Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events

Diverse interactions between bacteria and microalgae: A review for enhancing harmful algal bloom mitigation and biomass processing efficiency

The interactions between bacteria and microalgae play pivotal roles in resource allocation, biomass accumulation, nutrient recycling, and species succession in aquatic systems, offering ample opportunities to solve several social problems. The escalating threat of harmful algal blooms (HABs) in the aquatic environment and the lack of cheap and eco-friendly algal-biomass processing methods have been among the main problems, demanding efficient and sustainable solutions. In light of this, the application of algicidal bacteria to control HABs and enhance algal biomass processing has been promoted in the past few decades as potentially suitable mechanisms to solve those problems. Hence, this comprehensive review aims to explore the diverse interaction modes between bacteria and microalgae, ranging from synergistic to antagonistic, and presents up-to-date information and in-depth analysis of their potential biotechnological applications, particularly in controlling HABs and enhancing microalgal biomass processing. For instance, several studies revealed that algicidal bacteria can effectively inhibit the growth of Microcystis aeruginosa, a notorious freshwater HAB species, with an antialgal efficiency of 24.87 %-98.8 %. The review begins with an overview of the mechanisms behind algae-bacteria interactions, including the environmental factors influencing these dynamics and their broader implications for aquatic ecosystems. It then provides a detailed analysis of the role of algicidal bacteria in controlling harmful algal blooms, as well as their role in bioflocculation and the pretreatment of microalgal biomass. Additionally, the review identifies and discusses the constraints and challenges in the biotechnological application of these interactions. By exploring the strategic use of algicidal bacteria, this review not only underscores their importance in maintaining aquatic environmental health but also in enhancing biomass processing efficiency. It offers valuable insights into future research avenues and the potential scalability of these applications, both in situ and at an industrial level.

Microbiome signature of different stages of hypoxia event in Wonmun Bay

We investigated how microbial communities associated with different hypoxic stages respond to environmental changes across three water depths in Wonmun Bay, South Korea. Analysis of temperature, salinity, dissolved oxygen (DO), and nutrient concentrations revealed prominent seasonal shifts and strong stratification during summer hypoxia. Metabarcoding of prokaryotic 16 S rRNA genes and phototrophic eukaryotic chloroplasts along with quantitative PCR (qPCR) revealed variations in the abundance and composition of these communities. Chloroplast 16 S sequences in May were dominated by land plants (93% of Embryophyta), contrasting with the diverse phytoplankton taxa detected in other months. The water communities in May also had higher total microbial abundance than other months but significantly lower alpha diversity. These results suggest a major influence of freshwater discharge on water communities, pre-conditioning for hypoxia events by promoting organic matter decomposition coupled with DO consumption in bottom water. Subsequently, distinct microbial communities were observed across depths during hypoxia in June and July, while less variability was detected among different depths in September and later months when hypoxia events disappeared. Principal Coordinate analysis (PCoA) demonstrated the distinct patterns of microbial communities in May, June, and July from other months. Both sulfur-oxidizing and sulfate-reducing bacteria (SRB) were prevalent in June while the increase of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was observed in mid and bottom water in July. This data suggests the intricate interaction between sulfur and nitrogen-cycling microbes during the hypoxia events in Wonmun Bay. In conclusion, this study provides valuable insights into the microbial community responses to the varying environmental conditions at different stages of hypoxia events in eutrophic coastal ecosystems.

Quantification of Climate Footprints of Vibrio vulnificus in Coastal Human Communities of the United States Gulf Coast

The incidence of vibriosis is rising globally with evidence of climate variability influencing environmental processes that support growth of pathogenic Vibrio spp. The waterborne pathogen, Vibrio vulnificus can invade wounds and has one of the highest case fatality rates in humans. The bacterium cannot be eradicated from the aquatic environment, hence climate driven environmental conditions enhancing growth and dissemination of V. vulnificus need to be understood to provide preemptive assessment of its presence and distribution in aquatic systems. To achieve this objective, satellite remote sensing was employed to quantify the association of sea surface temperature (SST) and chlorophyll-a (chl-a) in locations with reported V. vulnificus infections. Monthly analysis was done in two populated regions of the Gulf of Mexico-Tampa Bay, Florida, and Galveston Bay, Texas. Results indicate warm water, characterized by a 2-month lag in SST, high concentration of phytoplankton, proxied for zooplankton using 1 month lagged chl-a values, was statistically linked to higher odds of V. vulnificus infection in the human population. Identification of climate and ecological processes thresholds is concluded to be useful for development of an heuristic prediction system designed to determine risk of infection for coastal populations.

Effects of turbulence on diatoms of the genus Pseudo-nitzschia spp. and associated bacteria

Turbulence is one of the least investigated environmental factors impacting the ecophysiology of phytoplankton, both at the community and individual species level. Here, we investigated, for the first time, the effect of a turbulence gradient (Reynolds number, from Reλ = 0 to Reλ = 360) on two species of the marine diatom Pseudo-nitzschia and their associated bacterial communities under laboratory conditions. Cell abundance, domoic acid (DA) production, chain formation, and Chl a content of P. fraudulenta and P. multiseries were higher for intermediate turbulence (Reλ = 160 or 240). DA was detectable only in P. multiseries samples. These observations were supported by transcriptomic analyses results, which suggested the turbulence related induction of the expression of the DA production locus, with a linkage to an increased photosynthetic activity of the total metatranscriptome. This study also highlighted a higher richness of the bacterial community associated with the nontoxic strain of P. fraudulenta in comparison to the toxic strain of P. multiseries. Bacillus was an important genus in P. multiseries cultures (relative abundance 15.5%) and its highest abundances coincided with the highest DA levels. However, associated bacterial communities of both Pseudo-nitzschia species did not show clear patterns relative to turbulence intensity.

