DNA‐stable isotope probing (DNA‐SIP) identifies marine sponge‐associated bacteria actively utilizing dissolved organic matter (DOM)

Abstract

Sponges possess exceptionally diverse associated microbial communities and play a major role in (re) cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge-associated community structure with DOM utilization is essential to understand host-microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA-stable isotope probing (DNA-SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled ( 12 C) and labelled ( 13 C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA-SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge-associated bacteria to the consumption of DOM.

Meta-transcriptomic comparison of two sponge holobionts feeding on coral- and macroalgal-dissolved organic matter

“…Additionally, other transcripts related to carbohydrate degradation pathways were upregulated in the coral- compared to the macroalgal-DOM treatment, including the gene encoding for malate dehydrogenase (MDH) , another enzyme that takes part in the TCA cycle, glucose 1-dehydrogenase (DHG) , which is involved in the PP pathway, and a phosphoglycerate mutase (GPMA) that contributes to glycolysis/gluconeogenesis. This corroborates our previous finding in which we identified bacterial groups with a predicted genomic repertoire for TCA cycle, glycolysis and PP pathway to be active DOM incorporators in P. angulospiculatus [ 29 ]. Furthermore, in the coral-DOM treatment we found activation of fatty-acid biosynthesis through expression of acyl carrier protein (ACP) [ 111 ], and of aromatic amino acids biosynthesis, through expression of 3-phosphoshikimate 1-carboxyvinyltransferase (AROA) [ 112 ].…”

“…However, to confirm putative physiological responses and metabolic pathways employed by both host and associated microbiota and transcend ‘potential functions’ of sponges derived from metagenomics studies, it is required that molecular sequence data are coupled to hypothesis- driven experimental studies [ 28 ]. Recently, sponge-associated bacterial taxa of the sponge Plakortis angulospiculatus were shown to have an active metabolism in DOM processing by coupling DNA sequencing and stable isotope probing (DNA-SIP), for the first time in a marine holobiont [ 29 ]. Transcriptional responses to DOM-feeding by sponge host and its associated microbiota are at present not yet described.…”

Anthracene and Pyrene Biodegradation Performance of Marine Sponge Symbiont Bacteria Consortium

“…Three different bacterial stocks were utilized, and their genotypes were determined using the PCR technique. Total DNA from sponge symbionts was extracted and amplified using a universal primer of the 16S rRNA gene with the forward sequence 5 -CCAGCAGCCGCGGTAATACG-3 attached to nucleotide bases 518-537 and the reverse sequence 5 -ATCGG(C/T)TACCTTGTTACGACTTC-3 attached to nucleotide bases 1513-1491 [11,28]. Marine sponge symbiont bacteria Sp1-Bc, Sp2-Ps, and Sp3-Ac (Table 3), methanol pa, n-hexane for GC, anthracene CAS number 000120-12-7 and pyrene CAS number 000129-00-0 (Supelco, Bellefonte, PA, USA), Na 2 SO 4 pa, aquabides, physiological 0.9% NaCl (commercially obtained, Supelco), materials for sponge morphology analysis, materials for standard biochemical tests following the guidelines in [59], and materials for genotypic analysis of bacterial isolates were also obtained.…”

“…This mucus is thought to be utilized by sponges to defend themselves against predators in their environments, including the presence of poisonous PAHs and heavy metals [11,26]. Fourth, sponges are able to absorb carbon components and convert them into energy for activities, including being able to absorb heavy metals [27][28][29][30]. Some scientific data have suggested this adaptability of sponges to be due to their old civilization.…”

Actinobacteria Associated with Marine Invertebrates: Diversity and Biological Significance

“…The phylum Porifera harbor dense and diverse bacterial communities. According to the literature review, about 40% of the sponge biomass was due to their associated bacteria [18]. The sponges are recognized for their potential source of bioactive metabolites.…”