Marine sponges as Chloroflexi hot-spots: Genomic insights and high resolution visualization of an abundant and diverse symbiotic clade

Abstract

Chloroflexi represent a widespread, yet enigmatic bacterial phylum. Meta-and single cell genomics were performed to shed light on the functional gene repertoire of Chloroflexi symbionts from the HMA sponge 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, and amino acid utilization as nutrient source by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding for co-factor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPRs-Cas systems, eukaryote-like repeat proteins and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by FISH-CLEM method. Chloroflexi cells were generally rod-shaped and about 1 μm in length, albeit displayed different and characteristic cellular morphotypes per each class. The extensive potential for carbohydrate degradation has been reported previously for Ca. 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 also contribute to DOM re-cycling and primary productivity in reef ecosystems via a pathway termed the “sponge loop”.

Vertical transmission of sponge microbiota is inconsistent and unfaithful

“…Many of the sponge-associated phyla include microbes with known symbiotic features and functional capabilities. For example, members of Poribacteria and Chlo-roflexi harbor eukaryote-like protein domains which are suspected to be involved in preventing phagocytosis by the sponge host [54, 55]. Several genomic features in Chloroflexi are related to energy and carbon converting pathways, including amino and fatty acid metabolism and respiration, that directly benefit the sponge host [55].…”

“…For example, members of Poribacteria and Chlo-roflexi harbor eukaryote-like protein domains which are suspected to be involved in preventing phagocytosis by the sponge host [54, 55]. Several genomic features in Chloroflexi are related to energy and carbon converting pathways, including amino and fatty acid metabolism and respiration, that directly benefit the sponge host [55]. Microbes from PAUC34f have the capacity to produce, transport and store polyphosphate granules, likely representing a phosphate reservoir for the sponge host in periods of deprivation [56].…”

Ecological and biotechnological aspects of Aplysina-associated microorganisms

“…This sponge species can be maintained in aquaria for several months, allowing investigations on nutrient fluxes (Maldonado et al, 2012), oxygen transport (Hoffmann et al, 2008), secondary metabolite production dynamics (Gerçe et al, 2009) and bacterial uptake (Wehrl et al, 2007). Furthermore, cumulative genomic information and advanced imaging techniques have deepened our understanding of this sponge's holobiont (Bayer, Kamke, et al, 2014;Burgsdorf et al, 2015;Jahn et al, 2016;Bayer et al, 2018;.…”

“…The knowledge on symbiont functions remains limited to date which is partly due to the fact that all of the highly abundant sponge symbionts remain recalcitrant to cultivation. Recent advances in multi-omics techniques however have revealed genetic features of sponge-associated microorganisms that facilitate their symbiotic lifestyle and contribute to the sponge metabolism Astudillo-García et al, 2018;Bayer et al, 2018;Karimi et al, 2018;Kiran et al, 2018;Podell et al, 2019). Some of these processes are illustrated in Figure 5, 1-5, and a few selected symbiotic taxa and their functions are discussed below.…”

“…Chloroflexi represent a taxonomically and physiologically diverse microbial phylum and include highly predominant symbionts of many high-microbial-abundance sponges (Schmitt et al, 2011). As sponge symbionts, they might synthesize amino acids from ammonia, aid in co-factor biosynthesis and secondary metabolite production (Sacristán-Soriano et al, 2011;Bayer et al, 2018), while degrading sponge-derived carbohydrates .…”