Succession of diversity, assembly mechanisms, and activities of the microeukaryotic community throughout Scrippsiella acuminata (Dinophyceae) bloom phases

Harmful algal bloom (HAB) is a rapidly expanding marine ecological hazard. Although numerous studies have been carried out about the ecological impact and the ecological mechanism of HAB outbreaks, few studies have comprehensively addressed the shifts of species composition, metabolic activity level, driving factors and community assembly mechanisms of microeukaryotic plankton in the course of the bloom event. To fill the gap of research, we conducted 18S ribosomal DNA and RNA sequencing during the initiation, development, sustenance and decline stages of a Scrippsiella acuminata (S. acuminata) bloom at the coastal sea of Fujian Province, China. We found that the bloom event caused a decrease in microeukaryotic plankton species diversity and increase in community homogeneity. Our results revealed that the RNA- and DNA-inferred communities were similar, but α-diversity was more dynamic in RNA- than in DNA-inferred communities. The main taxa with high projected metabolic activity (with RNA:DNA ratio as the proxy) during the bloom included dinoflagellates, Cercozoa, Chlorophyta, Protalveolata, and diatoms. The role of deterministic processes in microeukaryotic plankton community assembly increased during the bloom, but stochastic processes were always the dominant assembly mechanism throughout the bloom process. Our findings improve the understanding of temporal patterns, driving factors and assembly mechanisms underlying the microeukarytic plankton community in a dinoflagellate bloom.

Impact of wildfire ash on bacterioplankton abundance and community composition in a coastal embayment (Ría de Vigo, NW Spain)

Wildfire ash can have an impact on coastal prokaryotic plankton. To understand the extent to which community composition and abundance of coastal prokaryotes are affected by ash, two ash addition experiments were performed. Ash from a massive wildfire that took place in the Ría de Vigo watershed in October 2017 was added to natural surface water samples collected in the middle sector of the ría during the summer of 2019 and winter of 2020, and incubated for 72 h, under natural water temperature and irradiance conditions. Plankton responses were assessed through chlorophyll a and bacterial abundance measurements. Prokaryotic DNA was analyzed using 16S rRNA gene partial sequencing. In summer, when nutrient concentrations were low in the ría, the addition of ash led to an increase in phytoplankton and bacterial abundance, increasing the proportions of Alteromonadales, Flavobacteriales, and the potentially pathogenic Vibrio, among other taxa. After the winter runoff events, nutrient concentrations in the Ría de Vigo were high, and only minor changes in bacterial abundance were detected. Our findings suggest that the compounds associated with wildfire ash can alter the composition of bacterioplanktonic communities, which is relevant information for the management of coastal ecosystems in fire-prone areas.

Microalgae Inoculation Significantly Shapes the Structure, Alters the Assembly Process, and Enhances the Stability of Bacterial Communities in Shrimp-Rearing Water

Intensive shrimp farming may lead to adverse environmental consequences due to discharged water effluent. Inoculation of microalgae can moderate the adverse effect of shrimp-farming water. However, how bacterial communities with different lifestyles (free-living (FL) and particle-attached (PA)) respond to microalgal inoculation is unclear. In the present study, we investigated the effects of two microalgae (Nannochloropsis oculata and Thalassiosira weissflogii) alone or in combination in regulating microbial communities in shrimp-farmed water and their potential applications. PERMANOVA revealed significant differences among treatments in terms of time and lifestyle. Community diversity analysis showed that PA bacteria responded more sensitively to different microalgal treatments than FL bacteria. Redundancy analysis (RDA) indicated that the bacterial community was majorly influenced by environmental factors, compared to microalgal direct influence. Moreover, the neutral model analysis and the average variation degree (AVD) index indicated that the addition of microalgae affected the bacterial community structure and stability during the stochastic process, and the PA bacterial community was the most stable with the addition of T. weissflogii. Therefore, the present study revealed the effects of microalgae and nutrient salts on bacterial communities in shrimp aquaculture water by adding microalgae to control the process of community change. This study is important for understanding the microbial community assembly and interpreting complex interactions among zoo-, phyto-, and bacterioplankton in shrimp aquaculture ecosystems. Additionally, these findings may contribute to the sustainable development of shrimp aquaculture and ecosystem conservation.

Cyanobacterial extracellular antibacterial substances could promote the spread of antibiotic resistance: impacts and reasons

Many studies have shown that antibiotic resistance genes (ARGs) can be facilitated by a variety of antibacterial substances. Cyanobacteria are photosynthetic bacteria that are widely distributed in the ocean. Some extracellular substances produced by marine cyanobacteria have been found to possess antibacterial activity. However, the impact of these extracellular substances on ARGs is unclear. Therefore, we established groups of seawater microcosms that contained different concentrations (1000, 100, 10, 1, 0.1, 0.01, and 0 μg mL-1) of cyanobacterial extracellular substances (CES), and tracked the changes of 17 types of ARGs, the integron gene (intI1), as well as the bacterial community at different time points. The results showed that CES could enrich most ARGs (15/17) in the initial stage, particularly at low concentrations (10 and 100 μg mL-1). The correlation analysis showed a positive correlation between several ARGs and intI1. It is suggested that the abundance of intI1 increased with CES may contribute to the changes of these ARGs, and co-resistance of CES may be the underlying reason for the similar variation pattern of some ARGs. Moreover, the results of qPCR and high-throughput sequencing of 16S rRNA showed that CES had an inhibitory impact on the growth of bacterial communities. High concentrations of CES were found to alter the structure of bacterial communities. Co-occurrence networks showed that bacteria elevated in the high concentration group of CES and might serve as the potential hosts for a variety of ARGs. In general, marine cyanobacteria could play an important role in the global dissemination of ARGs and antibiotic-resistant bacteria (ARBs).

Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp

Reciprocal metabolite exchanges between diatoms and bacteria can enhance the growth of both partners and therefore fundamentally influence aquatic ecosystem productivity. Here, we examined the growth-promoting capabilities of 15 different bacterial isolates from the bacterial community associated with the marine diatom Actinocyclus sp. and investigated the magnitude and timing of their effect on the growth of this diatom. In the presence of its microbiome, Actinocyclus sp. growth was significantly enhanced relative to axenic cultures. Co-culture with each of the 15 bacterial isolates examined here (seven Rhodobacteraceae, four Vibrionaceae, two Pseudoalteromonadaceae, one Oceanospirillaceae and one Alteromonadaceae) increased the growth of the diatom host, with four isolates inducing rates of growth that were similar to those delivered by the diatom's full microbiome. However, the timing and duration of this effect differed between the different bacteria tested. Indeed, one Rhodobacteraceae and one Alteromonadaceae enhanced Actinocyclus sp. cell numbers between days 0-6 after co-incubation, five other Rhodobacteraceae promoted diatom cell numbers the most between days 8-12, whilst four Vibrionaceae, one Oceanospirillaceae and one Rhodobacteraceae enhanced Actinocyclus sp. cell abundance between days 14-16. These results are indicative of a succession of the growth-enhancing effects delivered by diverse bacteria throughout the Actinocyclus sp. life cycle, which will likely deliver sustained growth benefits to the diatom when its full microbiome is present.

