Algicidal and growth-inhibiting bacteria associated with seagrass and macroalgae beds in Puget Sound, WA, USA

Revealing the algicidal characteristics of Maribacter dokdonensis: An investigation into bacterial strain P4 isolated from Karenia mikimotoi bloom water

Harmful algal blooms (HABs) are a global environmental concern, causing significant economic losses in fisheries and posing risks to human health. Algicidal bacteria have been suggested as a potential solution to control HABs, but their algicidal efficacy is influenced by various factors. This study aimed to characterize a novel algicidal bacterium, Maribacter dokdonensis (P4), isolated from a Karenia mikimotoi (Hong Kong strain, KMHK) HAB and assess the impact of P4 and KMHK's doses, growth phase, and algicidal mode and the axenicity of KMHK on P4's algicidal effect. Our results demonstrated that the algicidal effect of P4 was dose-dependent, with the highest efficacy at a dose of 25% v/v. The study also determined that P4's algicidal effect was indirect, with the P4 culture and the supernatant, but not the bacterial cells, showing significant effects. The algicidal efficacy was higher when both P4 and KMHK were in the stationary phase. Furthermore, the P4 culture at the log phase could effectively kill KMHK cells at the stationary phase, with higher algicidal efficacy in the bacterial culture than that of the supernatant alone. Interestingly, P4's algicidal efficacy was significantly higher when co-culturing with xenic KMHK (~90% efficacy at day 1) than that with the axenic KMHK (~50% efficacy at day 1), suggesting the presence of other bacteria could regulate P4's algicidal effect. The bacterial strain P4 also exhibited remarkable algicidal efficacy on four other dinoflagellate species, particularly the armored species. These results provide valuable insights into the algicidal effect of M. dokdonensis on K. mikimotoi and on their interactions.

Response of the toxic dinoflagellate Alexandrium minutum to exudates of the eelgrass Zostera marina

Biotic interactions are a key factor in the development of harmful algal blooms. Recently, a lower abundance of planktonic dinoflagellates has been reported in areas dominated by seagrass beds, suggesting a negative interaction between both groups of organisms. The interaction between planktonic dinoflagellates and marine phanerogams, as well as the way in which bacteria can affect this interaction, was studied in two experiments using a non-axenic culture of the toxic dinoflagellate Alexandrium minutum exposed to increasing additions of eelgrass (Zostera marina) exudates from old and young leaves and to the presence or absence of antibiotics. In these experiments, A. minutum abundance, growth rate and photosynthetic efficiency (Fv/Fm), as well as bacterial abundance, were measured every 48 h. Toxin concentration per cell was determined at the end of both experiments. Our results demonstrated that Z. marina exudates reduced A. minutum growth rate and, in one of the experiments, also the photosynthetic efficiency. These results are not an indirect effect mediated by the bacteria in the culture, although their growth modify the magnitude of the negative impact on the dinoflagellate growth rate. No clear pattern was observed in the variation of toxin production with the treatments.

Manipulation of the seagrass-associated microbiome reduces disease severity

Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.

Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater?

Seagrass meadows provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of waterborne pathogens linked to infections in humans and marine organisms in their vicinity. Among potential drivers, seagrass phenolics released into seawater have been linked to pathogen suppression, but the potential involvement of the seagrass microbiome has not been investigated. We hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and the surrounding seawater, inhibit waterborne pathogens thereby contributing to their removal. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots. We assessed the antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and mined the metabolome of the most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also displayed remarkable activities. UPLC-MS/MS-based untargeted metabolomics analyses showed rich specialized metabolite repertoires with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome in suppression of pathogens in seawater. Such effect is beneficial for the health of ocean and human, especially in the context of climate change that is expected to exacerbate all infectious diseases. It may also assist future seagrass conservation and management strategies.

