Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere

Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.

Minimal cobalt metabolism in the marine cyanobacterium Prochlorococcus

Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genus Prochlorococcus retain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in a Prochlorococcus isolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate that Prochlorococcus MIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions of Prochlorococcus cobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally but Prochlorococcus biomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.

Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability

Vitamin B1 (B1 herein) is a vital enzyme cofactor required by virtually all cells, including bacterioplankton, which strongly influence aquatic biogeochemistry and productivity and modulate climate on Earth. Intriguingly, bacterioplankton can be de novo B1 synthesizers or B1 auxotrophs, which cannot synthesize B1 de novo and require exogenous B1 or B1 precursors to survive. Recent isolate-based work suggests select abundant bacterioplankton are B1 auxotrophs, but direct evidence of B1 auxotrophy among natural communities is scant. In addition, it is entirely unknown if bulk bacterioplankton growth is ever B1-limited. We show by surveying for B1-related genes in estuarine, marine, and freshwater metagenomes and metagenome-assembled genomes (MAGs) that most naturally occurring bacterioplankton are B1 auxotrophs. Pyrimidine B1-auxotrophic bacterioplankton numerically dominated metagenomes, but multiple other B1-auxotrophic types and distinct uptake and B1-salvaging strategies were also identified, including dual (pyrimidine and thiazole) and intact B1 auxotrophs that have received little prior consideration. Time-series metagenomes from the Baltic Sea revealed pronounced shifts in the prevalence of multiple B1-auxotrophic types and in the B1-uptake and B1-salvaging strategies over time. Complementarily, we documented B1/precursor limitation of bacterioplankton production in three of five nutrient-amendment experiments at the same time-series station, specifically when intact B1 concentrations were ≤3.7 pM, based on bioassays with a genetically engineered Vibrio anguillarum B1-auxotrophic strain. Collectively, the data presented highlight the prevalent reliance of bacterioplankton on exogenous B1/precursors and on the bioavailability of the micronutrients as an overlooked factor that could influence bacterioplankton growth and succession and thereby the cycling of nutrients and energy in aquatic systems.

Metagenomic analysis reveals potential interactions in an artificial coculture

Disentangling the interactions between cyanobacteria and associated bacterial community is important for understanding the mechanisms that mediate the formation of cyanobacterial blooms in freshwater ecosystems. Despite the fact that a metagenomic approach enables researchers to profile the structure of microbial communities associated with cyanobacteria, reconstructing genome sequences for all members remains inefficient, due to the inherent enormous microbial diversity. Here, we have established a stable coculture system under high salinity, originally from a mixture of an axenic cyanobacterium Synechococcus sp. PCC 7002 and a non-axenic bloom-forming cyanobacterium Microcystis colony. Metagenomic analysis showed that the coculture consists of S. sp. PCC 7002 and two heterotrophic bacteria, designated as Pseudomonas stutzeri TAIHU and Mesorhizobium sp. TAIHU, respectively. And near-complete genome sequences of both bacteria were reconstructed from the metagenomic dataset with an average completeness of 99.8%. Genome-wide pathway analysis revealed that M. sp. TAIHU carried all the genes involved in the de novo biosynthesis of cobalamin, which is required by S. sp. PCC 7002 for growth. To cope with the high salinity in the coculture, experimental evidence demonstrated that S. sp. PCC 7002 would synthesize the compatible solutes including sucrose and glucosylglycerol, which are supposed to be exploited by both heterotrophic bacteria as potential carbon and/or nitrogen sources. Furthermore, the genes encoding for the biosynthesis of the ectoine, another common osmolyte are found exclusively in P. stutzeri TAIHU, while the genes responsible for the catabolism of ectoine and its derives are present only in M. sp. TAIHU. These genomic evidence indicates beneficial interaction between three members in the coculture. Establishment of the coculture system with relative simplicity provides a useful model system for investigating the interspecies interactions, and genome sequences of both bacteria associated with Microcystis bloom described here will facilitate the researcher to elucidate the role of these heterotrophic bacteria in the formation and maintenance of cyanobacterial bloom in freshwater ecosystem.