Phytoplankton Producer Species and Transformation of Released Compounds over Time Define Bacterial Communities following Phytoplankton Dissolved Organic Matter Pulses

Phytoplankton-bacterium interactions are mediated, in part, by phytoplankton-released dissolved organic matter (DOMp). Two factors that shape the bacterial community accompanying phytoplankton are (i) the phytoplankton producer species, defining the initial composition of released DOMp, and (ii) the DOMp transformation over time. We added phytoplankton DOMp from the diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 to natural bacterial communities from the eastern Mediterranean and determined the bacterial responses over a time course of 72 h in terms of cell numbers, bacterial production, alkaline phosphatase activity, and changes in active bacterial community composition based on rRNA amplicon sequencing. Both DOMp types were demonstrated to serve the bacterial community as carbon and, potentially, phosphorus sources. Bacterial communities in diatom-derived DOM treatments maintained higher Shannon diversities throughout the experiment and yielded higher bacterial production and lower alkaline phosphatase activity compared to cyanobacterium-derived DOM after 24 h of incubation (but not after 48 and 72 h), indicating greater bacterial usability of diatom-derived DOM. Bacterial communities significantly differed between DOMp types as well as between different incubation times, pointing to a certain bacterial specificity for the DOMp producer as well as a successive utilization of phytoplankton DOM by different bacterial taxa over time. The highest differences in bacterial community composition with DOMp types occurred shortly after DOMp additions, suggesting a high specificity toward highly bioavailable DOMp compounds. We conclude that phytoplankton-associated bacterial communities are strongly shaped by the phytoplankton producer as well as the transformation of its released DOMp over time. IMPORTANCE Phytoplankton-bacterium interactions influence biogeochemical cycles of global importance. Phytoplankton photosynthetically fix carbon dioxide and subsequently release the synthesized compounds as dissolved organic matter (DOMp), which becomes processed and recycled by heterotrophic bacteria. Yet the importance of phytoplankton producers in combination with the time-dependent transformation of DOMp compounds on the accompanying bacterial community has not been explored in detail. The diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 belong to globally important phytoplankton genera, and our study revealed that DOMp of both species was selectively incorporated by the bacterial community. The producer species had the highest impact shortly after DOMp appropriation, and its effect diminished over time. Our results improve the understanding of the dynamics of organic matter produced by phytoplankton in the oceans as it is utilized and modified by cooccurring bacteria.

Microbial community structure and settlement induction capacity of marine biofilms developed under varied reef conditions

Coral larval settlement relies on biogenic cues such as those elicited by microbial biofilm communities, a crucial element of coral recruitment. Eutrophication can modify these biofilm-associated communities, but studies on how this affects coral larval settlement are limited. In this study, we developed biofilm communities on glass slides at four sites with increasing distance from a mariculture zone. Biofilms farthest from the mariculture area were more effective at inducing the settlement of Acropora tenuis larvae. These biofilms were characterized by a greater proportion of crustose coralline algae (CCA) and gammaproteobacterial taxa compared to biofilms from sites closer to the mariculture zone, which had a greater proportion of cyanobacteria and no CCA. These findings suggest that nutrient enrichment due to mariculture activities alters the composition of biofilm-associated microbiome at nearby reef sites and indirectly causes poor coral larval settlement.

Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations

The exchange of metabolites mediates algal and bacterial interactions that maintain ecosystem function. Yet, while thousands of metabolites are produced, only a few molecules have been identified in these associations. Using the ubiquitous microalgae Pseudo-nitzschia sp., as a model, we employed an untargeted metabolomics strategy to assign structural characteristics to the metabolites that distinguished specific diatom-microbiome associations. We cultured five species of Pseudo-nitzschia, including two species that produced the toxin domoic acid, and examined their microbiomes and metabolomes. A total of 4826 molecular features were detected by tandem mass spectrometry. Only 229 of these could be annotated using available mass spectral libraries, but by applying new in silico annotation tools, characterization was expanded to 2710 features. The metabolomes of the Pseudo-nitzschia-microbiome associations were distinct and distinguished by structurally diverse nitrogen compounds, ranging from simple amines and amides to cyclic compounds such as imidazoles, pyrrolidines and lactams. By illuminating the dark metabolomes, this study expands our capacity to discover new chemical targets that facilitate microbial partnerships and uncovers the chemical diversity that underpins algae-bacteria interactions.

Emerging harmful algal blooms caused by distinct seasonal assemblages of a toxic diatom

Diatoms in the Pseudo-nitzschia genus produce the neurotoxin domoic acid. Domoic acid bioaccumulates in shellfish, causing illness in humans and marine animals upon ingestion. In 2017, high domoic acid levels in shellfish meat closed shellfish harvest in Narragansett Bay, Rhode Island for the first and only time in history, although abundant Pseudo-nitzschia have been observed for over 60 years. To investigate whether an environmental factor altered endemic Pseudo-nitzschia physiology or new domoic acid-producing strain(s) were introduced to Narragansett Bay, we conducted weekly sampling from 2017 to 2019 and compared closure samples. Plankton-associated domoic acid was quantified by LC-MS/MS and Pseudo-nitzschia spp. were identified using a taxonomically improved high-throughput rDNA sequencing approach. Comparison with environmental data revealed a detailed understanding of domoic acid dynamics and seasonal multi-species assemblages. Plankton-associated domoic acid was low throughout 2017-2019, but recurred in fall and early summer maxima. Fall domoic acid maxima contained known toxic species as well as a novel Pseudo-nitzschia genotype. Summer domoic acid maxima included fewer species but also known toxin producers. Most 2017 closure samples contained the particularly concerning toxic species, P. australis, which also appeared infrequently during 2017-2019. Recurring Pseudo-nitzschia assemblages were driven by seasonal temperature changes, and plankton-associated domoic acid correlated with low dissolved inorganic nitrogen. Thus, the Narragansett Bay closures were likely caused by both resident assemblages that become toxic depending on nutrient status as well as the episodic introductions of toxic species from oceanographic and climatic shifts.