Nanoparticles, an Emerging Control Method for Harmful Algal Blooms: Current Technologies, Challenges, and Perspectives

Harmful algal blooms (HABs) are a global concern because they harm aquatic ecosystems and pose a risk to human health. Various physical, chemical, and biological approaches have been explored to control HABs. However, these methods have limitations in terms of cost, environmental impact, and effectiveness, particularly for large water bodies. Recently, the use of nanoparticles has emerged as a promising strategy for controlling HABs. Briefly, nanoparticles can act as anti-algae agents via several mechanisms, including photocatalysis, flocculation, oxidation, adsorption, and nutrient recovery. Compared with traditional methods, nanoparticle-based approaches offer advantages in terms of environmental friendliness, effectiveness, and specificity. However, the challenges and risks associated with nanoparticles, such as their toxicity and ecological impact, must be considered. In this review, we summarize recent research progress concerning the use of nanoparticles to control HABs, compare the advantages and disadvantages of different types of nanoparticles, discuss the factors influencing their effectiveness and environmental impact, and suggest future directions for research and development in this field. Additionally, we explore the causes of algal blooms, their harmful effects, and various treatment methods, including restricting eutrophication, biological control, and disrupting living conditions. The potential of photocatalysis for generating reactive oxygen species and nutrient control methods using nanomaterials are also discussed in detail. Moreover, the application of flocculants/coagulants for algal removal is highlighted, along with the challenges and potential solutions associated with their use. This comprehensive overview aims to contribute to the development of efficient and sustainable strategies for controlling HAB control.

Identification of a Bacillus thuringiensis Q1 compound with algicidal activity

Bacillus thuringiensis Q1, isolated from the eutrophic waters of the Haihe River in Tianjin, possesses remarkable algae dissolving character. We determined the lytic effect of B. thuringiensis Q1 fermentation broth, and it proved to be pH- and temperature-stable. Then, we investigated the structure of the algicidal compound by high performance liquid chromatography, gas chromatography tandem quadrupole mass spectrometry and fourier transform infrared spectroscopy, and identified as purine-derived C12H15O5N5. To further understand B. thuringiensis Q1, we performed genome sequencing and analysis. The genome was 5341610 bp, with 35.31% GC content. Some elements involved in algicidal activity, such as quorum sensing pathway and ABC transporter were predicted. Our results reveal that B. thuringiensis Q1 can be used for biological control of harmful algal blooms.

SoundToxins: A Research and Monitoring Partnership for Harmful Phytoplankton in Washington State

The more frequent occurrence of marine harmful algal blooms (HABs) and recent problems with newly-described toxins in Puget Sound have increased the risk for illness and have negatively impacted sustainable access to shellfish in Washington State. Marine toxins that affect safe shellfish harvest because of their impact on human health are the saxitoxins that cause paralytic shellfish poisoning (PSP), domoic acid that causes amnesic shellfish poisoning (ASP), diarrhetic shellfish toxins that cause diarrhetic shellfish poisoning (DSP) and the recent measurement of azaspiracids, known to cause azaspiracid poisoning (AZP), at low concentrations in Puget Sound shellfish. The flagellate, Heterosigma akashiwo, impacts the health and harvestability of aquacultured and wild salmon in Puget Sound. The more recently described flagellates that cause the illness or death of cultivated and wild shellfish, include Protoceratium reticulatum, known to produce yessotoxins, Akashiwo sanguinea and Phaeocystis globosa. This increased incidence of HABs, especially dinoflagellate HABs that are expected in increase with enhanced stratification linked to climate change, has necessitated the partnership of state regulatory programs with SoundToxins, the research, monitoring and early warning program for HABs in Puget Sound, that allows shellfish growers, Native tribes, environmental learning centers and citizens, to be the “eyes on the coast”. This partnership enables safe harvest of wholesome seafood for consumption in the region and helps to describe unusual events that impact the health of oceans, wildlife and humans.

Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding

During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful algal bloom (HAB) species. In this study, the presence of HAB species and their appearance patterns were investigated by employing molecular and light microscopy-based monitoring in Tokyo Bay, Japan. The potential co-appearance patterns between the HAB species, as well as with other eukaryotes and prokaryotes were investigated using correlation and association rule-based time-series analysis. In total, 40 unique HAB species were detected, including 12 toxin-producing HAB species previously not reported from the area. More than half of the HAB species were present throughout the sampling season (summer to autumn) and no structuring or succession patterns associated with the environmental conditions could be detected. Statistically significant (p < 0.05, rS ranging from −0.88 to 0.90) associations were found amongst the HAB species and other eukaryotic and prokaryotic species, including genera containing growth-limiting bacteria. However, significant correlations between species differed amongst the years, indicating that variability in environmental conditions between the years may have a stronger influence on the microalgal community structure and interspecies interactions than the variability during the sampling season. The association rule-based time-series analysis allowed the detection of a previously reported negative relationship between Synechococcus sp. and Skeletonema sp. in nature. Overall, the results support the applicability of metabarcoding and HTS-based microalgae monitoring, as it facilitates more precise species identification compared to light microscopy, as well as provides input for investigating potential interactions amongst different species/groups through simultaneous detection of multiple species/genera.