Identification and Regulation of Genes for Cobalamin Transport in the Cyanobacterium Synechococcus sp. Strain PCC 7002

The cyanobacterium Synechococcus sp. strain PCC 7002 is a cobalamin auxotroph and utilizes this coenzyme solely for the synthesis of l-methionine by methionine synthase (MetH). Synechococcus sp. strain PCC 7002 is unable to synthesize cobalamin de novo, and because of the large size of this tetrapyrrole, an active-transport system must exist for cobalamin uptake. Surprisingly, no cobalamin transport system was identified in the initial annotation of the genome of this organism. With more sophisticated in silico prediction tools, a btuB-cpdA-btuC-btuF operon encoding components putatively required for a B12 uptake (btu) system was identified. The expression of these genes was predicted to be controlled by a cobalamin riboswitch. Global transcriptional profiling by high-throughput RNA sequencing of a cobalamin-independent form of Synechococcus sp. strain PCC 7002 grown in the absence or presence of cobalamin confirmed regulation of the btu operon by cobalamin. Pérez et al. (A. A. Pérez, Z. Liu, D. A. Rodionov, Z. Li, and D. A. Bryant, J Bacteriol 198:2743-2752, 2016, http://dx.doi.org/10.1128/JB.00475-16) developed a cobalamin-dependent yellow fluorescent protein reporter system in a Synechococcus sp. strain PCC 7002 variant that had been genetically modified to allow cobalamin-independent growth. This reporter system was exploited to validate components of the btu uptake system by assessing the ability of targeted mutants to transport cobalamin. The btuB promoter and a variant counterpart mutated in an essential element of the predicted cobalamin riboswitch were fused to a yfp reporter. The combined data indicate that the btuB-cpdA-btuF-btuC operon in this cyanobacterium is transcriptionally regulated by a cobalamin riboswitch.

IMPORTANCE

With a cobalamin-regulated reporter system for expression of yellow fluorescent protein, genes previously misidentified as encoding subunits of a siderophore transporter were shown to encode components of cobalamin uptake in the cyanobacterium Synechococcus sp. strain PCC 7002. This study demonstrates the importance of experimental validation of in silico predictions and provides a general scheme for in vivo verification of similar cobalamin transport systems. A putative cobalamin riboswitch was identified in Synechococcus sp. strain PCC 7002. This riboswitch acts as a potential transcriptional attenuator of the btu operon that encodes the components of the cobalamin active-transport system.

Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo

The euryhaline cyanobacterium Synechococcus sp. strain PCC 7002 has an obligate requirement for exogenous vitamin B12 (cobalamin), but little is known about the roles of this compound in cyanobacteria. Bioinformatic analyses suggest that only the terminal enzyme in methionine biosynthesis, methionine synthase, requires cobalamin as a coenzyme in Synechococcus sp. strain PCC 7002. Methionine synthase (MetH) catalyzes the transfer of a methyl group from N(5)-methyl-5,6,7,8-tetrahydrofolate to l-homocysteine during l-methionine synthesis and uses methylcobalamin as an intermediate methyl donor. Numerous bacteria and plants alternatively employ a cobalamin-independent methionine synthase isozyme, MetE, that catalyzes the same methyl transfer reaction as MetH but uses N(5)-methyl-5,6,7,8-tetrahydrofolate directly as the methyl donor. The cobalamin auxotrophy of Synechococcus sp. strain PCC 7002 was complemented by using the metE gene from the closely related cyanobacterium Synechococcus sp. strain PCC 73109, which possesses genes for both methionine synthases. This result suggests that methionine biosynthesis is probably the sole use of cobalamin in Synechococcus sp. strain PCC 7002. Furthermore, a cobalamin-repressible gene expression system was developed in Synechococcus sp. strain PCC 7002 that was used to validate the presence of a cobalamin riboswitch in the promoter region of metE from Synechococcus sp. strain PCC 73109. This riboswitch acts as a cobalamin-dependent transcriptional attenuator for metE in that organism.