Specific bacterial microbiome enhances the sexual reproduction and auxospore production of the marine diatom, Odontella

Auxospore production is a sexual reproductive strategy by diatoms to re-attain normal size after the size-reducing effect of clonal reproduction. Aside from the minimum size threshold used as a sex clock by diatoms, the environmental or chemical triggers that can induce sex in diatoms are still not well understood. Here we investigated the influence of six marine bacteria from five families on the production of sexual cells and auxospores of the ubiquitous marine polar centric diatom, Odontella sp. Microbiome association and co-occurrence with the diatom in culture and in nature were investigated using 16S rRNA amplicon sequencing. Indole acetic acid (IAA) secretion, a phytohormone that regulates plants' growth and sexual development, was explored as a potential inducer of sexual reproduction in Odontella and compared between bacterial associates. We found that Odontella co-cultured with Flavobacteriaceae (Polaribacter and Cellulophaga) have significantly more sexual cells and auxospores than bacteria-free Odontella and Odontella co-cultured with other bacteria from Vibrionaceae (Vibrio), Pseudoalteromonadaceae (Pseudoalteromonas), Rhodobacteraceae (Sulfitobacter), or Planococcaceae (Planococcus) family. Differences in IAA secretion were observed between bacterial isolates, but this did not correspond consistently with the diatom's clonal growth or production of sexual cells and auxospores. Microbiome composition survey of Odontella cultures showed that the diatom harbors homologous sequences of the four bacterial isolates at varying proportions, with Sulfitobacter and Polaribacter at high abundances. Microbiome surveys at Santa Cruz Wharf, Monterey Bay, from 2014-2015 showed that Odontella abundance is positively correlated with Flavobacteriaceae and Rhodobacteraceae abundances. Our study demonstrates that specific members of the diatom microbiome can enhance the host's sexual reproduction, with the interkingdom interaction driven by partner compatibility and long-term association. Sex-enhancing bacteria may even be needed by the diatom host to carry out the optimal inducement of sex under normal conditions, allowing for size restitution and maintaining genetic diversity in culture and in nature.

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.

Cold-Active Shewanella glacialimarina TZS-4T nov. Features a Temperature-Dependent Fatty Acid Profile and Putative Sialic Acid Metabolism

Species of genus Shewanella are among the most frequently identified psychrotrophic bacteria. Here, we have studied the cellular properties, growth dynamics, and stress conditions of cold-active Shewanella strain #4, which was previously isolated from Baltic Sea ice. The cells are rod-shaped of ~2μm in length and 0.5μm in diameter, and they grow between 0 and 25°C, with an optimum at 15°C. The bacterium grows at a wide range of conditions, including 0.5–5.5% w/v NaCl (optimum 0.5–2% w/v NaCl), pH 5.5–10 (optimum pH 7.0), and up to 1mM hydrogen peroxide. In keeping with its adaptation to cold habitats, some polyunsaturated fatty acids, such as stearidonic acid (18:4n-3), eicosatetraenoic acid (20:4n-3), and eicosapentaenoic acid (20:5n-3), are produced at a higher level at low temperature. The genome is 4,456kb in size and has a GC content of 41.12%. Uniquely, strain #4 possesses genes for sialic acid metabolism and utilizes N-acetyl neuraminic acid as a carbon source. Interestingly, it also encodes for cytochrome c3 genes, which are known to facilitate environmental adaptation, including elevated temperatures and exposure to UV radiation. Phylogenetic analysis based on a consensus sequence of the seven 16S rRNA genes indicated that strain #4 belongs to genus Shewanella, closely associated with Shewanella aestuarii with a ~97% similarity, but with a low DNA–DNA hybridization (DDH) level of ~21%. However, average nucleotide identity (ANI) analysis defines strain #4 as a separate Shewanella species (ANI score=76). Further phylogenetic analysis based on the 92 most conserved genes places Shewanella strain #4 into a distinct phylogenetic clade with other cold-active marine Shewanella species. Considering the phylogenetic, phenotypic, and molecular characterization, we conclude that Shewanella strain #4 is a novel species and name it Shewanella glacialimarina sp. nov. TZS-4_T, where glacialimarina means sea ice. Consequently, S. glacialimarina TZS-4_T constitutes a promising model for studying transcriptional and translational regulation of cold-active metabolism.

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms

Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.

Temporal variability of free-living microbial culturability and community composition after an Akashiwo sanguinea bloom in Shenzhen, China

Dinoflagellate blooms currently caused serious environmental problems in different areas of the world. Recent studies revealed close relationship between dinoflagellate blooms and microbial community dynamics, while less attention has been paid on the bacterial culturability change associated with the bloom. Here, we investigated the temporal variation of microbial community composition and culturability during the decline stage of an Akashiwo sanguinea bloom occurred in Shenzhen, China. The daily microbial community phylogenetic structures in water samples collected during a four-day period after the bloom peak were assessed through 16S rRNA gene amplicons sequencing on the MiSeq (Illumina) platform. The environmental parameters, Chlorophyll a concentrations, and total viable and culturable bacterial densities were also measured. Our results showed that Gamma-proteobacteria comprising mostly of Pseudoalteromonadaceae and Vibrionaceae was the predominant microbial class in the post-bloom samples, except for the second day. During that day, the represented groups switched to Alpha-proteobacteria (Rhizobiales) and Beta-proteobacteria (Comamonadaceae), with the microbial culturability decreased. Total viable bacterial densities reached the maximum value on the third day, with Gamma-proteobacteria regained the dominance till the fourth day. The dramatic microbial community succession and culturability variation observed in this study indicated the complication of algae-bacteria interactions during dinoflagellate bloom.