Functional role of a novel algicidal compound produced by Pseudoruegeria sp. M32A2M on the harmful algae Alexandrium catenella

A marine phytoplankton dinoflagellate, Alexandrium sp. is known to cause worldwide harmful algal blooms, resulting in paralytic shellfish poisoning. In this study, we isolated a novel compound secreted by the marine bacterium Pseudoruegeria sp. M32A2M, and showed that it displays algicidal activity against A. catenella (group I). The molecular structure of the compound was analyzed by using ¹H nuclear magnetic resonance (NMR), ¹³C NMR, and gas chromatography-mass spectrometry, which revealed that the compound was a diketopiperazine, cyclo[Ala-Gly]. Cyclo[Ala-Gly] induced a rapid decrease in the active chlorophyll a content and maximal quantum yield of photosystem II, leading to membrane disintegration after 24 h of its treatment. It showed the highest algicidal effect against diketopiperazines and also showed specific algicidal activities against several dinoflagellate species, but not for diatom species. In particular, cyclo[Ala-Gly] caused the transcriptional downregulation of the photosynthesis-related membrane complex in A. catenella, but not in the diatom Chaetoceros simplex. Based on structural modeling, we elucidated that cyclo[Ala-Gly] has a structure similar to that of plastoquinone, which transfers electrons by binding to the photosystem II core proteins PsbA and PsbD. This suggests a novel role for cyclo[Ala-Gly] as a potential inhibitor of photosynthesis.

New horizons in developing cell lysis methods: A Review

Cell lysis is an essential step in many studies related to biology and medicine. Based on the scale and medium that cell lysis is carried out, there are three main types of the cell lysis: 1) lysis of the cells in the surrounding environment, 2) lysis of the isolated or cultured cells and 3) Single cell lysis. Conventionally, several cell lysis methods have been developed, such as freeze-thawing, bead beating, incursion in liquid nitrogen, sonication and enzymatic and chemical based approaches. In recent years, various novel technologies have been employed to develop new methods of cell lysis. The aim of studies in this field is to introduce more precise and efficient tools or to reduce the costs of cell lysis procedures. Nanostructure based lysis methods, acoustic oscillation, electrical current, irradiation, bacteria-mediated cell lysis, magnetic ionic liquids, bacteriophage genes, monolith columns, hydraulic forces and steam explosion are some examples of new developed cell lysis methods. Beside the significant advances in this field, there are still many challenges and the tools must be further improved. This article is protected by copyright. All rights reserved.

Predictable Changes in Eelgrass Microbiomes with Increasing Wasting Disease Prevalence across 23° Latitude in the Northeastern Pacific

Predicting outcomes of marine disease outbreaks presents a challenge in the face of both global and local stressors. Host-associated microbiomes may play important roles in disease dynamics but remain understudied in marine ecosystems. Host–pathogen–microbiome interactions can vary across host ranges, gradients of disease, and temperature; studying these relationships may aid our ability to forecast disease dynamics. Eelgrass, Zostera marina, is impacted by outbreaks of wasting disease caused by the opportunistic pathogen Labyrinthula zosterae. We investigated how Z. marina phyllosphere microbial communities vary with rising wasting disease lesion prevalence and severity relative to plant and meadow characteristics like shoot density, longest leaf length, and temperature across 23° latitude in the Northeastern Pacific. We detected effects of geography (11%) and smaller, but distinct, effects of temperature (30-day max sea surface temperature, 4%) and disease (lesion prevalence, 3%) on microbiome composition. Declines in alpha diversity on asymptomatic tissue occurred with rising wasting disease prevalence within meadows. However, no change in microbiome variability (dispersion) was detected between asymptomatic and symptomatic tissues. Further, we identified members of Cellvibrionaceae, Colwelliaceae, and Granulosicoccaceae on asymptomatic tissue that are predictive of wasting disease prevalence across the geographic range (3,100 kilometers). Functional roles of Colwelliaceae and Granulosicoccaceae are not known. Cellvibrionaceae, degraders of plant cellulose, were also enriched in lesions and adjacent green tissue relative to nonlesioned leaves. Cellvibrionaceae may play important roles in disease progression by degrading host tissues or overwhelming plant immune responses. Thus, inclusion of microbiomes in wasting disease studies may improve our ability to understand variable rates of infection, disease progression, and plant survival.

