco-systems biology: towards an understanding of community function

“…Similar spatio-temporal variation has been observed from a functional point of view [69]. Comparative metagenomics approaches [24,25,29] recently charted the molecular basis of spatial functional variation of environments from the kilometre [25,42,70] to centimetre [38] and even millimetre scale [71] (Fig.3), and with timeseries metagenomics studies underway [28], studying temporal (and spatio-temporal [72]) aspects should become possible at the molecular level. The recent development of phylochips, metagenome-based microarrays and high-throughput sequencing-based monitoring will further expedite the amount of dynamic data that is available (for example, Refs [73][74][75][76][77]; reviewed in Refs [78,79]).…”

“…group III, could be a cornerstone species that carries out the fixation of nitrogen for the other community members that lack these pathways [26]. In an analysis of four gut symbionts in a gutless worm, evidence was found for syntrophic cycling of sulphate and sulphide (or other intermediate sulphur compounds) between gammaproteobacterial and deltaproteobacterial symbionts and for the existence of additional hydrogen syntrophy [38]. Finally, metabolic network reconstruction from the genome analysis of two endosymbionts (Candidatus Baumannia cicadellinicola and Candidatus Sulcia muelleri) in a sharpshooter revealed not only their role in providing nutrients, vitamins and cofactors to the host, but also their extensive metabolic cooperation -for example, in amino acid biosynthesis and complementing genome reduction between the two bacteria [39,40].…”

Proteomics of marine bacteria

“…Low and high salt concentrations 2-D PAGE and MALDI-MS [52] Heat shock 2-D DIGE and [ 35 S]methionine pulse-labelling combined with 2-D PAGE and MALDI-MS [54] Biofilm-specific proteins 2-D PAGE and MALDI-MS/MS or nano-LC-ESI-MS [79] Aerobic and anaerobic conditions 2-D PAGE and MALDI-MS [90] Cell isolation of symbiotic cells Cell density centrifugation to separate bacterial cell populations [14,15] Cell disruption of mixed bacterial assemblages Sonication with different lysis buffers [122] Image analysis Quantitative analysis of 2-D maps [37] Gel-image warping and quantitative analysis [38] 2 Marine genome sequencing projects…”

“…With 7.145 megabases, R. baltica SH1 has one of the largest circular bacterial genomes sequenced so far. The partial sequencing of the first genomes of individual uncultured marine bacteria, the symbionts of the deep sea tube worm Riftia pachyptila [14,127] and of the marine oligochaete Olavius algarvensis were recently published [15].…”

Metagenomics: A Quantum Jump from Bacterial Genomics

“…Two nearly complete and two partial genomes of the oligochaetes' predominant symbionts were assembled using shotgun sequencing of a bacteria-enriched sample combined with nucleotide-signature based binning. Metabolic pathway reconstruction from the sequenced genomes revealed all the four symbionts to be capable of autotrophic carbon fixation and provide multiple sources of organic carbon to their host as two of them are sulfuroxidizing and two sulfate-reducing bacteria [20].…”