Dynamics of microcystins and saxitoxin in the Indian River Lagoon, Florida

Harmful algal blooms that can produce toxins are common in the Indian River Lagoon (IRL), which covers ~250 km of Florida's east coast. The current study assessed the dynamics of microcystins and saxitoxin in six segments of the IRL: Banana River Lagoon (BRL), Mosquito Lagoon (ML), Northern IRL (NIRL), Central IRL (CIRL), Southern IRL (SIRL), and the St. Lucie Estuary (SLE). Surface water samples (n = 40) collected during the 2018 wet and 2019 dry season were analyzed to determine associations between toxins and temperature, salinity, pH, oxygen saturation, concentrations of dissolved nutrients and chlorophyll-a, presence of biosynthetic genes for toxins, relative abundance of planktonic species, and composition of the microbial community. The potential toxicity of samples was assessed using multiple mammalian cell lines. Enzyme-Linked Immunosorbent Assays were used to determine concentrations of microcystins and saxitoxin. Overall, the microcystins concentration ranged between 0.01-85.70 µg/L, and saxitoxin concentrations ranged between 0.01-2.43 µg/L across the IRL. Microcystins concentrations were 65% below the limit of quantification (0.05 µg/L), and saxitoxin concentrations were 85% below the limit of detection (0.02 µg/L). Microcystins concentrations were higher in the SLE, while saxitoxin was elevated in the NIRL and BRL. Cytotoxicity related to the presence of microcystins was seen in the SLE during the wet season. No significant patterns between cytotoxicity and saxitoxin were identified. Dissolved nutrients were identified as the most highly related parameters, explaining 53% of microcystin and 47% of saxitoxin variability. Multivariate models suggested cyanobacteria, flagellates, ciliates, and diatoms as the subset of microorganisms whose abundances were maximally correlated with saxitoxin and microcystins concentrations. Lastly, biosynthetic genes for microcystins were detected in the SLE and for saxitoxin in the BRL and NIRL. These results highlight the synergistic roles environmental and biological parameters play in influencing the dynamics of toxin production by harmful algae in the IRL.

Presence and abundance of bacteria with the Type VI secretion system in a coastal environment and in the global oceans

Marine bacteria employ various strategies to maintain their competitive advantage over others in a mixed community. The use of Type VI Secretion Systems (T6SS), a protein secretion apparatus used as a molecular weapon for interbacterial competition and eukaryotic interactions, is one of the competitive strategies that is least studied among heterotrophic bacteria living in the water column. To get an insight into the temporal and spatial distribution of bacteria with T6SS in this portion of the marine environment, we examine the presence and abundance of T6SS-bearing bacteria at both local and global scales through the use of metagenome data from water samples obtained from the coast of Monterey Bay and the TARA Oceans project. We also track the abundance of T6SS-harboring bacteria through a two-year time series of weekly water samples in the same coastal site to examine the environmental factors that may drive their presence and abundance. Among the twenty-one T6SS-bearing bacterial genera examined, we found several genera assume a particle-attached lifestyle, with only a few genera having a free-living lifestyle. The abundance of T6SS-harboring bacteria in both niches negatively correlates with the abundance of autotrophs. Globally, we found that T6SS genes are much more abundant in areas with low biological productivity. Our data suggest that T6SS-harboring bacteria tend to be abundant spatially and temporally when organic resources are limited. This ecological study agrees with the patterns observed from several in vitro studies; that T6SS could be an adaptive strategy employed by heterotrophic bacteria to obtain nutrients or reduce competition when resources are in limited quantity.

Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM

To study the response of bacteria to different size-fractions of naturally occurring dissolved organic matter (DOM), a natural prokaryotic community from North Atlantic mesopelagic waters (1000 m depth) was isolated and grown in (i) 0.1-μm filtered seawater (CONTROL), (ii) the low-molecular-weight (<1 kDa) DOM fraction (L-DOM), and (iii) the recombination of high- (>1 kDa) and low-molecular-weight DOM fractions (H + L-DOM), to test the potential effect of ultrafiltration on breaking the DOM size continuum. Prokaryotic abundance and leucine incorporation were consistently higher in the H + L-DOM niche than in the L-DOM and CONTROL treatments, suggesting a different interaction with each DOM fraction and the disruption of the structural DOM continuum by ultrafiltration, respectively. Rhodobacterales (Alphaproteobacteria) and Flavobacteriales (Bacteroidetes) were particularly enriched in L-DOM and closely related to the colored DOM (CDOM) fraction, indicating the tight link between these groups and changes in DOM aromaticity. Conversely, some other taxa that were rare or undetectable in the original bacterial community were enriched in the H + L-DOM treatment (e.g., Alteromonadales belonging to Gammaproteobacteria), highlighting the role of the rare biosphere as a seed bank of diversity against ecosystem disturbance. The relationship between the fluorescence of protein-like CDOM and community composition of populations in the H + L-DOM treatment suggested their preference for labile DOM. Conversely, the communities growing on the L-DOM niche were coupled to humic-like CDOM, which may indicate their ability to degrade more reworked DOM and/or the generation of refractory substrates (as by-products of the respiration processes). Most importantly, L- and/or H + L-DOM treatments stimulated the growth of unique bacterial amplicon sequence variants (ASVs), suggesting the potential of environmental selection (i.e., changes in DOM composition and availability), particularly in the light of climate change scenarios. Taken together, our results suggest that different size-fractions of DOM induced niche-specialization and differentiation of mesopelagic bacterial communities.

Bacterioplankton assembly and interspecies interactions follow trajectories of Gymnodinium-diatom bloom

The underlying mechanisms of bacterioplankton community assembly and interspecies interactions during harmful algal blooms remain largely unclear. Using 16S rRNA gene amplicon sequencing, we analyzed the bacterioplankton communities over the continuous course of saxitoxin-producing Gymnodinium catenatum blooms and two diatom (i.e., Skeletonema costatum and Chaetoceros curvisetus) blooms in an anthropogenically controlled and eutrophic bay, East China Sea. The succession of bacterioplankton communities correlated with changes in the dynamics of algal species. Deterministic versus stochastic bacterioplankton community assemblage processes were quantified, demonstrating that stochastic processes increased when algal blooms happened. The occurrence of algal blooms caused weaker bacterioplankton interspecies interactions and higher degrees of cooperative activities, changed keystone taxa and diminished the stability of bacterial communities. These findings consequently have important implications for our understanding of bacterioplankton community ecology during algal blooms.