IMPORTANCE The roles of marine microbiomes in disease remain poorly understood due, in part, to the challenging nature of sampling at appropriate spatiotemporal scales and across natural gradients of disease throughout host ranges. This is especially true for marine vascular plants like eelgrass (Zostera marina) that are vital for ecosystem function and biodiversity but are susceptible to rapid decline and die-off from pathogens like eukaryotic slime-mold Labyrinthula zosterae (wasting disease). We link bacterial members of phyllosphere tissues to the prevalence of wasting disease across the broadest geographic range to date for a marine plant microbiome-disease study (3,100 km). We identify Cellvibrionaceae, plant cell wall degraders, enriched (up to 61% relative abundance) within lesion tissue, which suggests this group may be playing important roles in disease progression. These findings suggest inclusion of microbiomes in marine disease studies will improve our ability to predict ecological outcomes of infection across variable landscapes spanning thousands of kilometers.

Algicidal Bacteria: A Review of Current Knowledge and Applications to Control Harmful Algal Blooms

Interactions between bacteria and phytoplankton in aqueous ecosystems are both complex and dynamic, with associations that range from mutualism to parasitism. This review focuses on algicidal interactions, in which bacteria are capable of controlling algal growth through physical association or the production of algicidal compounds. While there is some evidence for bacterial control of algal growth in the field, our understanding of these interactions is largely based on laboratory culture experiments. Here, the range of these algicidal interactions is discussed, including specificity of bacterial control, mechanisms for activity, and insights into the chemical and biochemical analysis of these interactions. The development of algicidal bacteria or compounds derived from bacteria for control of harmful algal blooms is reviewed with a focus on environmentally friendly or sustainable methods of application. Potential avenues for future research and further development and application of bacterial algicides for the control of algal blooms are presented.

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds

Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.

Mitigation of harmful algal blooms caused by Alexandrium catenella and reduction in saxitoxin accumulation in bivalves using cultivable seaweeds

Alexandrium catenella is a harmful algal bloom (HAB)-forming dinoflagellate that causes significant damage to the cultivation and harvest of shellfish due to its synthesis of paralytic shellfish toxins.  To evaluate the potential for macroalgae aquaculture to mitigate A. catenella blooms, we determined the effects of three cultivable macroalgae - Saccharina latissima (sugar kelp), Chondrus crispus (Irish moss), and Ulva spp. - on A. catenella in culture- and field-based experiments.  Co-culture growth assays of A. catenella exposed to environmentally realistic concentrations of each macroalgae showed that all species except low levels of C. crispus caused cell lysis and significant reductions in A. catenella densities relative to control treatments of 17-74% in 2-3 days and 42-96% in ~one week (p<0.05 for all assays). In a toxin accumulation experiment, S. latissima significantly lessened (p<0.05) saxitoxin (STX) accumulation in blue mussels (Mytilus edulis), keeping levels (71.80±1.98 µg STX 100 g^-1) below US closure limits (80 µg STX 100 g^-1) compared to the untreated control (93.47±8.11 µg STX 100 g^-1). Bottle incubations of field-collected, bloom populations of A. catenella experienced significant reductions in cell densities of up to 95% when exposed to aquaculture concentrations of all three macroalgae (p<0.005 for all). The stocking of aquacultured S. latissima within mesocosms containing a bloom population of A. catenella (initial density: 3.2 × 10⁴ cells L^-1) reduced the population of A. catenella by 73% over 48 h (p<0.005) while Ulva addition caused a 54% reduction in A. catenella over 96 h (p<0.01).  Among the three seaweeds, their ordered ability to inhibit A. catenella was S. latissima > Ulva spp. > C. crispus. Seaweeds' primary anti-A. catenella activity were allelopathic, while nutrient competition, pH elevation, and macroalgae-attached bacteria may have played a contributory role in some experiments. Collectively, these results suggest that the integration of macroalgae with shellfish-centric aquaculture establishments should be considered as a non-invasive, environmentally friendly, and potentially profit-generating measure to mitigate A. catenella-caused damage to the shellfish aquaculture industry.

