Synechococcus-like cyanobacteria are vital to aquatic ecosystems. Taxonomists have begun to reassign genomic clades within this group to new taxa. This process depends on genomic data from diverse habitats. Here, we present a metagenome-assembled genome of a Synechococcus sp. strain from the Tennessee River Basin, an ecosystem under-represented in databases.

ABSTRACT Clear Lake is a large, natural eutrophic lake located in northern California, United States. Persistent, toxic cyanobacterial blooms have been reported in the lake since 2011. However, our understanding of the spatiotemporal distribution of toxin-producing genera and their interaction with the biotic and abiotic environment is limited. Moreover, few studies have addressed how the co-occurring microbial communities respond to these toxic cyanobacterial blooms. Using multi-domain 16S/18S rRNA gene amplicon sequencing, a strong seasonal succession within the cyanobacterial and co-occurring eukaryotic assemblage was identified, which was primarily explained by variation in total phosphorus (~30%, P < 0.001) and temperature (~15%, P < 0.01). Cyanobacterial seasonal succession was often initiated by proliferation of diazotrophs ( Dolichospermum and Nodularia ) with concomitant increases in total nitrogen, followed by blooms of non-diazotrophs, such as Microcystis, Limnothrix, and Planktothrix . The picocyanobacterium Cyanobium , previously undocumented in the lake, was a dominant summer taxon in the western part of Clear Lake, accounting for ~45%–80% relative abundance of the cyanobacterial reads. Seasonal succession within the eukaryotic assemblage was influenced by photosynthetic chlorophytes and diatoms, as well as mixotrophic ciliates and cryptophytes. Among all toxin-producing cyanobacterial genera, Microcystis abundance was most strongly correlated with microcystin concentrations ( P < 0.001), both of which appeared to influence co-occurring eukaryotes. Finally, using putative relationships based on correlation of sequence abundance and environmental variables, several potential grazers of Microcystis were identified, including cyclopoid copepods and Cryptomonas . These correlations need further confirmation and experimental work to validate the nature of the relationships. IMPORTANCE Clear Lake is an important habitat for fish and wildlife, which also provides a myriad of human benefits, such as recreation, irrigation, and drinking water. Moreover, the lake is vital for tribal tradition and cultural practices. However, since the last decade, the lake has experienced recurring harmful algal blooms with toxin levels that frequently exceed California voluntary guidance levels. These high toxin concentrations pose a substantial threat to the residents, visitors, and tribal sustenance fishing and beneficial uses. However, significant gaps remain in our understanding of these toxic algal bloom dynamics and their interaction with the abiotic and biotic environments. This study characterized the seasonal and spatial patterns in the distribution of bloom-causing cyanobacteria and identified Microcystis as the major toxin producer in Clear Lake. Additionally, the co-occurring bacterial and eukaryotic microbial communities were also characterized, and their potential interactions with the cyanobacterial assemblage were identified and discussed.

Decades of research has been devoted to understanding the occurrence, distribution, and activity of different N2-fixers in the oceans. Marine N2-fixing diatom symbioses involving the heterocyst-forming cyanobacterium Richelia are widespread, yet often go undetected. Some of the diatom-Richelia symbioses have the advantage to be identified by microscopy, however, observations alone cannot inform on the metabolic state of a cell. Here, we developed nine new specific quantitative PCR assays that detect three common symbiotic Richelia strains (ReuHH01, RintRC01, RrhiSC01) of diatoms based on molecular markers for: a high affinity phosphate transporter (pstS), an iron transporter (exbB), and a constitutively expressed gene (rnpA, protein component of ribonuclease P). We first tested the new assays in the lab, including a diel experiment to elucidate the temporal dynamics of gene expression for each molecular marker, then applied the new assays to field collected samples. In the field we also made microscopy observations of the diatom-Richelia symbioses and measured bulk N2 and Carbon (C) fixation rates with stable isotope labelling incubations. The number of genes encoding the molecular markers varied; typically, fewer in the endobiont strains. Detection in field samples based on qPCR was consistent with microscopy observations. The environmental gene expression for all the new targets, and additionally nifH for N2 fixation (nitrogenase) were low, and highest expression was detected in the upper water column (0-40 m) consistent with higher densities of the Richelia by qPCR and microscopy observations. Low in situ bulk rates of N2 and C fixation corroborated the aforementioned low nifH expression. Expression of both nifH and pstS was temporally regulated in the lab experiment of the facultative symbiotic Richelia strain RrhiSC01 with higher expression in the early and late photoperiods, respectively. The nine new assays are an improvement over the previous assays based on the nifH gene as cross-reactivity between Richelia strains is minimum, expression can be normalized to rnpA, and expression is informative of the symbiont nutrient status.

