ORIGINAL RESEARCH published: 08 June 2021 doi: 10.3389/fmicb.2021.674004 Prokaryotic, Fungal, and Unicellular Eukaryotic Core Communities Across Three Sympatric Marine Sponges From the Southwestern Atlantic Coast Are Dominated Largely by Deterministic Assemblage Processes Cristiane C. P. Hardoim 1*, Gisele Lôbo-Hajdu 2, Márcio R. Custódio 3 and Pablo R. Hardoim 4 1 Institute of Biosciences, São Paulo State University, São Paulo, Brazil, 2 Department of Genetic, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil, 3 Department of Physiology, Biosciences Institute and NP-Biomar, Center for Marine Biology, University of São Paulo, São Paulo, Brazil, 4 Department of R&D, Biopromo, São Edited by: Paulo, Brazil Laura Steindler, University of Haifa, Israel Marine sponges are known to harbor a diverse and complex microbiota; however, a vast Reviewed by: Beate M. Slaby, majority of surveys have been investigating the prokaryotic communities in the north GEOMAR Helmholtz Center for hemisphere and Australia. In addition, the mechanisms of microbial community assembly Ocean Research Kiel, Germany Marta Turon, are poorly understood in this pivotal player of the ecosystem. Thus, this survey addressed UiT The Arctic University of Norway, the holobiome of the sponge species in the São Paulo region (Brazil) for the first time and Norway investigated the contribution of neutral and niche processes of prokaryotic, fungal, and *Correspondence: unicellular eukaryotic assemblage in three sympatric species Aplysina caissara, Aplysina Cristiane C. P. Hardoim [email protected] fulva, and Tedania ignis along with environmental samples. The compositions of the holobiome associated with the sponges and detected in environmental samples were Specialty section: This article was submitted to strikingly different. Remarkably, between 47 and 88% of the assigned operational Microbial Symbioses, taxonomic units (OTUs) were specifically associated with sponge species. Moreover, a section of the journal around 77, 69, and 53% of the unclassified OTUs from prokaryotic, fungal, and unicellular Frontiers in Microbiology eukaryotic communities, respectively, showed less than 97% similarity with well-known Received: 28 February 2021 Accepted: 19 April 2021 databases, suggesting that sponges from the southwestern Atlantic coast are an important Published: 08 June 2021 source of microbial novelty. These values are even higher, around 80 and 61% of the Citation: unclassified OTUs, when excluding low abundance samples from fungal and unicellular Hardoim CCP, Lôbo-Hajdu G, Custódio MR and Hardoim PR (2021) eukaryotic datasets, respectively. Host species were the major driver shaping the sponge- Prokaryotic, Fungal, and Unicellular associated microbial community. Deterministic processes were primarily responsible for Eukaryotic Core Communities Across the assembly of microbial communities in all sponge species, while neutral processes of Three Sympatric Marine Sponges From the Southwestern Atlantic prokaryotic and fungal community assembly were also detected in the sympatric A. caissara Coast Are Dominated Largely by and T. ignis replicates, respectively. Most of the species-rich sponge-associated lineages Deterministic Assemblage Processes. Front. Microbiol. 12:674004. from this region are also found in the Northern seas and many of them might play essential doi: 10.3389/fmicb.2021.674004 roles in the symbioses, such as biosynthesis of secondary metabolites that exhibit Frontiers in Microbiology | www.frontiersin.org 1 June 2021 | Volume 12 | Article 674004 Hardoim et al. Niche-Based Holobiome of Marine Sponges antimicrobial and antiviral activities, as well as provide protection against host predation. Overall, in this study the microbiota was assembled by interactions with the host sponge in a deterministic-based manner; closely related sponge species shared a strong phylogenetic signal in their associated prokaryotic and fungal community traits and Brazilian sponges were a reservoir of novel microbial species. Keywords: microbial community assembly, stochastic process, deterministic process, neutral community model, Brazilian coast, co-evolution, Porifera holobiome INTRODUCTION important roles are played by the unicellular eukaryotic community for ecosystem functioning, the assembly of these Marine sponges harbor abundant, diverse, and complex communities are dominated by stochastic processes. microbiomes, which include bacteria and archaea (Taylor et al., The mechanisms of the community assembly responsible 2007; Thomas et al., 2016). Based on the abundance, these for shaping the structure of the sponge microbiomes continue animals have been classified into high microbe abundance to remain uncertain. Hosts and their microbiomes