Hiding in plain sight: Shellfish-killing phytoplankton in Washington State

Summer bivalve shellfish mortalities have been observed in Puget Sound for nearly a century and attempts to understand and mitigate these losses have been only partially successful. Likewise, the understanding of the environmental conditions triggering shellfish mortalities and successful strategies for their mitigation are incomplete. In the literature, phytoplankton have played only a cursory role in summer shellfish mortalities in Washington State because spawning stress and bacteria were thought to be the primary causes. In recent years, the occurrence of Protoceratium reticulatum (Claparede & Lachmann) Buetschli and Akashiwo sanguinea (Hirasaka) Hansen & Moestrup, have been documented by the SoundToxins research and monitoring partnership in increasing numbers and duration and have been associated with declining shellfish health or mortality at various sites in Puget Sound. Blooms of these species occur primarily in summer months and have been shown to cause mass mortalities of shellfish in the U.S. and other parts of the world. In 2016-2017, yessotoxins (YTX) were measured in several species of Puget Sound bivalve shellfish, with a maximum concentration of 2.20 mg/kg in blue mussels, a value below the regulatory limit of 3.75 mg/kg established by the European Union for human health protection but documented to cause shellfish mortalities in other locations around the world. In July 2019, a bloom of P. reticulatum coincided with a summer shellfish mortality event, involving a dramatic surfacing of stressed, gaping Manila clams, suggesting that YTX could be the cause. YTX concentrations in their tissues were measured at a maximum of 0.28 mg/kg and histology of these clams demonstrated damage to digestive glands. A culture of P. reticulatum, isolated from North Bay during this massive bloom and shellfish mortality event, showed YTX reaching 26.6 pg/cell, the highest recorded toxin quota measured in the U.S. to date. Concentrations of YTX in phytoplankton samples reached a maximum of 920 ng/L during a P. reticulatum bloom in Mystery Bay on 13 August 2019 when cell abundance reached 1.82 million cells/L. The highest cellular YTX quota during that bloom that lasted into September was 10.8 pg/cell on 3 Sept 2019. Shellfish producers in Washington State have also noted shellfish larvae mortalities due to A. sanguinea passing through filtration intake systems into hatchery facilities. Early warning of shellfish-killing harmful algal bloom (HAB) presence in Puget Sound, through partnerships such as SoundToxins, provides options for shellfish growers to mitigate their effects through early harvest, movement of shellstock to upland facilities, or enhanced filtration at aquaculture facilities.

Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides

The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and ¹H, ¹³C, and two-dimensional nuclear magnetic resonance spectroscopy, including ¹H-¹⁵N heteronuclear multiple bond correlation analysis. MS 1056 contains a β-amino acid residue with an alkyl side chain of C₁₅, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC₅₀ values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator

Microbes and seagrass establish symbiotic relationships constituting a functional unit called the holobiont that reacts as a whole to environmental changes. Recent studies have shown that the seagrass microbial associated community varies according to host species, environmental conditions and the host’s health status, suggesting that the microbial communities respond rapidly to environmental disturbances and changes. These changes, dynamics of which are still far from being clear, could represent a sensitive monitoring tool and ecological indicator to detect early stages of seagrass stress. In this review, the state of art on seagrass holobiont is discussed in this perspective, with the aim of disentangling the influence of different factors in shaping it. As an example, we expand on the widely studied Halophila stipulacea’s associated microbial community, highlighting the changing and the constant components of the associated microbes, in different environmental conditions. These studies represent a pivotal contribution to understanding the holobiont’s dynamics and variability pattern, and to the potential development of ecological/ecotoxicological indices. The influences of the host’s physiological and environmental status in changing the seagrass holobiont, alongside the bioinformatic tools for data analysis, are key topics that need to be deepened, in order to use the seagrass-microbial interactions as a source of ecological information.

