A pathway to improve seaweed aquaculture through microbiota manipulation

Bacteria on the foundational kelp in kelp forest ecosystems: Insights from culturing, whole genome sequencing and metabolic assays

In coastal marine ecosystems, kelp forests serve as a vital habitat for numerous species and significantly influence local nutrient cycles. Bull kelp, or Nereocystis luetkeana, is a foundational species in the iconic kelp forests of the northeast Pacific Ocean and harbours a complex microbial community with potential implications for kelp health. Here, we report the isolation and functional characterisation of 16 Nereocystis-associated bacterial species, comprising 13 Gammaproteobacteria, 2 Flavobacteriia and 1 Actinomycetia. Genome analyses of these isolates highlight metabolisms potentially beneficial to the host, such as B vitamin synthesis and nitrogen retention. Assays revealed that kelp-associated bacteria thrive on amino acids found in high concentrations in the ocean and in the kelp (glutamine and asparagine), generating ammonium that may facilitate host nitrogen acquisition. Multiple isolates have genes indicative of interactions with key elemental cycles in the ocean, including carbon, nitrogen and sulphur. We thus report a collection of kelp-associated microbial isolates that provide functional insight for the future study of kelp-microbe interactions.

Adverse Environmental Perturbations May Threaten Kelp Farming Sustainability by Exacerbating Enterobacterales Diseases

Globally kelp farming is gaining attention to mitigate land-use pressures and achieve carbon neutrality. However, the influence of environmental perturbations on kelp farming remains largely unknown. Recently, a severe disease outbreak caused extensive kelp mortality in Sanggou Bay, China, one of the world's largest high-density kelp farming areas. Here, through in situ investigations and simulation experiments, we find indications that an anomalously dramatic increase in elevated coastal seawater light penetration may have contributed to dysbiosis in the kelp Saccharina japonica's microbiome. This dysbiosis promoted the proliferation of opportunistic pathogenic Enterobacterales, mainly including the genera Colwellia and Pseudoalteromonas. Using transcriptomic analyses, we revealed that high-light conditions likely induced oxidative stress in kelp, potentially facilitating opportunistic bacterial Enterobacterales attack that activates a terrestrial plant-like pattern recognition receptor system in kelp. Furthermore, we uncover crucial genotypic determinants of Enterobacterales dominance and pathogenicity within kelp tissue, including pathogen-associated molecular patterns, potential membrane-damaging toxins, and alginate and mannitol lysis capability. Finally, through analysis of kelp-associated microbiome data sets under the influence of ocean warming and acidification, we conclude that such Enterobacterales favoring microbiome shifts are likely to become more prevalent in future environmental conditions. Our study highlights the need for understanding complex environmental influences on kelp health and associated microbiomes for the sustainable development of seaweed farming.

Co-occurrence of native and invasive macroalgae might be facilitated under global warming

Climate change is driving compositional shifts in ecological communities directly by affecting species and indirectly through changes in species interactions. For example, competitive hierarchies can be inversed when competitive dominants are more susceptible to climate change. The brown seaweed Fucus vesiculosus is a foundation species in the Baltic Sea, experiencing novel interactions with the invasive red seaweed Gracilaria vermiculophylla, which is known for its high tolerance to environmental stress. We investigated the direct and interactive effects of warming and co-occurrence of the two algal species on their performance, by applying four climate change-relevant temperature scenarios: 1) cooling ) 2 °C below ambient - representing past conditions), 2) ambient summer temperature (18 °C), 3) IPCC RCP2.6 warming scenario (1 °C above ambient), and 4) RCP8.5 warming (3 °C above ambient) for 30 days and two compositional levels (mono and co-cultured algae) in a fully-crossed design. The RCP8.5 warming scenario increased photosynthesis, respiration, and nutrients' uptake rates of mono- and co-cultured G. vermiculophylla while growth was reduced. An increase in photosynthesis and essential nutrients' uptake and, at the same time, a growth reduction might result from increasing stress and energy demand of G. vermiculophylla under warming. In contrast, the growth of mono-cultured F. vesiculosus significantly increased in the highest warming treatment (+3 °C). The cooling treatment (-2 °C) exerted a slight negative effect only on co-cultured F. vesiculosus photosynthesis, compared to the ambient treatment. Interestingly, at ambient and warming (RCP2.6 and RCP8.5 scenarios) treatments, both F. vesiculosus and G. vermiculophylla appear to benefit from the presence of each other. Our results suggest that short exposure of F. vesiculosus to moderate or severe global warming scenarios may not directly affect or even slightly enhance its performance, while G. vermiculophylla net performance (growth) could be directly hampered by warming.

