Specific plasmid patterns and high rates of bacterial co‐occurrence within the coral holobiont

Abstract

Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co‐occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns. Proxies for two broad‐host‐range (BHR) plasmid groups, IncP‐1β and PromA, were screened. Both groups were significantly (up to 252 and 100%, respectively) more abundant in coral mucus than in seawater. Notably, the PromA plasmid group was detected only in coral mucus samples. The core bacteriome of M. hispida mucus was composed primarily of members of the Proteobacteria, followed by those of Firmicutes. Significant host specificity and co‐occurrences among different groups of the dominant phyla (e.g., Bacillaceae and Pseudoalteromonadaceae and the genera Pseudomonas, Bacillus, and Vibrio) were detected. These relationships were observed for both the most abundant phyla and the bacteriome core, in which most of the operational taxonomic units showed intertaxa correlations. The observed evidence of host‐specific bacteriome and co‐occurrence (and potential symbioses or niche space co‐dominance) among the most dominant members indicates a taxonomic selection of members of the stable bacterial community. In parallel, host‐specific plasmid patterns could also be, independently, related to the assembly of members of the coral microbiome.

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere

“…This is the first report of a persistent bacterial phylotype within this group across coral species and a broad range of geographical and depth reef locations. However, members of the family Alteromonadaceae have been previously reported to occur in the core microbiome of other coral species ( 52 ) and in early life stages of coral ( 50 , 53 ) and to be important in chemical defenses against pathogenesis in crustaceans ( 54 ). A search comparison of the sequence of this phylotype in the BLAST Nucleotide database (National Center of Biotechnology Information [NCBI] [see Table S3 at https://figshare.com/s/ffadfdf1a1bab8a37088 ]) showed close affiliation to an uncultured bacterium, a member of the Symbiodinium core microbiome ( 55 ), and to Alteromonas sp.…”

Coral Bacterial-Core Abundance and Network Complexity as Proxies for Anthropogenic Pollution

“…Considering the complex nature of the coral and its associated bacterial-microbiome relationships, the core bacteriome, i.e., the set of bacterial species shared among multiple microbial assemblages ( Turnbaugh et al, 2007 ; Shade and Handelsman, 2012 ), as well the core dynamics, networks and their transmission to the coral offspring ( Ainsworth et al, 2015 ; Kellogg et al, 2017 ; Leite et al, 2017 , 2018 ; van de Water et al, 2017 ) represent a good target to simplify analyses and identify key players within a community. This selective approach focuses only on the persistent members of the bacteriome ( Astudillo-García et al, 2017 ).…”

“…In parallel, the transient bacteriome, shaped mostly by environmental sources and forces ( van de Water et al, 2017 ), is likely associated with strategic mechanisms for the holobiont to quickly acclimate to changes in the environment ( Webster and Reusch, 2017 ), and this part of the bacteriome is also a good target to explore. Knowledge of how the core ( Ainsworth et al, 2015 ; Kellogg et al, 2017 ; Leite et al, 2017 , 2018 ) and the transient communities are affected by local (e.g., oil and organic matter) and global (e.g., climate changes) impacts ( Shade and Handelsman, 2012 ; Santos et al, 2014 , 2015 ; Mustafa et al, 2016 ) and how this may affect the health of the metaorganism may provide valuable insights for subsequent studies of possible manipulation of beneficial microorganisms ( Peixoto et al, 2017 ), as proposed by Shade and Handelsman (2012) , Damjanovic et al (2017) , and Peixoto et al (2017) .…”

“…Our group has previously described the bacterial core associated with mucus of the coral Mussismilia hispida ( Leite et al, 2018 ), showing that members of this core are present in different coral life stages and are transmitted to the coral offspring through their gametes ( Leite et al, 2017 ). Here, we explored how the diversity and the interactions among members of bacterial core, and also the variable populations, can be affected by a gradient of space (representing also a gradient of anthropogenic influence, through the influence of the Buranhém River) and time.…”

The microbiome of pest insects: it is not just bacteria

“…Microbial interactions influence both how communities are formed (Dini‐Andreote et al., , ; Jia et al., ) and how they respond (Jurburg et al., ; Mallon et al., ). Such patterns have also been observed in microbial communities associated with hosts such as plants (Wang et al., ), corals (Leite et al., ,), and birds (van Veelen et al., ), indicating that similar rules drive microbiome assembly in several habitats.…”