Distribution of Growth-Inhibiting Bacteria against the Toxic Dinoflagellate Alexandrium catenella (Group I) in Akkeshi-Ko Estuary and Akkeshi Bay, Hokkaido, Japan

The distribution of growth-inhibiting bacteria (GIB) against the toxic dinoflagellate Alexandrium catenella (Group I) was investigated targeting seagrass leaves and surface waters at the seagrass bed of Akkeshi-ko Estuary and surface waters of nearshore and offshore points of Akkeshi Bay, Japan. Weekly samplings were conducted from April to June in 2011. GIBs were detected from surface of leaves of the seagrass Zostera marina in Akkeshi-ko Estuary (7.5 × 105–4.7 × 106 colony-forming units: CFU g−1 wet leaf) and seawater at the stations in Akkeshi Bay (6.7 × 100–1.1 × 103 CFU mL−1). Sequence analyses revealed that the same bacterial strains with the same 16S rRNA sequences were isolated from the surface biofilm of Z. marina and the seawater in the Akkeshi Bay. We therefore strongly suggested that seagrass beds are the source of algicidal and growth-inhibiting bacteria in coastal ecosystems. Cells of A.catenella were not detected from seawaters in Akkeshi-ko Estuary and the coastal point of Akkeshi Bay, but frequently detected at the offshore point of Akkeshi Bay. It is suggested that A.catenella populations were suppressed by abundant GIBs derived from the seagrass bed, leading to the less toxin contamination of bivalves in Akkeshi-ko Estuary.

Distribution of Harmful Algal Growth-Limiting Bacteria on Artificially Introduced Ulva and Natural Macroalgal Beds

The intensity and frequency of harmful algal blooms (HABs) have increased, posing a threat to human seafood resources due to massive kills of cultured fish and toxin contamination of bivalves. In recent years, bacteria that inhibit the growth of HAB species were found to be densely populated on the biofilms of some macroalgal species, indicating the possible biological control of HABs by the artificial introduction of macroalgal beds. In this study, an artificially created Ulva pertusa bed using mobile floating cages and a natural macroalgal bed were studied to elucidate the distribution of algal growth-limiting bacteria (GLB). The density of GLB affecting fish-killing raphidophyte Chattonella antiqua, and two harmful dinoflagellates, were detected between 106 and 107 CFU g−1 wet weight on the biofilm of artificially introduced U. pertusa and 10 to 102 CFU mL−1 from adjacent seawater; however, GLB found from natural macroalgal species targeted all tested HAB species (five species), ranging between 105 and 106 CFU g−1 wet weight in density. These findings provide new ecological insights of GLB at macroalgal beds, and concurrently demonstrate the possible biological control of HABs by artificially introduced Ulva beds.

Cell density-dependent suppression on the development and photosynthetic activities of Sargassum fusiformis embryos by dinoflagellate Karenia mikimotoi

Lots of research has demonstrated that macroalgae can strongly inhibit the growth of harmful algal bloom (HAB) species in general. However, the effects of HABs or HAB-forming species on macrophytes are still largely uncharacterized until now. In the present study, the effects of the dinoflagellate Karenia mikimotoi cell density gradient, live cell suspension (LC), ruptured cell suspension (RC) as well as the cell-free supernatant (FC) of K. mikimotoi at 1000 μg Chla l-1 (~1.0 × 105 cells ml-1) on the development and photosynthesis of Sargassum fusiforme embryos were investigated in a series of laboratory experiments. The results showed that co-cultivation with K. mikimotoi at 500 μg Chla l-1(~5.0 × 104 cells ml-1) and higher cell densities significantly (P<0.05) inhibited the development, pigment content and photosynthetic activities of the embryos. In addition, the inhibitory effects increased with increased cell densities and prolonged exposure time. Compared to the embryos cultured with the F/2 medium (Control), exposure to LC, RC and FC of K. mikimotoi at 1000 μg Chla l-1for 2 weeks all led to decreased relative growth rate (RGR), chlorophyll (Chl) a content, carotenoids (Car) content and photosynthetic activities of the embryos, with LC and RC exhibiting the maximal and the minimal suppression. The dominant inhibitory effects of FC on the embryos indicated that the suppression was mainly caused by the allelochemicals, while the slightest inhibitory effects of RC on the embryos suggested that some intracellular growth-promoting substances were synchronously released when K. mikimotoi cells lyzed. In addition, the most severe growth suppression of embryos by LC indicated that intact cell contact by K. mikimotoi probably also contributed to the inhibitory effects. These results indicated that a dense HAB formed by K. mikimotoi could seriously suppress the development and photosynthesis of S. fusiforme embryos and eventually reduce the seedlings stock.

