Draft genome and description of Waterburya agarophytonicola gen. nov. sp. nov. (Pleurocapsales, Cyanobacteria): a seaweed symbiont

Seasonal Cycles in a Seaweed Holobiont: A Multiyear Time Series Reveals Repetitive Microbial Shifts and Core Taxa

Seasonality is an important natural feature that drives cyclic environmental changes. Seaweed holobionts, inhabiting shallow waters such as rocky shores and mud flats, are subject to seasonal changes in particular, but little is known about the influence of seasonality on their microbial communities. In this study, we conducted a three-year time series, sampling at two-month intervals, to assess the seasonality of microbial epibiota in the seaweed holobiont Gracilaria vermiculophylla. Our results reveal pronounced seasonal shifts that are both taxonomic and functional, oscillating between late winter and early summer across consecutive years. While epibiota varied taxonomically between populations, they were functionally similar, indicating that seasonal variability drives functional changes, while spatial variability is more redundant. We also identified seasonal core microbiota that consistently (re)associated with the host at specific times, alongside a permanent core that is present year-round, independent of season or geography. These findings highlight the dynamic yet resilient nature of seaweed holobionts and demonstrate that their epibiota undergo predictable changes. Therewith, this research offers important insights into the temporal dynamics of seaweed-associated microbiota and demonstrates that the relationship between seaweed host and its epibiota is not static but naturally subject to an ongoing seasonal succession process.

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.

Epiphytic Bacterial Community Analysis of Ulva prolifera in Garorim and Muan Bays, Republic of Korea

The bacterial communities related to seaweed can vary considerably across different locations, and these variations influence the seaweed's nutrition, growth, and development. To study this further, we evaluated the bacteria found on the green marine seaweed Ulva prolifera from Garorim Bay and Muan Bay, two key locations on Republic of Korea's west coast. Our analysis found notable differences in the bacterial communities between the two locations. Garorim Bay hosted a more diverse bacterial population, with the highest number of ASVs (871) compared to Muan Bay's 156 ASVs. In Muan Bay, more than 50% of the bacterial community was dominated by Pseudomonadota. On the other hand, Garorim Bay had a more balanced distribution between Bacteroidota and Pseudomonadota (37% and 35.5%, respectively). Additionally, Cyanobacteria, particularly Cyanothece aeruginosa, were found in significant numbers in Garorim Bay, making up 8% of the community. Mineral analysis indicated that Garorim Bay had higher levels of S, Na, Mg, Ca, and Fe. Function-wise, both locations exhibited bacterial enrichment in amino acid production, nucleosides, and nucleotide pathways. In conclusion, this study broadens our understanding of the bacterial communities associated with Ulva prolifera in Korean waters and provides a foundation for future research on the relationships between U. prolifera and its bacteria.

Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon exchange in the marine cyanolichen Lichina pygmaea

Lichens are exemplar symbioses based upon carbon exchange between photobionts and their mycobiont hosts. Historically considered a two-way relationship, some lichen symbioses have been shown to contain multiple photobiont partners; however, the way in which these photobiont communities react to environmental change is poorly understood. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores where it is submerged in seawater during every tidal cycle. Recent work has indicated that L. pygmaea has a complex photobiont community including the cyanobionts Rivularia and Pleurocapsa. We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont at high and low tide to investigate community response to immersion in seawater. Carbon exchange in L. pygmaea is a dynamic process, influenced by both tidal cycle and the biology of the individual symbiotic components. The mycobiont and two cyanobiont partners exhibit distinct transcriptional responses to seawater hydration. Sugar-based compatible solutes produced by Rivularia and Pleurocapsa in response to seawater are a potential source of carbon to the mycobiont. We propose that extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea and is analogous to uptake of plant-derived carbon in ectomycorrhizal symbioses.

Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy

Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and terrestrial systems. Despite their well-known significance, their taxonomy remains problematic and is the subject of much research. Taxonomic issues of Cyanobacteria have consequently led to inaccurate curation within known reference databases, ultimately leading to problematic taxonomic assignment during diversity studies. Recent advances in sequencing technologies have increased our ability to characterize and understand microbial communities, leading to the generation of thousands of sequences that require taxonomic assignment. We herein propose CyanoSeq (https://zenodo.org/record/7569105), a database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. The taxonomy of CyanoSeq is based on the current state of cyanobacterial taxonomy, with ranks from the domain to genus level. Files are provided for use with common naive Bayes taxonomic classifiers, such as those included in DADA2 or the QIIME2 platform. Additionally, FASTA files are provided for creation of de novo phylogenetic trees with (near) full-length 16S rRNA gene sequences to determine the phylogenetic relationship of cyanobacterial strains and/or ASV/OTUs. The database currently consists of 5410 cyanobacterial 16S rRNA gene sequences along with 123 Chloroplast, Bacterial, and Vampirovibrionia (formally Melainabacteria) sequences.

A pathway to improve seaweed aquaculture through microbiota manipulation

Eukaryotic hosts are associated with microbial communities that are critical to their function. Microbiota manipulation using beneficial microorganisms, for example, in the form of animal probiotics or plant growth-promoting microorganisms (PGPMs), can enhance host performance and health. Recently, seaweed beneficial microorganisms (SBMs) have been identified that promote the growth and development and/or improve disease resistance of seaweeds. This knowledge coincides with global initiatives seeking to expand and intensify seaweed aquaculture. Here, we provide a pathway with the potential to improve commercial cultivation of seaweeds through microbiota manipulation, highlighting that seaweed restoration practices can also benefit from further understanding SBMs and their modes of action. The challenges and opportunities of different approaches to identify and apply SBMs to seaweed aquaculture are discussed.

Elevated Temperature-Induced Epimicrobiome Shifts in an Invasive Seaweed Gracilaria vermiculophylla

Epibacterial communities on seaweeds are affected by several abiotic factors such as temperature and acidification. Due to global warming, surface seawater temperatures are expected to increase by 0.5-5 °C in the next century. However, how epibacterial communities associated with seaweeds will respond to global warming remains unknown. In this study, we investigated the response of epibacterial communities associated with the invasive Gracilaria vermiculophylla exposed to 3 °C above ambient temperature for 4 months using a benthocosm system in Kiel, Germany, and 16S rRNA gene amplicon sequencing. The results showed that elevated temperature affected the beta-diversity of the epibacterial communities. Some potential seaweed pathogens such as Pseudoalteromonas, Vibrio, Thalassotalea, and Acinetobacter were identified as indicator genera at the elevated temperature level. Thirteen core raw amplicon sequence variants in the elevated temperature group were the same as the populations distributed over a wide geographical range, indicating that these core ASVs may play an important role in the invasive G. vermicullophylla. Overall, this study not only contributes to a better understanding of how epibacterial communities associated with G. vermiculophylla may adapt to ocean warming, but also lays the foundation for further exploration of the interactions between G. vermiculophylla and its epimicrobiota.