Abstract
The kelp forest of the Pacific temperate rocky marine coastline of Monterey Bay in California is a dominant habitat for large brown macro-algae in the order of Laminariales. It is probably one of the most species-rich, structurally complex and productive ecosystems in temperate waters and well-studied in terms of trophic ecology. However, still little is known about the microorganisms thriving in this habitat. A growing body of evidence suggests that bacteria associated with macro-algae represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological purposes. Those microorganisms are most likely attracted by algae through secretion of specific carbohydrates and proteins that trigger them to attach to the algal surface and to form biofilms. The algae might then employ those bacteria as biofouling control, using their antimicrobial secondary metabolites to defeat other bacteria or eukaryotes. We here analyzed biofilm samples from the brown macro-algae Macrocystis pyrifera sampled in November 2014 in the kelp forest of Monterey Bay by a metagenomic shotgun and amplicon sequencing approach, focusing on Planctomycetes and Verrucomicrobia from the PVC superphylum. Although not very abundant, we were able to find novel Planctomycetal and Verrucomicrobial species by an innovative binning approach. All identified species harbor secondary metabolite related gene clusters, contributing to our hypothesis that through inter-species interaction, microorganisms might have a substantial effect on kelp forest wellbeing and/or disease-development.
Highlights
Submarine kelp forests are one of the most species-rich, structurally complex, and productive ecosystems in temperate waters. They are extremely well studied in terms of trophic ecology (Dayton and Tegner, 1984; Steneck et al, 2002; Estes et al, 2004; Graham, 2004) and provide habitat and nutrition to diverse communities extending from microorganisms to mammals
We here analyzed the biofilm community of M. pyrifera sampled from Monterey Bay kelp forest in November 2014 on multiple levels: Amplicon sequences, unassembled metagenomic shotgun reads, and assembled metagenome (Figure 2, Supplementary Figures 1, 2)
The overall trend of this community profile was confirmed by the Least Common Ancestor (LCA) taxonomic classification of a metagenomic shotgun sequencing dataset (KelpA) obtained from the same sample (Figure 2B), albeit with pronounced differences in the exact proportions of each bacterial fraction
Summary
Submarine kelp forests are one of the most species-rich, structurally complex, and productive ecosystems in temperate waters. The resulting read subsets were individually reassembled using SPAdes v.3.7.1 (Bankevich et al, 2012) and utilizing the scaffolds of the respective purified preliminary bin as “untrusted reference.” For final purification, new coverage profiles were calculated based on bowtie2 mappings and analyzed in order to identify scaffolds displaying differential coverage between datasets KelpA and KelpB, indicating putative contaminating genome fragments in each bin.
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