Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning

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.

Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co‐occurring macroalgae

“…At more detailed taxonomic resolution, similarity in composition across kelp is more striking. For example, Verrucomicrobia and Planctomycetes are predominately represented by characteristic genera, including Rubritalea and Persicirhabdus (Verrucomicrobia) and Blastopirellula (Planctomycetes; Bengtsson & Øvreås, ; Bengtsson et al., ; Lemay et al., ; Vollmers, Frentrup, Rast, Jogler, & Kaster, ; Figure and Figure ; Table ). Within the Gammaproteobacteria, Granulosicoccus is highly abundant and is indicative of annual kelp (Lemay et al., ), and dominant in early season samples of Laminaria (Bengtsson et al., ).…”

Kelp beds and their local effects on seawater chemistry, productivity, and microbial communities

“…The significant differences in carbon and nitrogen biogeochemistry that we measured inside vs. outside of the kelp bed coincided with the strongest microbial contrasts. Kelp-bed-enriched taxa included Flavobacteriaceae, which are often hosted by Macrocystis (Michelou et al 2013, Vollmers et al 2017, Minich et al 2018, are usually aerobic (McBride 2014), and were also an abundant component in the Monterey Bay, California kelp bed (Wilson et al 2018). All nine taxa that had a significantly greater relative abundance inside kelp beds were found on either Nereocystis or Macrocystis in a study of surface-associated microbes (Weigel and Pfister 2019).…”

“…All nine taxa that had a significantly greater relative abundance inside kelp beds were found on either Nereocystis or Macrocystis in a study of surface-associated microbes (Weigel and Pfister 2019). Kelp-bed-enriched taxa included Flavobacteriaceae, which are often hosted by Macrocystis (Michelou et al 2013, Vollmers et al 2017, Minich et al 2018, are usually aerobic (McBride 2014), and were also an abundant component in the Monterey Bay, California kelp bed (Wilson et al 2018). Microbes in association with Macrocystis were enriched in nitrogen metabolic functions compared to surrounding seawater (Minich et al 2018), which may contribute to increased nitrogen recycling and the pattern of increased 15 N NH4 within the kelp bed.…”

Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy

“…Each metagenome was then binned using Maxbin v.2.1.1 (Wu et al, 2016). Bins were subsequently decontaminated using a z-score based differential coverage approach previously described (Vollmers et al, 2017b;Pratscher et al, 2018). Bins with a high likelihood of originating from the same species were identified based on similarity of coverage profiles across all time points and subsamples, as well as by the presence of nearly identical universal marker genes.…”