Environmental shaping of sponge associated archaeal communities

Abstract

Background: Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood.

Methodology/principal findings: We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA) gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA) generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum.

Conclusion/significance: The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition of their associated archaeal communities, thereby improving their fitness in impacted environments.

Figure 1. Location of sampling sites, seawater trophic status and planktonic microbiological parameters in Rio de Janeiro.

(A) The location of Guanabara Bay in South America is indicated on the map (upper left corner). The map on the upper right corner shows the location of Guanabara Bay in reference to Rio de Janeiro state. The lower panel shows a detailed map of Guanabara Bay and the location of the two sampling sites: the pillar 92 of the Rio-Niterói Bridge, the inner bay site (P92) and the Cagarras Archipelago (CA), the outer bay site. (B) Ammonium, phosphate and chlorophyll a concentrations in seawater inside (black bars) and outside Guanabara Bay (gray bars). (C) Planktonic prokaryotic abundance and production inside (black bars) and outside the bay (gray bars).

Figure 2. Sponge species, population and community structure.

(A) Hymeniacidon heliophila (B) Paraleucilla magna (C) Petromica citrina (D) Indexes of whole sponge community structure: Shannon's diversity H' (bits per individual), species richness (number of species) and total sponge density (number of individuals per square meter) (E) Abundance of H. heliophila (H.h.), P. magna (P.m.) and P. citrina (P.c.) (number of individuals per square meter) (F) Dominance (% of total sponge cover) of H. heliophila, P. magna and P. citrina inside (black columns) and outside Guanabara Bay (gray columns). N.S., not significant. Error bars  =  standard deviation.

Figure 3. Planktonic archaeal communities.

(A) Phylogenetic construction: Neighbour-joining 16S rRNA unrooted tree (•) inner bay (P92) clones (○) Cagarras Archipelago (CA) clones (B) Rarefaction analysis at 97% stringency (•) inner bay (P92) sequences (○) Cagarras Archipelago (CA) sequences.

Figure 4. Sponge Crenarchaeota communities.

(A) Neighbour-joining 16S rRNA phylogenetic tree. Sponge archaeal clones (▪) HhP92, (□) HhCA, (▴) PmP92, (Δ) PmCA and (◊) PcCA Venn diagram with OTUs grouped at 97% similarity in (B) Archaea related to seawater and sponges from the Cagarras Archipelago and (C) Archaea related to seawater and sponges from P92. Hh, Hymeniacidon heliophila; Pm, Paraleucilla magna; Pc, Petromica citrina; CA, Cagarras Archipelago; P92, inner bay site.

Figure 5. Phylogenetic relationships of sponge archaeal amoA genes.

Unrooted neighbour-joining phylogenetic tree (▪) HhP92, (□) HhCA, (Δ) PmCA and (◊) PcCA. Hh, Hymeniacidon heliophila; Pm, Paraleucilla magna; Pc, Petromica citrina; CA, Cagarras Archipelago; P92, inner bay site.

Figure 6. Match between archaeal communities in sponges and seawater samples.

(A) Similarity between archaeal communities. Principal coordinates plots (PCA) were generated using the pairwise unweighted UniFrac distances. (B) Community tree showing the similarity of the samples under the Yue & Clayton theta structural diversity measure. Hh, Hymeniacidon heliophila; Pm, Paraleucilla magna; Pc, Petromica citrina; SW, seawater; CA, Cagarras Archipelago; P92, inner bay site.