Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons

Abstract

The phylogenetic diversity of microorganisms in marine sponges is becoming increasingly well described, yet relatively little is known about the activities of these symbionts. Given the seemingly favourable environment provided to microbes by their sponge hosts, as indicated by the extraordinarily high abundance of sponge symbionts, we hypothesized that the majority of spongeassociated bacteria are active in situ. To test this hypothesis we compared, for the first time in sponges, 16S rRNA gene-vs 16S rRNA-derived bacterial community profiles to gain insights into symbiont composition and activity, respectively. Clone libraries revealed a highly diverse bacterial community in Ancorina alata, and a much lower diversity in Polymastia sp., which were identified by electron microscopy as a high-and a low-microbial abundance sponge, respectively. Substantial overlap between DNA and RNA libraries was evident at both phylum and phylotype levels, indicating in situ activity for a large fraction of sponge-associated bacteria. This active fraction included uncultivated, sponge-specific lineages within, for example, Actinobacteria, Chloroflexi and Gemmatimonadetes. This study shows the potential of RNA vs DNA comparisons based on the 16S rRNA gene to provide insights into the activity of sponge-associated microorganisms.

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

“…It seems that these candidate phyla are generally not diverse but widespread among sponges. The SAUL lineage was found before in sponges (Taylor et al, 2007;Kamke et al, 2010) and, according to previous phylogenetic analyses, belongs to the Planctomycetes-VerrucomicrobiaChlamydiae (PVC) superphylum (Wagner and Horn 2006). However, it remains unclear whether the SAUL lineage falls within one of the phyla in this group or whether it represents a novel candidate phylum alongside Poribacteria and WS3 in the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum.…”

“…There are four notable exceptions with much fewer Plus-OTUs: Polymastia sp., Cymbastela coralliophila, Stylissa massa and Xestospongia sp. A possible explanation, at least for the first two mentioned sponges, is that they are low microbial abundance sponges that contain less diverse microbiota with a different compositional profile to high microbial abundance sponges (Hentschel et al, 2003;Kamke et al, 2010). The core bacterial community consists of only three 97%, eight 95% and 18 different 90% OTUs (Table 2).…”

“…The term 'sponge-specific' was introduced for these clusters to describe a phylogenetically complex community that is repeatedly detected in sponges around the world but that is different from microbial seawater communities (Hentschel et al, 2002;Taylor et al, 2007). Interestingly, sponge-specific microbes are mainly found in high microbial abundance sponges whereas low microbial abundance sponges usually have a much lower microbial diversity and a different microbial profile (Hentschel et al, 2006;Kamke et al, 2010). Given the observed uniformity of spongespecific communities, the aim of this study was to identify geographical or host-dependent bacterial subpopulations in sponges and to define the bacterial core community that is shared among most sponges as well as the species-specific community that is unique to a certain sponge species.…”

Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins

“…Corinaldesi et al 2014). Based on these considerations, we elected to more closely target the metabolically--active fraction of the prokaryotic communities inhabiting the sediments of three DHABs by investigating the diversity of bulk rRNA as a general marker of metabolic activity (Campbell et al 2009;Kamke et al 2010;Jones & Lennon 2011;Blazewicz et al 2013;Kang et al 2013). We recognize that this approach runs the risk of missing taxa that are alive, but whose activity levels are so low that their signatures may not appear in the rRNA libraries.…”

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

“…Historically, rRNA analyses have been used to quantify populations' growth rates in mixed microbial communities (for example, Poulsen et al, 1993;Muttray et al, 2001), but recent application has shifted toward the more qualitative approach using rRNA to identify currently active microbial populations in a mixed community (for example, Jones and Lennon, 2010;Kamke et al, 2010;Campbell et al, 2011;DeAngelis et al, 2011;Gaidos et al, 2011;Reid et al, 2011;Baldrian et al, 2012;Mannisto et al, 2012;Mattila et al, 2012;Simister et al, 2012;Campbell and Kirchman, 2013;Hunt et al, 2013;Yarwood et al, 2013). Two principal lines of evidence used to support rRNA as an indicator of current activity originate from earlier studies testing how rRNA scales with growth rate.…”