Biogeographic patterns of abundant and rare bacterial and microeukaryotic subcommunities in connected freshwater lake zones subjected to different levels of nutrient loading

AIMS

To reveal whether the patterns of abundant and rare subcommunity composition of both bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading in freshwater lakes.

METHODS AND RESULTS

We investigated the abundant and rare subcommunity composition of both bacteria and microeukaryotes in two connected zones (Meiliang Bay (MLB) and Xukou Bay (XKB)) of a large shallow freshwater Lake Taihu via the high-throughput sequencing of bacterial 16S rRNA and microeukaryotic 18S rRNA genes. Even though these two lake zones are connected and share a species bank, they diverge in community composition. Significantly higher alpha diversity was observed for the abundant bacterial subcommunity in the MLB. However, no significant difference in alpha diversity between the rare bacterial subcommunities, as well as both rare and abundant microeukaryotic subcommunities were observed between MLB and XKB. It is demonstrated that both environmental factors and geographic distance play central roles in controlling the rare and abundant microbial subcommunities in the two connected lake zones.

CONCLUSIONS

The abundant subcommunity composition of bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading. Dispersal limitation plays a vital role in shaping microbial communities even in connected zones of freshwater lakes.

SIGNIFICANCE AND IMPACT OF THE STUDY

Leading to a comprehensive understanding of the characteristics of microbial community in connected lake regions with different levels of nutrient loading.

Major imprint of surface plankton on deep ocean prokaryotic structure and activity

Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep-sea physicochemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4,000 m) free-living and particle-attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as changes in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physicochemical conditions. Amino acid-like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200-1,000 m) communities, suggesting a direct connectivity through fast-sinking particles that escape mesopelagic transformations. Finally, we identified a pool of endemic deep-sea prokaryotic taxa (including potentially chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physicochemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters.

Diatom-Derived Polyunsaturated Aldehydes Are Unlikely to Influence the Microbiota Composition of Laboratory-Cultured Diatoms

Diatom-derived oxylipins, including polyunsaturated aldehydes (PUA), are considered to have infochemical, allelochemical and bacteriostatic properties, with plausible roles as grazing deterrents and regulators of inter- and intraspecific competition. However, the extent and mechanisms of how PUA influence diatom–bacteria interactions remain unresolved. In this study, impacts on the diversity of the associated bacterial communities (microbiota) of two contrasting Skeletonema marinoi strains (a PUA and a non-PUA producer) were investigated under three nitrate conditions in batch culture. Further, the response of the culture microbiota was studied when spiked with PUA at ecologically relevant concentrations (86nM octadienal and 290nM heptadienal). Of the 741 identified OTUs, Proteobacteria was the most abundant phylum (62.10%), followed by Bacteroidetes (12.33%) and Firmicutes (6.11%). Escherichia/Shigella were the most abundant genera for all treatments. Similar communities were present in both spiked and non-spiked cultures suggesting they can tolerate PUA exposure at realistic concentrations. This study suggests that PUA are not major drivers of diatom–bacteria interactions in laboratory cultures.

Environmental Reservoirs of Vibrio cholerae: Challenges and Opportunities for Ocean-Color Remote Sensing

The World Health Organization has estimated the burden of the on-going pandemic of cholera at 1.3 to 4 million cases per year worldwide in 2016, and a doubling of case-fatality-rate to 1.8% in 2016 from 0.8% in 2015. The disease cholera is caused by the bacterium Vibrio cholerae that can be found in environmental reservoirs, living either in free planktonic form or in association with host organisms, non-living particulate matter or in the sediment, and participating in various biogeochemical cycles. An increasing number of epidemiological studies are using land- and water-based remote-sensing observations for monitoring, surveillance, or risk mapping of Vibrio pathogens and cholera outbreaks. Although the Vibrio pathogens cannot be sensed directly by satellite sensors, remotely-sensed data can be used to infer their presence. Here, we review the use of ocean-color remote-sensing data, in conjunction with information on the ecology of the pathogen, to map its distribution and forecast risk of disease occurrence. Finally, we assess how satellite-based information on cholera may help support the Sustainable Development Goals and targets on Health (Goal 3), Water Quality (Goal 6), Climate (Goal 13), and Life Below Water (Goal 14).

Abiotic environmental factors override phytoplankton succession in shaping both free-living and attached bacterial communities in a highland lake

Bacterial communities are an important part of biological diversity and biogeochemical cycling in aquatic ecosystems. In this study, the relationship amongst the phytoplankton species composition and abiotic environmental factors on seasonal changes in the community composition of free-living and attached bacteria in Lake Erhai were studied. Using Illumina high-throughput sequencing, we found that the impact of environmental factors on both the free-living and attached bacterial community composition was greater than that of the phytoplankton community, amongst which total phosphorus, Secchi disk, water temperature, dissolved oxygen and conductivity strongly influenced bacterial community composition. Microcystis blooms associated with subdominant Psephonema occurred during the summer and autumn, and Fragilaria, Melosira and Mougeotia were found at high densities in the other seasons. Only small numbers of algal species-specific bacteria, including Xanthomonadaceae (Proteobacteria) and Alcaligenaceae (Betaproteobacteria), were tightly coupled to Microcystis and Psephonema during Microcystis blooms. Redundancy analysis showed that although the composition of the bacterial communities was controlled by species composition mediated by changes in phytoplankton communities and abiotic environmental factors, the impact of the abiotic environment on both free-living and attached bacterial community compositions were greater than the impact of the phytoplankton community. These results suggest that the species composition of both free-living and attached bacterial communities are affected by abiotic environmental factors, even when under strong control by biotic factors, particularly dominant genera of Microcystis and Psephonema during algal blooms.

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea

The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO₂^-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.

