Hologenome theory supported by cooccurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa)

Abstract

The siphonous algae of the Caulerpa genus harbor internal microbial communities hypothesized to play important roles in development, defense and metabolic activities of the host. Here, we characterize the endophytic bacterial community of four Caulerpa taxa in the Mediterranean Sea, through 16S rRNA amplicon sequencing. Results reveal a striking alpha diversity of the bacterial communities, similar to levels found in sponges and coral holobionts. These comprise (1) a very small core community shared across all hosts (< 1% of the total community), (2) a variable portion (ca. 25%) shared by some Caulerpa taxa but not by all, which might represent environmentally acquired bacteria and (3) a large (>70%) species-specific fraction of the community, forming very specific clusters revealed by modularity in networks of cooccurrence, even in areas where distinct Caulerpa taxa occurred in sympatry. Indirect inferences based on sequence homology suggest that these communities may play an important role in the metabolism of their host, in particular on their ability to grow on anoxic sediment. These findings support the hologenome theory and the need for a holistic framework in ecological and evolutionary studies of these holobionts that frequently become invasive.

The Use of Bioinformatic Tools in Symbiosis and Co-Evolution Studies

“…These processes of co-evolution have been documented by several studies carried out in the organization and composition of host microorganisms (microbiome) in different species [1][2][3][4]. The microbiome is currently considered a functional organ which is fundamental for the host organism, given that studies have shown that this organ is highly dynamic and adaptable, likewise plays an important role in physiological adaptation processes, metabolism, and development [1,2,[4][5][6]. The study of the role of the microbiome for years was limited to those organisms that could be susceptible to culture, the use of techniques based on molecular information (AFLP and RFLP) and denaturing gradient gel electrophoresis (DGGE) could reveal the presence of some species not cultured, but the gel resolution was being the main limitation since a single band could contain more than one sequence [7].…”

“…Higher multicellular organisms have coexisted and co-evolved with resident microorganisms in a relatively harmonious relationship over millions of years, forming a complex organism called holobiont. These processes of co-evolution have been documented by several studies carried out in the organization and composition of host microorganisms (microbiome) in different species [1][2][3][4]. The microbiome is currently considered a functional organ which is fundamental for the host organism, given that studies have shown that this organ is highly dynamic and adaptable, likewise plays an important role in physiological adaptation processes, metabolism, and development [1,2,[4][5][6].…”

“…The study of the role of the microbiome for years was limited to those organisms that could be susceptible to culture, the use of techniques based on molecular information (AFLP and RFLP) and denaturing gradient gel electrophoresis (DGGE) could reveal the presence of some species not cultured, but the gel resolution was being the main limitation since a single band could contain more than one sequence [7]. The development of genomic tools such as the new generation sequencing platforms (NGS) has allowed a better resolution of the diversity present in a given sample through what is known as metagenomics [2,[7][8][9][10]. These same sequencing platforms have allowed not only observing the diversity of a host or environment, but also the functional role of microorganisms as well as their possible interactions with physiological processes or biogeochemical cycles through metatranscriptomics [1,2,4,9].…”

“…The development of genomic tools such as the new generation sequencing platforms (NGS) has allowed a better resolution of the diversity present in a given sample through what is known as metagenomics [2,[7][8][9][10]. These same sequencing platforms have allowed not only observing the diversity of a host or environment, but also the functional role of microorganisms as well as their possible interactions with physiological processes or biogeochemical cycles through metatranscriptomics [1,2,4,9]. The understanding of the composition of microorganisms, functions, interactions, and other biological processes through NGS has been done through the development of different bioinformatics tools, which make use of large amounts of information and are able to compare them through different data bases [3,9,11].…”

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“…Bacteria are capable of regulating mineralization of organic matter, nutrient cycling and energy transfer through bacterial metabolism and utilization of their molecules 11 . Bacterial communities associated with seaweeds can be species specific, varieties specific 12,13 or they can also be made of different bacteria but with similar metabolic functions 14 .…”