Clear Lake in Lake County, CA, USA has experienced highly toxic cyanobacterial blooms for more than a decade, with multiple cyanobacterial taxa and cyanotoxins appearing sporadically, typically throughout much of the early-spring to late-fall seasons. Recurring blooms have been attributed to high internal nutrient loads within the lake, with hydrography and hydrology playing important but still poorly documented roles in controlling the availability of growth-limiting elements to the phytoplankton community. The lake is approximately 180 km2 in areal extent and composed of three somewhat disjointed lobes, or 'Arms'. The large size of the lake presents a formidable task for synoptic lakewide surveys and for understanding the specific features that stimulate the development and magnitude of harmful blooms. We conducted a study in August of 2020 that involved the use of an autonomous underwater vehicle and deployment of a hand-held water column profiler to describe the lakewide status of various biological, chemical, and physical features. Discrete water samples were also collected from ten stations located throughout the lake to produce a near-synoptic depiction of lake status. Additionally, a mechanically driven, continuously monitoring water-column profiler was deployed at a central lake location to document short-term temporal (minutes to months) changes in water-column structure and chemistry. Wind was a dominant feature affecting the lake's chemistry and biology during the study, resulting in massive concentrations and dramatic spatial heterogeneity of phytoplankton biomass and cyanotoxins in the eastern and southeastern Arms of the lake, and confirmed by the analysis of discrete water samples. Unique insight into the processes leading to or prolonging blooms was revealed by the water column profiler, which demonstrated rapid development (within a few hours) of suboxic conditions during periods of calm winds. We speculate that these quiescent periods are fundamental events in the lake's ecology, resulting in episodic 'pulses' of nutrient release from the sediments, which can stimulate or refuel blooms of cyanobacteria in the water column.

While the ecological role that Trichodesmium sp. play in nitrogen fixation has been widely studied, little information is available on potential specialized metabolites that are associated with blooms and standing stock Trichodesmium colonies. While a collection of biological material from a T. thiebautii bloom event from North Padre Island, Texas, in 2014 indicated that this species was a prolific producer of chlorinated specialized metabolites, additional spatial and temporal resolution was needed. We have completed these metabolite comparison studies, detailed in the current report, utilizing LC-MS/MS-based molecular networking to visualize and annotate the specialized metabolite composition of these Trichodesmium blooms and colonies in the Gulf of Mexico (GoM) and other waters. Our results showed that T. thiebautii blooms and colonies found in the GoM have a remarkably consistent specialized metabolome. Additionally, we isolated and characterized one new macrocyclic compound from T. thiebautii, trichothilone A (1), which was also detected in three independent cultures of T. erythraeum. Genome mining identified genes predicted to synthesize certain functional groups in the T. thiebautii metabolites. These results provoke intriguing questions of how these specialized metabolites affect Trichodesmium ecophysiology, symbioses with marine invertebrates, and niche development in the global oligotrophic ocean.

Marine N2-fixing cyanobacteria, including the unicellular genus Crocosphaera, are considered keystone species in marine food webs. Crocosphaera are globally distributed and provide new sources of nitrogen and carbon, which fuel oligotrophic microbial communities and upper trophic levels. Despite their ecosystem importance, only one pelagic, oligotrophic, phycoerythrin-rich species, Crocosphaera watsonii, has ever been identified and characterized as widespread. Herein, we present a new species, named Crocosphaera waterburyi, enriched from the North Pacific Ocean. C. waterburyi was found to be phenotypically and genotypically distinct from C. watsonii, active in situ, distributed globally, and preferred warmer temperatures in culture and the ocean. Additionally, C. waterburyi was detectable in 150- and 4000-meter sediment export traps, had a relatively larger biovolume than C. watsonii, and appeared to aggregate in the environment and laboratory culture. Therefore, it represents an additional, previously unknown link between atmospheric CO2 and N2 gas and deep ocean carbon and nitrogen export and sequestration.

