Environmental Shaping of Sponge Associated Archaeal Communities

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

Bacterial community composition shifts in the gut of Periplaneta americana fed on different lignocellulosic materials

ABSTRACT: Cockroaches are insects that can accommodate diets of different composition, including lignocellulosic materials. Digestion of these compounds is achieved by the insect’s own enzymes and also by enzymes produced by gut symbionts. The presence of different and modular bacterial phyla on the cockroach gut tract suggests that this insect could be an interesting model to study the organization of gut bacterial communities associated with the digestion of different lignocellulosic diets. Thus, changes in the diversity of gut associated bacterial communities of insects exposed to such diets could give useful insights on how to improve hemicellulose and cellulose breakdown systems. In this work, through sequence analysis of 16S rRNA clone libraries, we compared the phylogenetic diversity and composition of gut associated bacteria in the cockroach Periplaneta americana collected in the wild-types or kept on two different diets: sugarcane bagasse and crystalline cellulose. These high fiber diets favor the predominance of some bacterial phyla, such as Firmicutes, when compared to wild-types cockroaches. Our data show a high bacterial diversity in P. americana gut, with communities composed mostly by the phyla Bacteroidetes, Firmicutes, Proteobacteria and Synergistetes. Our data show that the composition and diversity of gut bacterial communities could be modulated by diet composition. The increased presence of Firmicutes in sugarcane bagasse and crystalline cellulose-fed animals suggests that these bacteria are strongly involved in lignocellulose digestion in cockroach guts. BACKGROUND: Cockroaches are omnivorous animals that can incorporate in their diets food of different composition, including lignocellulosic materials. Digestion of these compounds is achieved by the insect’s own enzymes and also by enzymes produced by gut symbiont. However, the influence of diet with different fiber contents on gut bacterial communities and how this affects the digestion of cockroaches is still unclear. The presence of some bacterial phyla on gut tract suggests that cockroaches could be an interesting model to study the organization of gut bacterial communities during digestion of different lignocellulosic diets. Knowledge about the changes in diversity of gut associated bacterial communities of insects exposed to such diets could give interesting insights on how to improve hemicellulose and cellulose breakdown systems. METHODOLOGY/PRINCIPAL FINDINGS: We compared the phylogenetic diversity and composition of gut associated bacteria in the cockroach P. americana caught on the wild or kept on two different diets: sugarcane bagasse and crystalline cellulose. For this purpose we constructed bacterial 16S rRNA gene libraries which showed that a diet rich in cellulose and sugarcane bagasse favors the predominance of some bacterial phyla, more remarkably Firmicutes, when compared to wild cockroaches. Rarefaction analysis, LIBSHUFF and UniFrac PCA comparisons showed that gene libraries of wild insects were the most diverse, followed by sugarcane bagasse fed and then cellulose fed animals. It is also noteworthy that cellulose and sugarcane bagasse gene libraries resemble each other. CONCLUSION/SIGNIFICANCE: Our data show a high bacterial diversity in P. americana gut, with communities composed mostly by the phyla Bacteroidetes, Firmicutes, Proteobacteria and Synergistetes. The composition and diversity of gut bacterial communities could be modulated by font of diet composition. The increased presence of Firmicutes in sugarcane bagasse and crystalline cellulose-fed animals suggests that these bacteria are strongly involved in lignocellulose digestion in cockroach guts

Planktonic archaeal communities.

<p>(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.</p

Match between archaeal communities in sponges and seawater samples.

<p>(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, <i>Hymeniacidon heliophila</i>; Pm, <i>Paraleucilla magna</i>; Pc, <i>Petromica citrina</i>; SW, seawater; CA, Cagarras Archipelago; P92, inner bay site.</p

Sponge <i>Crenarchaeota</i> communities.

<p>(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) <i>Archaea</i> related to seawater and sponges from the Cagarras Archipelago and (C) <i>Archaea</i> related to seawater and sponges from P92. Hh, <i>Hymeniacidon heliophila</i>; Pm, <i>Paraleucilla magna</i>; Pc, <i>Petromica citrina</i>; CA, Cagarras Archipelago; P92, inner bay site.</p

Phylogenetic relationships of sponge archaeal <i>amoA</i> genes.

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

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

<p>(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 <i>a</i> 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).</p

Sponge species, population and community structure.

<p>(A) <i>Hymeniacidon heliophila</i> (B) <i>Paraleucilla magna</i> (C) <i>Petromica citrina</i> (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 <i>H. heliophila</i> (<i>H.h</i>.), <i>P. magna</i> (<i>P.m.</i>) and <i>P. citrina</i> (<i>P.c</i>.) (number of individuals per square meter) (F) Dominance (% of total sponge cover) of <i>H. heliophila, P. magna</i> and <i>P. citrina</i> inside (black columns) and outside Guanabara Bay (gray columns). N.S., not significant. Error bars  =  standard deviation.</p