are ecological (HMA) and low microbe abundance (LMA) sponges (Hentschel systems structured by multitrophic interactions governed by et al., 2003). The diversity of bacteria associated with sponges deterministic and stochastic processes (Miller et al., 2018). has been extensively investigated followed by archaea (Taylor Deterministic processes assume that species traits, interspecies et al., 2007; Hardoim et al., 2012; Hentschel et al., 2012; Webster interactions such as mutualism, competition, predation, and and Taylor, 2012; Thomas et al., 2016). The prokaryotic community trade-offs, environmental factors such as nutrient heterogeneity, from 268 sponge species collected from several locations pH, temperature, moisture, and salinity, and host environments encompassed 60 to 72 recognized and candidate phyla (Moitinho- shape the microbial community structure (i.e., species Silva et al., 2017a). A previous prokaryotic survey of three composition and abundance distributions; Vellend, 2010; Zhou sympatric marine sponges from the southwestern Atlantic coast and Ning, 2017). On the other hand, stochastic processes, of Brazil (São Paulo state) revealed a total of 51 associated such as birth, death, immigration and emigration, spatiotemporal phyla (Hardoim et al., 2021). Among them, Nanoarchaeota, variation, and/or historical contingency also play a role in Elusimicrobiota, Parcubacteria, and others were detected for community assembly (Chen et al., 2017; Zhou and Ning, 2017). the first time. Moreover, a high degree of novel prokaryotic Both processes are recognized as occurring simultaneously in diversity was also associated with these marine sponges. shaping the assembly of microbial communities (Gravel et al., Much less attention has been given to microbial eukaryotic 2006; Chase and Myers, 2011; Stegen et al., 2016). Therefore, communities associated with marine sponges, especially regarding each ecological process of selection, dispersal, diversification, their ecology and function with their hosts (Taylor et al., 2007; and drift might affect the microbial species on its own terms. Webster and Taylor, 2012; Thomas et al., 2016). To date, very Furthermore, studies have shown that microbial species can few studies have applied high-throughput sequencing technology be partitioned into habitat generalists and specialists, on the to study both fungal and other microbial eukaryotic communities basis of their distinct capacities to respond to environmental associated with marine sponges. The fungi associated with challenges (Pandit et al., 2009; Székely and Langenheder, 2014). sponges were considered to have high host-specificity (De Mares Often, habitat generalists have broad environmental tolerances et al., 2017), low host-specificity (Nguyen and Thomas, 2018), and can occur in many habitats, whereas habitat specialists or no specificity at all Naim( et al., 2017). For fungal assemblages are more restricted in sites, due to their narrow environmental associated with sponges, two genes have been routinely used, tolerances (Pandit et al., 2009). Hence, habitat generalists and the 18S rRNA gene and internal transcribed spacer (ITS) of specialists might respond distinctively under changing the ribosomal RNA gene operon (De Mares et al., 2017; Naim environmental conditions. For the sponge microbiome, the et al., 2017; Nguyen and Thomas, 2018). Overall, the associated influences of deterministic and stochastic processes affecting fungi are phylogenetically diverse and both Ascomycota and the distribution of habitat generalists and specialists Basidiomycota were the dominant phyla (De Mares et al., 2017; remain unknown. Naim et al., 2017; Nguyen and Thomas, 2018). The microbial diversity and community composition of the The unicellular eukaryotic community associated with marine three domains of life have rarely been assessed for the same sponges is largely unknown. Recently, this community was host sponges and, to the best of our knowledge, have never assessed with 18S rRNA gene metabarcoding analysis in sympatric been assessed for southwestern Atlantic species. Thus, in the species and showed no host-specificity De( Mares et al., 2017). present study, the bacteria, archaea, fungi, and unicellular Besides, there was no significant difference between eukaryotic eukaryotic communities associated with Aplysina caissara, communities detected in seawater and those associated with Aplysina fulva, and Tedania ignis were investigated. Aplysina the sponge hosts, indicating no selection by the host. Overall, caissara is so far considered endemic to the southern and members of 94 eukaryotic phyla and approximate phylum-level southeastern Brazilian coast (Pinheiro and Hajdu, 2001; Pinheiro groups were detected