Julie B. Olson

Diversity, structure and convergent evolution of the global sponge microbiome

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host–microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the worlds oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.

Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.

Background Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. Methodology/Principal Findings We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil). Conclusions/Significance The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient environment, allowed us to differentiate resident symbionts from potentially transient or prey bacteria. Pairing replicated clone library construction with rapid community profiling via T-RFLP analyses will greatly facilitate future studies of sponge-microbe symbioses.

Microbial ecology of corals, sponges, and algae in mesophotic coral environments

Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.

Molecular Comparison of Bacterial Communities within Iron-Containing Flocculent Mats Associated with Submarine Volcanoes along the Kermadec Arc

ABSTRACT Iron oxide sheaths and filaments are commonly found in hydrothermal environments and have been shown to have a biogenic origin. These structures were seen in the flocculent material associated with two submarine volcanoes along the Kermadec Arc north of New Zealand. Molecular characterization of the bacterial communities associated with the flocculent samples indicated that no known Fe-oxidizing bacteria dominated the recovered clone libraries. However, clones related to the recently described Fe-oxidizing bacterium Mariprofundus ferrooxydans were obtained from both the iron-containing flocculent (Fe-floc) and sediment samples, and peaks corresponding to Mariprofundus ferrooxydans, as well as the related clones, were observed in several of our terminal restriction fragment length polymorphism profiles. A large group of epsilonproteobacterial sequences, for which there is no cultured representative, dominated clones from the Fe-floc libraries and were less prevalent in the sediment sample. Phylogenetic analyses indicated that several operational taxonomic units appeared to be site specific, and statistical analyses of the clone libraries found that all samples were significantly different from each other. Thus, the bacterial communities in the Fe-floc samples were not more closely related to each other than to the sediment communities.

Investigating Bacterial Sources of Toxicity as an Environmental Contributor to Dopaminergic Neurodegeneration

Parkinson disease (PD) involves progressive neurodegeneration, including loss of dopamine (DA) neurons from the substantia nigra. Select genes associated with rare familial forms of PD function in cellular pathways, such as the ubiquitin-proteasome system (UPS), involved in protein degradation. The misfolding and accumulation of proteins, such as α-synuclein, into inclusions termed Lewy Bodies represents a clinical hallmark of PD. Given the predominance of sporadic PD among patient populations, environmental toxins may induce the disease, although their nature is largely unknown. Thus, an unmet challenge surrounds the discovery of causal or contributory neurotoxic factors that could account for the prevalence of sporadic PD. Bacteria within the order Actinomycetales are renowned for their robust production of secondary metabolites and might represent unidentified sources of environmental exposures. Among these, the aerobic genera, Streptomyces, produce natural proteasome inhibitors that block protein degradation and may potentially damage DA neurons. Here we demonstrate that a metabolite produced by a common soil bacterium, S. venezuelae, caused DA neurodegeneration in the nematode, Caenorhabditis elegans, which increased as animals aged. This metabolite, which disrupts UPS function, caused gradual degeneration of all neuronal classes examined, however DA neurons were particularly vulnerable to exposure. The presence of DA exacerbated toxicity because neurodegeneration was attenuated in mutant nematodes depleted for tyrosine hydroxylase (TH), the rate-limiting enzyme in DA production. Strikingly, this factor caused dose-dependent death of human SH-SY5Y neuroblastoma cells, a dopaminergic line. Efforts to purify the toxic activity revealed that it is a highly stable, lipophilic, and chemically unique small molecule. Evidence of a robust neurotoxic factor that selectively impacts neuronal survival in a progressive yet moderate manner is consistent with the etiology of age-associated neurodegenerative diseases. Collectively, these data suggest the potential for exposures to the metabolites of specific common soil bacteria to possibly represent a contributory environmental component to PD.

Occurrence of deep-water Lophelia pertusa and Madrepora oculata in the Gulf of Mexico

One of the critical information needs identified at the 2003 Deep-Sea Corals Workshop in Galway, Ireland, was to locate and chart deep-sea corals in order to develop reliable estimates of their distribution and abundance. While reports of deep-sea corals from the Gulf of Mexico date back to the 1860s, relatively little is known about their distribution or abundance. This paper attempts to provide a current assessment of the occurrence of Lophelia pertusa and Madrepora oculata in water depths greater than 200 m in the Gulf of Mexico by summarizing records from (1) published material, (2) the 2003 National Museum of Natural History Taxonomic Database, (3) findings obtained during the September-October 2003 NOAA-OE RV Ronald H. Brown cruise RB-03-07-leg-2 in the northern Gulf, and (4) from various unpublished sources.

Molecular community profiling reveals impacts of time, space, and disease status on the bacterial community associated with the Caribbean sponge Aplysina cauliformis.