A halo of reduced dinoflagellate abundances in and around eelgrass beds

Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for 13 major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least 15 m outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming harmful algal blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting.

A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems

Changing ecological communities in response to anthropogenic activities and climate change has become a worldwide problem. The eutrophication of waterbodies in freshwater and seawater caused by the effects of human activities and nutrient inputs could result in harmful algae blooms (HABs), decreases water quality, reductions in biodiversity and threats to human health. Rapid and accurate monitoring and assessment of aquatic ecosystems are imperative. Environmental DNA (eDNA) analysis using high-throughput sequencing has been demonstrated to be an effective and sensitive assay for detecting and monitoring single or multiple species in different samples. In this study, we review the potential applications of eDNA approaches in controlling and mitigating eutrophication and HABs in freshwater and marine ecosystems. We use recent studies to highlight how eDNA methods have been shown to be a useful tool for providing comprehensive data in studies of eutrophic freshwater and marine environments. We also provide perspectives on using eDNA techniques to reveal molecular mechanisms in biological processes and mitigate eutrophication and HABs in aquatic ecosystems. Finally, we discuss the feasible applications of eDNA for monitoring biodiversity, surveying species communities and providing instructions for the conservation and management of the environment by integration with traditional methods and other advanced techniques.

The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning

This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.

Questiomycins, Algicidal Compounds Produced by the Marine Bacterium Alteromonas sp. D and Their Production Cue

Questiomycin A (1) along with three new compounds, questiomycins C–E (2–4), were isolated from culture of Alteromonas sp. D, an algicidal marine bacterium, guided by algal lethality assay using the raphidophyte, Chattonella antiqua, one of the causative organisms of harmful algal bloom. The structures of 1–4 were assigned on the basis of their spectrometric and spectroscopic data. Compounds 1 to 4 exhibited algicidal activity against C. antiqua with LC₅₀ values ranging from 0.18 to 6.37 μM. Co-cultivation experiment revealed that 1 was produced only when the microalgae and the bacterium are in close contact, suggesting that some interactions between them trigger the biosynthesis of questiomycins. These results suggested that the algicidal bacteria such as Alteromonas sp. D can control microalgae chemically in marine ecosystem.

Rapid Metabolome and Bioactivity Profiling of Fungi Associated with the Leaf and Rhizosphere of the Baltic Seagrass Zostera marina

Zostera marina (eelgrass) is a marine foundation species with key ecological roles in coastal habitats. Its bacterial microbiota has been well studied, but very little is known about its mycobiome. In this study, we have isolated and identified 13 fungal strains, dominated by Penicillium species (10 strains), from the leaf and the root rhizosphere of Baltic Z. marina. The organic extracts of the fungi that were cultured by an OSMAC (One-Strain–Many-Compounds) regime using five liquid culture media under both static and shaking conditions were investigated for their chemical and bioactivity profiles. All extracts showed strong anti-quorum sensing activity, and the majority of the Penicillium extracts displayed antimicrobial or anti-biofilm activity against Gram-negative environmental marine and human pathogens. HPLC-DAD-MS-based rapid metabolome analyses of the extracts indicated the high influence of culture conditions on the secondary metabolite (SM) profiles. Among 69 compounds detected in all Penicillium sp. extracts, 46 were successfully dereplicated. Analysis of SM relatedness in culture conditions by Hierarchical Cluster Analysis (HCA) revealed generally low similarity and showed a strong effect of medium selection on chemical profiles of Penicillium sp. This is the first study assessing both the metabolite and bioactivity profile of the fungi associated with Baltic eelgrass Z. marina.