Oligoagars and microbial agents show potential for Porphyra disease prevention

Disease is a major concern in Porphyra aquaculture, particularly during the early shell-borne conchocelis (SBC) seedling stage. To explore prevention strategies for Porphyra diseases, this study explored the potential of using oligoagars (OA) and microbial agents (MA) to treat SBC of Neoporphyra haitanensis in an aquaculture environment. The impact of these treatments on the phycosphere microbial community was analyzed, and the resistance of the treated Porphyra conchocelis to the pathogenic bacterium Vibrio mediterranei 117-T6 (which causes yellow spot disease) was tested in the lab. Results showed that OA reduced α-diversity while enriching Rhodobacteriaceae, and MA increased stability and relative abundance of Bacteroidetes (including Flavobacteria). Furthermore, compared to the control group, the abundance of pathogenic microorganisms and virulence functional genes decreased while defense-related functional gene abundance increased significantly in the groups treated with OA and MA. Most importantly, the OA and MA treatments improved resistance to Vm117-T6, with survival rates of 70% (OA) and 80% (MA), compared to 15% in the control group. Overall, the findings suggest that OA and MA treatments have great potential for preventing Porphyra disease, as they improve phycosphere microorganisms and increase algae resistance to pathogenic bacteria.

The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity

Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.

Naturally occurring beneficial bacteria Vibrio alginolyticus X-2 protects seaweed from bleaching disease

Microbiome manipulation is gaining fresh attention as a way to mitigate diseases in aquaculture. The commercially farmed seaweed Saccharina japonica suffers from a bacterial-induced bleaching disease, which has major implications for the reliable supply of healthy sporelings. Here, we identify a beneficial bacterium, Vibrio alginolyticus X-2 that significantly reduces the risk of bleaching disease. By combining infection assays and multi-omic analyses, we provide evidence to suggest that the underlying protective mechanisms of V. alginolyticus X-2 involve maintaining epibacterial communities, increasing the gene expression of S. japonica related to immune and stress protection pathways, and stimulating betaine concentrations in S. japonica holobionts. Thus, V. alginolyticus X-2 can elicit a suite of microbial and host responses to mitigate the bleaching disease. Our study provides insights into disease control in farmed S. japonica through the application of beneficial bacteria. IMPORTANCE Beneficial bacteria can elicit a suite of microbial and host responses to enhance the resistance to bleaching disease.

Successional dynamics of the cultivated kelp microbiome

Kelp are important primary producers that are colonized by diverse microbes that can have both positive and negative effects on their hosts. The kelp microbiome could support the burgeoning kelp cultivation sector by improving host growth, stress tolerance, and resistance to disease. Fundamental questions about the cultivated kelp microbiome still need to be addressed before microbiome-based approaches can be developed. A critical knowledge gap is how cultivated kelp microbiomes change as hosts grow, particularly following outplanting to sites that vary in abiotic conditions and microbial source pools. In this study we assessed if microbes that colonize kelp in the nursery stage persist after outplanting. We characterized microbiome succession over time on two species of kelp, Alaria marginata and Saccharina latissima, outplanted to open ocean cultivation sites in multiple geographic locations. We tested for host-species specificity of the microbiome and the effect of different abiotic conditions and microbial source pools on kelp microbiome stability during the cultivation process. We found the microbiome of kelp in the nursery is distinct from that of outplanted kelp. Few bacteria persisted on kelp following outplanting. Instead, we identified significant microbiome differences correlated with host species and microbial source pools at each cultivation site. Microbiome variation related to sampling month also indicates that seasonality in host and/or abiotic factors may influence temporal succession and microbiome turnover in cultivated kelps. This study provides a baseline understanding of microbiome dynamics during kelp cultivation and highlights research needs for applying microbiome manipulation to kelp cultivation.