Reports of marine sponge diseases have increased in recent years, but few etiologic agents have been identified. Aplysina red band syndrome (ARBS), a condition observed in the Caribbean sponge Aplysina cauliformis, is characterized by a rust-colored leading margin. Culture-independent methods (terminal restriction fragment length polymorphism and clone library analyses) were used to assess bacterial communities associated with healthy and ARBS-affected sponges from two locations over 2 years. Although the bacterial communities associated with healthy and ARBS-affected sponges were significantly different, the sponges maintained a core bacterial community across space, time, and health status. Ten terminal restriction fragments were shown to change significantly between sponge health conditions, with six increasing in abundance with disease and four decreasing. The prevalence of the photosymbiont Synechococcus spongiarum decreased with ARBS infection, suggesting a functional consequence of disease. After cultivating a red-pigmented Leptolyngbya strain from ARBS lesions, transmission studies were conducted to determine whether this organism was the ARBS pathogen. Despite significantly increased abundance of Leptolyngbya spp. in diseased sponges, signs of ARBS were not observed in healthy sponges following 24 days of contact with the cultured strain. Additional work with this model system is needed to increase our understanding of the dynamics of marine diseases.

Unique Actinomycetes from Marine Caves and Coral Reef Sediments Provide Novel PKS and NRPS Biosynthetic Gene Clusters

In the ever-expanding search for novel bioactive molecules and enzymes, marine actinomycetes have proven to be a productive source. While open reef sediment and sponge-associated actinomycetes have been extensively examined, their marine cave counterparts remain unevaluated. Anchialine cave systems in the Bahamas offered an ideal setting to evaluate the occurrence and variation within sediment-associated actinomycete communities. While in close geographical proximity to open reef environments, these systems provide a specialized environmental niche devoid of light and direct exposure to nutrient input. In the present study, selective isolation techniques and molecular methods were used to test the hypothesis that variable distribution of actinomycetes and secondary metabolite gene clusters occur between open reef and marine cave systems. The results indicated that differences exist within the culturable sediment-associated actinomycete communities between marine caves and open reef systems, with members of the genus Streptomyces dominating cultures from open reef sediments and a more diverse suite of actinomycetes isolated from marine cave sediment samples. Within the cave isolates, members of the proposed genus Solwaraspora were the most represented. Based on PKS- and NRPS-gene-targeted PCR amplification and sequencing, geographic variation in the occurrence of these biosynthetic pathways was also observed. These findings indicate that marine cave systems are a lucrative source in the search for novel secondary metabolite producers with biotechnological applications and that environmental and geographic factors likely affect the occurrence of these biosynthetic pathways.

Slowing PCR ramp speed reduces chimera formation from environmental samples

Chimeric sequences falsely increase the apparent diversity within samples. To examine chimera formation in PCR products from environmental DNA, clone libraries were prepared using different ramp speeds to reach the designated temperatures for each step of the PCR program. Slowing the thermocycler ramp speed to 1 °C s(-1) reduced chimera formation.

Trade-Offs in Defensive Metabolite Production But Not Ecological Function in Healthy and Diseased Sponges

Diseases of marine organisms, and sponges in particular, are increasingly reported worldwide. Prior research indicates that the survival of sponges on reefs is due largely to their production of biologically active secondary metabolites that provide protection from a diversity of stressors. Aplysina Red Band Syndrome (ARBS) is an emerging disease affecting Caribbean rope sponges (Aplysina spp.), but it is not known whether secondary metabolites play a role in disease susceptibility and resistance. To investigate whether differences in secondary metabolites may explain variability in susceptibility to ARBS in Aplysina cauliformis, we used high performance liquid chromatography (HPLC) to generate chemical profiles from healthy tissue in both healthy and diseased sponges, and quantified peak areas for 15 metabolites. Analyses of healthy and diseased sponges revealed qualitative and quantitative differences in their chemical profiles. Aplysamine-1 and fistularin-3 were produced in significantly higher concentrations by healthy sponges, whereas aerothionin and 11-oxoaerothionin were found only in diseased sponges. At natural concentrations, extracts from both healthy and diseased sponges deterred feeding by an omnivorous reef fish. Fistularin-3 deterred feeding at concentrations found in healthy sponges, but not at concentrations found in diseased sponges. Aerothionin deterred feeding at concentrations found in diseased sponges, and may at least partially replace the loss of fistularin-3 as a feeding deterrent compound following pathogenesis, suggesting a trade-off in the production of feeding deterrent compounds. Extracts from healthy and diseased sponges inhibited bacterial growth, and both aplysamine-1 and fistularin-3 displayed selective antibacterial activity. Despite differences in secondary metabolite production between healthy and diseased sponges, the stress associated with ARBS does not appear to compromise the ability of A. cauliformis to maintain defenses against some of its natural enemies.