Community Structure of Bacteria Associated With Drifting Sargassum horneri, the Causative Species of Golden Tide in the Yellow Sea

Golden tides dominated by Sargassum spp. are occurring at an accelerated rate worldwide. In China, Sargassum has started to bloom in the Yellow Sea and led to tremendous economic losses, but the underlying biological causes and mechanisms are still unclear. Although algae-associated bacteria were suggested to play crucial roles in algal blooms, the profiles of bacteria associated with drifting Sargassum remain unexplored. In this study, the community structures and functions of Sargassum-associated bacteria were analyzed using the high-throughput sequencing data of the V5–V7 hypervariable region of the 16S rRNA gene. Molecular identification revealed that the golden tide analyzed in the Yellow Sea was dominated by a single species, Sargassum horneri. They were a healthy brown color nearshore but were yellow offshore with significantly decreased chlorophyll contents (P < 0.01), which indicates that yellow S. horneri was under physiological stress. The structural and functional analyses of bacterial communities indicated that the drifting S. horneri had an obvious selectivity on their associated bacteria against surrounding seawater. Although the bacterial communities phylogenetically differed between brown and yellow S. horneri (P < 0.01), their dominant functions were all nitrogen and iron transporters, which strongly indicates microbial contribution to blooming of the algal host. For the first time, potential epiphytic and endophytic bacteria associated with Sargassum were independently analyzed by a modified co-vortex method with silica sand. We showed that the composition of dominant endophytes, mainly Bacillus and Propionibacterium, was relatively consistent regardless of host status, whereas the epiphytic operational taxonomic units (OTUs) greatly varied in response to weakness of host status; however, dominant functions were consistent at elevated intensities, which might protect the host from stress related to nitrogen or iron deficiency. Thus, we propose that host physiological status at different intensities of functional demands, which were related to variable environmental conditions, may be a critical factor that influences the assembly of epiphytic bacterial communities. This study provided new insight into the structure and potential functions of associated bacteria with golden tide blooms.

Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations.

A Time Series of Water Column Distributions and Sinking Particle Flux of Pseudo-Nitzschia and Domoic Acid in the Santa Barbara Basin, California

Water column bulk Pseudo-nitzschia abundance and the dissolved and particulate domoic acid (DA) concentrations were measured in the Santa Barbara Basin (SBB), California from 2009–2013 and compared to bulk Pseudo-nitzschia cell abundance and DA concentrations and fluxes in sediment traps moored at 147 m and 509 m. Pseudo-nitzschia abundance throughout the study period was spatially and temporally heterogeneous (<200 cells L⁻¹ to 3.8 × 10⁶ cells L⁻¹, avg. 2 × 10⁵ ± 5 × 10⁵ cells L⁻¹) and did not correspond with upwelling conditions or the total DA (tDA) concentration, which was also spatially and temporally diverse (<1.3 ng L⁻¹ to 2.2 × 10⁵ ng L⁻¹, avg. 7.8 × 10³ ± 2.2 × 10⁴ ng L⁻¹). We hypothesize that the toxicity is likely driven in part by specific Pseudo-nitzschia species as well as bloom stage. Dissolved (dDA) and particulate (pDA) DA were significantly and positively correlated (p < 0.01) and both comprised major components of the total DA pool (pDA = 57 ± 35%, and dDA = 42 ± 35%) with substantial water column concentrations (>1000 cells L⁻¹ and tDA = 200 ng L⁻¹) measured as deep as 150 m. Our results highlight that dDA should not be ignored when examining bloom toxicity. Although water column abundance and pDA concentrations were poorly correlated with sediment trap Pseudo-nitzschia abundance and fluxes, DA toxicity is likely associated with senescent blooms that rapidly sink to the seafloor, adding another potential source of DA to benthic organisms.

Pseudo-nitzschia, Nitzschia, and domoic acid: New research since 2011

Some diatoms of the genera Pseudo-nitzschia and Nitzschia produce the neurotoxin domoic acid (DA), a compound that caused amnesic shellfish poisoning (ASP) in humans just over 30 years ago (December 1987) in eastern Canada. This review covers new information since two previous reviews in 2012. Nitzschia bizertensis was subsequently discovered to be toxigenic in Tunisian waters. The known distribution of N. navis-varingica has expanded from Vietnam to Malaysia, Indonesia, the Philippines and Australia. Furthermore, 15 new species (and one new variety) of Pseudo-nitzschia have been discovered, bringing the total to 52. Seven new species were found to produce DA, bringing the total of toxigenic species to 26. We list all Pseudo-nitzschia species, their ability to produce DA, and show their global distribution. A consequence of the extended distribution and increased number of toxigenic species worldwide is that DA is now found more pervasively in the food web, contaminating new marine organisms (especially marine mammals), affecting their physiology and disrupting ecosystems. Recent findings highlight how zooplankton grazers can induce DA production in Pseudo-nitzschia and how bacteria interact with Pseudo-nitzschia. Since 2012, new discoveries have been reported on physiological controls of Pseudo-nitzschia growth and DA production, its sexual reproduction, and infection by an oomycete parasitoid. Many advances are the result of applying molecular approaches to discovering new species, and to understanding the population genetic structure of Pseudo-nitzschia and mechanisms used to cope with iron limitation. The availability of genomes from three Pseudo-nitzschia species, coupled with a comparative transcriptomic approach, has allowed advances in our understanding of the sexual reproduction of Pseudo-nitzschia, its signaling pathways, its interactions with bacteria, and genes involved in iron and vitamin B₁₂ and B₇ metabolism. Although there have been no new confirmed cases of ASP since 1987 because of monitoring efforts, new blooms have occurred. A massive toxic Pseudo-nitzschia bloom affected the entire west coast of North America during 2015-2016, and was linked to a 'warm blob' of ocean water. Other smaller toxic blooms occurred in the Gulf of Mexico and east coast of North America. Knowledge gaps remain, including how and why DA and its isomers are produced, the world distribution of potentially toxigenic Nitzschia species, the prevalence of DA isomers, and molecular markers to discriminate between toxigenic and non-toxigenic species and to discover sexually reproducing populations in the field.

Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system

Eastern boundary upwelling systems (EBUSs) are among the most productive marine environments in the world. The Canary Current upwelling system off the coast of Mauritania and Morocco is the second most productive of the four EBUS, where nutrient‐rich waters fuel perennial phytoplankton blooms, evident by high chlorophyll a concentrations off Cape Blanc, Mauritania. High primary production leads to eutrophic waters in the surface layers, whereas sinking phytoplankton debris and horizontally dispersed particles form nepheloid layers (NLs) and hypoxic waters at depth. We used Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD‐FISH) in combination with fatty acid (measured as methyl ester; FAME) profiles to investigate the bacterial and archaeal community composition along transects from neritic to pelagic waters within the “giant Cape Blanc filament” in two consecutive years (2010 and 2011), and to evaluate the usage of FAME data for microbial community studies. We also report the first fatty acid profile of Pelagibacterales strain HTCC7211 which was used as a reference profile for the SAR11 clade. Unexpectedly, the reference profile contained low concentrations of long chain fatty acids 18:1 cis11, 18:1 cis11 11methyl, and 19:0 cyclo11–12 fatty acids, the main compounds in other Alphaproteobacteria. Members of the free‐living SAR11 clade were found at increased relative abundance in the hypoxic waters in both years. In contrast, the depth profiles of Gammaproteobacteria (including Alteromonas and Pseudoalteromonas), Bacteroidetes, Roseobacter, and Synechococcus showed high abundances of these groups in layers where particle abundance was high, suggesting that particle attachment or association is an important mechanisms of dispersal for these groups. Collectively, our results highlight the influence of NLs, horizontal particle transport, and low oxygen on the structure and dispersal of microbial communities in upwelling systems.

Daily variation in the prokaryotic community during a spring bloom in shelf waters of the East China Sea

To understand prokaryotic responses during a spring bloom in offshore shelf waters, prokaryotic parameters were measured daily at a station located in the middle of the East China Sea over a six-week period from March 25 to May 19. The site experienced a phytoplankton bloom in late April, triggering changes in prokaryotic abundance and production after a lag of approximately one week. Before the bloom, changes in prokaryotic composition were small. Both during the bloom and in the post-bloom period, successive changes among bacterial groups were apparent. A SAR11 group became more dominant during the bloom period, and diverse groups belonging to the Flavobacteriia occurred dominantly during both the bloom and post-bloom periods. However, bacterial community changes at the species level during the bloom and post-bloom periods occurred rapidly in a time scale of a few days. Especially, NS5, NS4 and Formosa bacteria belonging to Flavobacteriia and bacteria belonging to Halieaceae and Arenicellaceae families of Gammaproteobacteria showed a successive pattern with large short-term variation during the period. The changes in prokaryotic composition were found to be related to phytoplankton biomass and composition, as well as seawater temperature and variations in nutrients.

A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data

The successional dynamics of microbial communities are influenced by the synergistic interactions of physical and biological factors. In our motivating data, ocean microbiome samples were collected from the Santa Cruz Municipal Wharf, Monterey Bay at multiple time points and then 16S ribosomal RNA (rRNA) sequenced. We develop a Bayesian semiparametric regression model to investigate how microbial abundance and succession change with covarying physical and biological factors including algal bloom and domoic acid concentration level using 16S rRNA sequencing data. A generalized linear regression model is built using the Laplace prior, a sparse inducing prior, to improve estimation of covariate effects on mean abundances of microbial species represented by operational taxonomic units (OTUs). A nonparametric prior model is used to facilitate borrowing strength across OTUs, across samples and across time points. It flexibly estimates baseline mean abundances of OTUs and provides the basis for improved quantification of covariate effects. The proposed method does not require prior normalization of OTU counts to adjust differences in sample total counts. Instead, the normalization and estimation of covariate effects on OTU abundance are simultaneously carried out for joint analysis of all OTUs. Using simulation studies and a real data analysis, we demonstrate improved inference compared to an existing method.

Blurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routine monitoring for either toxin. Dinophysis shellfish toxins (DSTs) and freshwater microcystins are also present within SFB, but not routinely monitored. Acute exposure to any of these toxin groups has severe consequences for marine organisms and humans, but chronic exposure to sub-lethal doses, or synergistic effects from multiple toxins, are poorly understood and rarely addressed. This study documents the occurrence of domoic acid and microcystins in SFB from 2011 to 2016, and identifies domoic acid, microcystins, DSTs, and PSTs in marine mussels within SFB in 2012, 2014, and 2015. At least one toxin was detected in 99% of mussel samples, and all four toxin suites were identified in 37% of mussels. The presence of these toxins in marine mussels indicates that wildlife and humans who consume them are exposed to toxins at both sub-lethal and acute levels. As such, there are potential deleterious impacts for marine organisms and humans and these effects are unlikely to be documented. These results demonstrate the need for regular monitoring of marine and freshwater toxins in SFB, and suggest that co-occurrence of multiple toxins is a potential threat in other ecosystems where freshwater and seawater mix.

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×10⁸ cell/L, respectively. The cell concentration was positively correlated with COD_Mn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)

Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.

Patterns of bacterial diversity in the marine planktonic particulate matter continuum

Depending on their relationship with the pelagic particulate matter, planktonic prokaryotes have traditionally been classified into two types of communities: free-living (FL) or attached (ATT) to particles, and are generally separated using only one pore-size filter in a differential filtration. Nonetheless, particulate matter in the oceans appears in a continuum of sizes. Here we separated this continuum into six discrete size-fractions, from 0.2 to 200 μm, and described the prokaryotes associated to each of them. Each size-fraction presented different bacterial communities, with a range of 23-42% of unique (OTUs) in each size-fraction, supporting the idea that they contained distinct types of particles. An increase in richness was observed from the smallest to the largest size-fractions, suggesting that increasingly larger particles contributed new niches. Our results show that a multiple size-fractionation provides a more exhaustive description of the bacterial diversity and community structure than the use of only one filter. In addition, and based on our results, we propose an alternative to the dichotomy of FL or ATT lifestyles, in which we differentiate the taxonomic groups with preference for the smaller fractions, those that do not show preferences for small or large fractions, and those that preferentially appear in larger fractions.