A horizon scan of priorities for coastal marine microbiome research

Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microbes in ecosystem function. This is particularly relevant in ocean environments, where microbes constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate the Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (e.g. fisheries, water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the ‘microbiome’) and their hosts or environment – termed the ‘holobiont’. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here we evaluated the current state of knowledge on coastal marine microbiome research and identified key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research

A horizon scan of priorities for coastal marine microbiome research

Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microbes in ecosystem function. This is particularly relevant in ocean environments, where microbes constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate the Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (e.g. fisheries, water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the ‘microbiome’) and their hosts or environment – termed the ‘holobiont’. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here we evaluated the current state of knowledge on coastal marine microbiome research and identified key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research

Microbial Communities with Emphasis on Coral Disease-Associated Bacteria within Florida Reef Sponges

Previous studies have shown that bacteria associated with coral diseases are not found in the surrounding water column at detectable levels, yet at the same time, coral diseases are becoming more prominent. Sponges are coral reef residents, which expel filtered seawater that is practically sterile of microbes. Therefore sponges harbor very diverse and abundant microbial communities. This leads to the possibility that coral disease associated bacteria (CDAB) may be present within reef sponge microcosms. In order to identify internal microbes, nonculturable techniques including fluorescent in situ hybridization (FISH), electron microscopy (EM) and 16S small subunit (SSU) rRNA gene cloning and sequencing were applied to local Florida reef sponges Agelas tubulata, Amphimedon compressa and Aplysina fistularis. This study targeted potential coral bacterial pathogens with FISH including Aurantimonas coralicida, Cytophaga sp., Desulfvibrio spp., Firmicutes, Serrattia marcescans, and Vibrio shiloni AK-1. All of the targeted coral disease associated bacteria were found within A. compressa and A. tubulata with FISH, but not in every individual. Differences in the spatial arrangement of targeted microbes were also seen within these sponge hosts. For instance, the two anaerobic bacteria Desulfovibrio spp. and S. marcescans were found in aggragates. In addition, electron microscopy revealed a higher abundance of bacteria in Applysina fistularis choanosome compared to the ectosome

Florida reef sponges harbor coral disease-associated microbes

Sponges can filter large volumes of seawater and accumulate highly diverse and abundant microbial communities within their tissue. Culture-independent techniques such as fluorescent in situ hybridization (FISH), 16S small subunit (SSU) rRNA gene analyses, and transmission electron microscopy (TEM) were applied to characterize the presence and distribution of microbes within sponges abundant on south Florida reefs. This study found that coral disease-associated bacteria (CDAB) are harbored within Agelas tubulata and Amphimedon compressa. FISH probes detected several potential bacterial pathogens such as Aurantimonas coralicida, Cytophaga sp., Desulfovibrio spp, Serratia marcescans, and Vibrio mediterranei within A. compressa and A. tubulata host sponges. Spatial differences in the distribution of targeted bacteria were seen within sponge hosts. Transmission electron microscopy of A. compressa indicated there was a higher concentration of bacteria in the choanosome compared to the ectosome. These observed spatial distributions support the presence of internal sponge niches, which could play a role in the location of the CDAB within the sponges.13 page(s