Dynamics of seagrass bed microbial communities in artificial Chattonella blooms: A laboratory microcosm study

The influence of algicidal and growth-inhibiting bacteria in a seagrass (Zostera marina) bed, and their capability of controlling blooms of the fish-killing raphidophyte flagellate, Chattonella antiqua, were examined in laboratory microcosm experiments. Bacterial communities in seawater collected from the seagrass bed and Z. marina biofilm suppressed artificial Chattonella blooms in the presence of their natural competitors and predators. Phylogenetic analysis suggest that considerable numbers of bacteria that suppress Chattonella, including algicidal or growth-inhibiting bacteria isolated from seagrass biofilm and seawater from the seagrass bed, are members of Proteobacteria that can decompose lignocellulosic compounds. A direct comparison of partial 16S rRNA gene sequences (500 bp) revealed that the growth-limiting bacterium (strain ZM101) isolated from Z. marina biofilm belonged to the genus Phaeobacter (Alphaproteobacteria) showed 100% similarity with strains of growth-limiting bacteria isolated from seawater of both the seagrass bed and nearshore region, suggesting that the origin of these growth-limiting bacteria are the seagrass biofilm or seawater surrounding the seagrass bed. This study demonstrates that Chattonella growth-limiting bacteria living on seagrass biofilm and in the adjacent seawater can suppress Chattonella blooms, suggesting the possibility of Chattonella bloom prevention through restoration, protection, or introduction of seagrass in coastal areas.

Surface chemical defence of the eelgrass Zostera marina against microbial foulers

Plants rely on both mechanical and chemical defence mechanisms to protect their surfaces against microorganisms. The recently completed genome of the eelgrass Zostera marina, a marine angiosperm with fundamental importance for coastal ecosystems, showed that its re-adaptation from land to the sea has led to the loss of essential genes (for chemical communication and defence) and structural features (stomata and thick cuticle) that are typical of terrestrial plants. This study was designed to understand the molecular nature of surface protection and fouling-control strategy of eelgrass against marine epiphytic yeasts. Different surface extraction methods and comparative metabolomics by tandem mass spectrometry (LC-MS/MS) were used for targeted and untargeted identification of the metabolite profiles of the leaf surface and the whole tissue extracts. Desorption electrospray ionization-imaging mass spectrometry (DESI-IMS) coupled with traditional bioassays revealed, for the first time, the unique spatial distribution of the eelgrass surface-associated phenolics and fatty acids, as well as their differential bioactivity against the growth and settlement of epiphytic yeasts. This study provides insights into the complex chemical defence system of the eelgrass leaf surface. It suggests that surface-associated metabolites modulate biotic interactions and provide chemical defence and structural protection to eelgrass in its marine environment.

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

Macroalgae variably promote and deter microbial growth through release of organic carbon and antimicrobial compounds into the water column. Consequently, macroalgae influence the microbial composition of the surrounding water column and biofilms on nearby surfaces. Here, we use manipulative experiments to test the hypotheses that (i) Nereocystis luetkeana and Mastocarpus sp. macroalgae alter the water column microbiota in species-specific manner, that (ii) neighbouring macroalgae alter the bacterial communities on the surface (epibiota) of actively growing Nereocystis luetkeana meristem fragments (NMFs), and that (iii) neighbours alter NMF growth rate. We also assess the impact of laboratory incubation on macroalgal epibiota by comparing each species to wild counterparts. We find strong differences between the Nereocystis and Mastocarpus epibiota that are maintained in the laboratory. Nereocystis and Mastocarpus alter water column bacterial community composition and richness in a species specific manner, but cause only small compositional shifts on NMF surfaces that do not differ by species, and do not change richness. Co-incubation with macroalgae results in significant change in abundance of fivefold more genera in the water column compared to NMF surfaces, although the direction (i.e., enrichment or reduction) of shift is generally consistent between the water and NMF surfaces. Finally, NMFs grew during the experiment, but growth did not depend on the presence or identity of neighbouring macroalgae. Thus, macroalgae exhibit a strong and species-specific influence on the water column microbiota, but a much weaker influence on the epibiota of neighbouring macroalgae. Overall, these results support the idea that macroalgae surfaces are highly selective and demonstrate that modulations of macroalgal microbiota operate within an overarching paradigm of host species specificity.

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe-plant mutualisms support the health and growth of aquatic plants.