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Archaea is a poorly studied domain associated with sponges. Many questions that have been addressed for bacteria still remain largely unknown for archaea. In this study, we analyzed the archaeal communities of 17 tropical sponge species from Nha Trang Bay (Vietnam) using archaea specific primers. We recorded patterns of diversity and spatial stability of these microbial communities and compared the results obtained with the bacterial communities, already reported in our previous study. In our study species, Shannon diversity was always lower for archaeal than for bacterial communities. The differences in alpha diversity as well as the presence of indicator phyla reported for the bacterial domain in High Microbial Abundance (HMA) and Low Microbial Abundance (LMA) could not be confirmed for the archaeal communities. Host identity was the main factor structuring the archaeal assemblages. Sponge archaea core was formed by few but very abundant ZOTUs, which contribute with a high proportion to the relative archaea abundance. The inclusion of the obtained sequences into phylogenetic trees allowed finding out whether or not they belonged to the so-called sponge clusters (SC). Our results showed that most of the Thaumarchaeota and Euryarchaeota sequences were more closely related to environmental samples than to SC, suggesting that they might be acquired from the seawater, which need to be verified. However, representatives of Woesarchaeota, which were major members of the archaea microbiome of two sponge species, formed a monophyletic tree, distantly related to any known environmental sequence.

Sponge diversity has been reported to decrease from well-preserved to polluted environments, but whether diversity and intra-species variation of their associated microbiomes also change as function of environmental quality remains unknown. Our study aimed to assess whether microbiome composition and structure are related to the proliferation of some sponges and not others under degraded conditions. We characterized the most frequent sponges and their associated bacteria in two close areas (impacted and well-preserved) of Nha Trang Bay (Indo-Pacific). Sponge assemblages were richer and more diverse in the well-preserved reefs, but more abundant (individuals/m. transect) in the impacted environments, where two species (Clathria reinwardti and Amphimedon paraviridis) dominated. Sponge microbiomes from the polluted zones had, in general, lower bacterial diversity and core size and consequently, higher intra-species dispersion than microbiomes of sponges from the well-preserved environments. Microbial communities reflect the reduction of diversity and richness shown by their host sponges. In this sense, sponges with less complex and more variable microbiomes proliferate under degraded environmental conditions, following the ecological paradigm that negatively correlates community diversity and environmental degradation. Thereby, the diversity and structure of sponge microbiomes might indirectly determine the presence and proliferation of sponge species in certain habitats.

Sponges are key organisms in the marine benthos where they play essential roles in ecological processes such as creating new niches, competition for resources, and organic matter recycling. Despite the increasing number of taxonomical studies, many sponge species remain hidden, whether unnoticed or cryptic. The occurrence of cryptic species may confound ecological studies by underestimating biodiversity. In this study, we monitored photographically growth, fusions, fissions, and survival of two morphologically cryptic species Hemimycale mediterranea Uriz, Garate & Agell, 2017 and H. columella (Bowerbank, 1874). Additionally, we characterized the main environmental factors of the corresponding species habitats, trying to ascertain whether some abiotic factors were correlated with the distribution of these species. Sponge monitoring was performed monthly. Seawater samples were collected the same monitoring days in the vicinity of the target sponges. Results showed contrasting growth and survival patterns for each species: H. mediterranea totally disappeared after larval release while 64% of individuals of H. columella survived the entire two years we monitored. The species also differed in the number of fissions and fusions. These events were evenly distributed throughout the year in the H. mediterranea population but concentrated in cold months in H. columella. No measured environmental factor correlated with H. mediterranea growth rates, while temperature and dissolved organic nitrogen were negatively correlated with H. columella growth rates. The strong differences in depth distribution, survival, growth, fusions, and fissions found between these two cryptic species, highlights the importance of untangling cryptic species before ecological studies are performed in particular when these species share geographical distribution.

The bioactivity of the most abundant sponges from three communities in a Mediterranean cave was assessed by Microtox® assay in two seasons, spring (June) and autumn (November). We quantified bioactivity as a proxy for the investment in production of biologically active substances, and we related sponge bioactivity to growth form, growth rates, and physical contacts of each species with other species. We established a threshold for classifying a species as bioactive based on a comparison between the results of the Microtox® and the sea urchin embryo toxicity bioassay. A total of 30 species were included in the study, of which 50% were bioactive in some community or season. Significant ecological (between communities) and seasonal variation in mean bioactivity was found. When sponge bioactivity was related to sponge growth shape, it was found that the encrusting species tended to be more toxic than the non-encrusting ones. There was a negative relationship between bioactivity and sponge growth, suggesting a trade-off in energy allocation to defence and to other biological functions. Furthermore, a negative correlation was found between bioactivity and positive associations with other species. These results highlight the important role of chemically-mediated interactions in cave communities.