Here, we describe the metagenome-assembled genome (MAG) HetDA_ MAG_MS6. HetDA_MAG_MS6 was obtained from an enrichment of the heterocystous diazotroph HetDA, which was isolated near Station ALOHA. The MAG was placed in the Cyclobacteriaceae family and is predicted to be a chemoorganoheterotroph with the potential for ammonia uptake, phosphonate transport, and sulfolipid biosynthesis.

We present a metagenome-assembled genome (MAG), HetDA_MAG_MS8, that was determined to be unique via relative evolutionary divergence (RED) scores and average nucleotide identity (ANI) values. HetDA_MAG_MS8 is in the order Nevskiales , genus Oceanococcus , and was assembled from a heterocytous cyanobiont enrichment from the Hawaii Ocean Time Series.

Here, we describe the metagenome-assembled genome (MAG) HetDA_MAG_SS2, in the family Cyclobacteriaceae . It was found in association with a HetDA cyanobiont isolated from a Station ALOHA Trichodesmium colony. Annotation suggests that HetDA_MAG_SS2 is a chemoorganoheterotroph with the potential for lithoheterotrophy, containing genes for aerobic respiration, mixed acid fermentation, dissimilatory nitrate reduction to ammonium, and sulfide oxidation.

The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed selection at cool and warm temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Curiously, the genomes of all 11 isolates were almost identical (average nucleotide identities of >99.99%, with >99% of the genome aligning) and no differences in gene content or single nucleotide variants were associated with either cool or warm temperature phenotypes. Despite a very high level of genomic similarity, sequenced epigenomes for two strains showed differences in methylation on genes associated with photosynthesis. These corresponded to measured differences in photophysiology, suggesting a potential pathway for future mechanistic research into thermal microdiversity. Our study demonstrates that present-day marine microbial populations can harbor cryptic but environmentally relevant thermotypes which may increase their resilience to future rising temperatures.

Here, we present a draft genome in the order Rhizobiales and family Devosiaceae. This draft genome comes from an enrichment of a heterocystous, cyanobacterial diazotroph (HetDA) that was originally living in association with Trichodesmium species. This Rhizobiales organism is proposed to be an anoxygenic phototroph capable of dissimilatory nitrate reduction to ammonia (DNRA).

We performed deep metagenomic sequencing on hydrocarbon-degrading marine microcosms designed to experimentally determine the effect of photo-oxidation on oil biodegradation dynamics. Assembly, binning, and dereplication yielded 73 unique metagenome-assembled genomes (MAGs) from 6 phyla, of which 61 are predicted to be over 90% complete.

Diazotrophic cyanobacteria play a vital role in the nitrogen influx of the global marine ecosystem. In July 2010, colonies of Trichodesmium spp. were picked near Station ALOHA in the oligotrophic North Pacific Subtropical Gyre, and a novel heterocystous diazotroph (strain HetDA_MAG_MS3) belonging to the genus Rivularia was found living in close association; it was cultured and sequenced.

Here, we present HetDA_MAG_SS10, a metagenome-assembled genome (MAG) from an enrichment of a heterocystous diazotroph originally living in association with Trichodesmium spp. obtained near Station ALOHA in the North Pacific Ocean. HetDA_MAG_SS10, an alphaproteobacterium in the order Micavibrionales , is proposed to be photoheterotrophic via rhodopsin and has the potential for dimethylsulfoniopropionate (DMSP) demethylation.

The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.

Marine N 2 -fixing cyanobacteria, including the unicellular genus Crocosphaera , are considered keystone species in marine food webs. Crocosphaera are globally distributed and provide new sources of nitrogen (N) and carbon (C), which fuel oligotrophic microbial communities and upper trophic levels. Despite their ecosystem importance, only one species, Crocosphaera watsonii , has ever been identified and characterized as widespread in the oligotrophic oceans. Herein, we present a novel species, candidatus Crocosphaera waterburyi ( C. waterburyi hereafter), enriched from the North Pacific Ocean, active in situ , and globally distributed in environmental datasets. C. waterburyi is morphologically, phylogenetically, and physiologically distinct from C. watsonii ; therefore, description of this novel species provides a new window into previously uncharacterized diversity and ecology of unicellular N 2 -fixing cyanobacterial taxa and further highlights their importance in the global N cycle.

Cyanobacteria of the genus Trichodesmium provide about 80 Tg of fixed nitrogen to the surface ocean per year and contribute to marine biogeochemistry, including the sequestration of carbon dioxide and mobilization of particulate iron. Trichodesmium fixes nitrogen in the daylight, despite the incompatibility of the nitrogenase enzyme with oxygen produced during photosynthesis. While the mechanisms protecting nitrogenase remain unclear, all proposed strategies require considerable resource investment. Here we describe a crucial benefit of daytime nitrogen fixation in Trichodesmium spp. that may counteract these costs. We analysed diel proteomes of cultured and field populations of Trichodesmium in comparison with the marine diazotroph Crocosphaera watsonii WH8501, which fixes nitrogen at night. Trichodesmium’s proteome is extraordinarily dynamic and demonstrates simultaneous photosynthesis and nitrogen fixation, resulting in balanced particulate organic carbon and particulate organic nitrogen production. Unlike Crocosphaera, which produces large quantities of glycogen as an energy store for nitrogenase, proteomic evidence is consistent with the idea that Trichodesmium reduces the need to produce glycogen by supplying energy directly to nitrogenase via soluble ferredoxin charged by the photosynthesis protein PsaC. This minimizes ballast associated with glycogen, reducing cell density and decreasing sinking velocity, thus supporting Trichodesmium’s niche as a buoyant, high-light-adapted colony forming cyanobacterium. To occupy its niche of simultaneous nitrogen fixation and photosynthesis, Trichodesmium appears to be a conspicuous consumer of iron, and has therefore developed unique iron-acquisition strategies, including the use of iron-rich dust. Particle capture by buoyant Trichodesmium colonies may therefore increase the residence time and degradation of mineral iron in the euphotic zone. These findings describe how cellular biochemistry defines and reinforces the ecological and biogeochemical function of these keystone marine diazotrophs, particularly their role as a microbial link in the nitrogen, carbon, and iron cycles.

Cluster 5 Synechococcus species are widely acknowledged for their broad distribution and biogeochemical importance. In particular, subcluster 5.2 strains inhabit freshwater, estuarine, and marine environments but are understudied, compared to other subclusters. Here, we present the genome for Synechococcus sp. strain LA31, a strain that was recently isolated from Narragansett Bay, Rhode Island, USA.

Cyanobacteria of the genus Trichodesmium provide about 80 Tg of fixed nitrogen to the surface ocean per year and contribute to marine biogeochemistry, including the sequestration of carbon dioxide. Trichodesmium fixes nitrogen in the daylight, despite the incompatibility of the nitrogenase enzyme with oxygen produced during photosynthesis. While the mechanisms protecting nitrogenase remain unclear, all proposed strategies require considerable resource investment. Here we identify a crucial benefit of daytime nitrogen fixation in Trichodesmium spp. that may counteract these costs. We analysed diel proteomes of cultured and field populations of Trichodesmium in comparison with the marine diazotroph Crocosphaera watsonii WH8501, which fixes nitrogen at night. Trichodesmium's proteome is extraordinarily dynamic and demonstrates simultaneous photosynthesis and nitrogen fixation, resulting in balanced particulate organic carbon and particulate organic nitrogen production. Unlike Crocosphaera, which produces large quantities of glycogen as an energy store for nitrogenase, proteomic evidence is consistent with the idea that Trichodesmium reduces the need to produce glycogen by supplying energy directly to nitrogenase via soluble ferredoxin charged by the photosynthesis protein PsaC. This minimizes ballast associated with glycogen, reducing cell density and decreasing sinking velocity, thus supporting Trichodesmium's niche as a buoyant, high-light-adapted colony forming cyanobacterium. To occupy its niche of simultaneous nitrogen fixation and photosynthesis, Trichodesmium appears to be a conspicuous consumer of iron, and has therefore developed unique iron-acquisition strategies, including the use of iron-rich dust. Particle capture by buoyant Trichodesmium colonies may increase the residence time and degradation of mineral iron in the euphotic zone. These findings describe how cellular biochemistry defines and reinforces the ecological and biogeochemical function of these keystone marine diazotrophs. The cyanobacterium Trichodesmium fixes nitrogen exclusively during the day to reduce glycogen ballast and remain buoyant in the surface ocean, where it occupies a specialized niche based on colony formation, high-light adaptation and mineral-dust utilization.

Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO 2 , NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.