IMPORTANCE

Synechococcus sp. strain PCC 7002 is a cobalamin auxotroph because, like eukaryotic marine algae, it uses a cobalamin-dependent methionine synthase (MetH) for the final step of l-methionine biosynthesis but cannot synthesize cobalamin de novo Heterologous expression of metE, encoding cobalamin-independent methionine synthase, from Synechococcus sp. strain PCC 73109, relieved this auxotrophy and enabled the construction of a truly autotrophic Synechococcus sp. strain PCC 7002 more suitable for large-scale industrial applications. Characterization of a cobalamin riboswitch expands the genetic toolbox for Synechococcus sp. strain PCC 7002 by providing a cobalamin-repressible expression system.

Chemistry of personalized solar energy

Personalized energy (PE) is a transformative idea that provides a new modality for the planet's energy future. By providing solar energy to the individual, an energy supply becomes secure and available to people of both legacy and nonlegacy worlds and minimally contributes to an increase in the anthropogenic level of carbon dioxide. Because PE will be possible only if solar energy is available 24 h a day, 7 days a week, the key enabler for solar PE is an inexpensive storage mechanism. HY (Y = halide or OH(-)) splitting is a fuel-forming reaction of sufficient energy density for large-scale solar storage, but the reaction relies on chemical transformations that are not understood at the most basic science level. Critical among these are multielectron transfers that are proton-coupled and involve the activation of bonds in energy-poor substrates. The chemistry of these three italicized areas is developed, and from this platform, discovery paths leading to new hydrohalic acid- and water-splitting catalysts are delineated. The latter water-splitting catalyst captures many of the functional elements of photosynthesis. In doing so, a highly manufacturable and inexpensive method for solar PE storage has been discovered.

Isolation and characterization of outer and inner envelope membranes of cyanelles from a glaucocystophyte, Cyanophora paradoxa

Envelope membranes were isolated by sucrose density gradient floatation centrifugation from the homogenate of cyanelles prepared from Cyanophora paradoxa. Two yellow bands were separated after 40 h of centrifugation. The buoyant density of one of the two fractions (fraction Y2) coincided with that of inner envelope membranes of spinach or plasma membranes of cyanobacteria. The other yellow fraction (fraction Y1) migrated to top of sucrose-gradient even at 0% sucrose. Pigment analysis revealed that the heavy yellow fraction was rich in zeaxanthin while the light fraction was rich in beta-carotene, and the both fractions contained practically no chlorophylls. Another yellow fraction (fraction Y3) was isolated from the phycobiliprotein fraction, which was the position where the sample was placed for gradient centrifugation. Its buoyant density and absorption spectra were similar to outer membranes of cyanobacteria. We have assigned fractions Y2 and Y3 as inner and outer envelope membrane fractions of cyanelles, respectively. Protein compositions were rather different between the two envelope membranes indicating little cross-contamination among the fractions.

Role of marine cyanobacteria in trace metal bioavailability in seawater

In seawater, several trace metals with biological significance are highly complexed with organic matter. Marine cyanobacteria are an important phytoplanktonic group, with the ability to release trace metal-binding compounds to the seawater medium, which in turn modulates their bioavailability and influences their biogeochemical cycles. Such interactions may allow cyanobacteria to more easily access less available trace metals essential for their metabolic processes, or, conversely, keep the toxic forms of the trace metals from reaching intolerable levels. In this minireview, Cu and Fe interactions with cyanobacteria received special attention, although other trace metals (Co, Pb, Zn, and Cd) are also covered. Recent research has shed light on many aspects of trace metal-cyanobacteria ecology in seawater; nevertheless, the biochemical processes behind this dynamics and the structure of the vast majority of the metal binding compounds remain unclear.

Marine and freshwater cyanophages in a Laurentian Great Lake: evidence from infectivity assays and molecular analyses of g20 genes

While it is well established that viruses play an important role in the structure of marine microbial food webs, few studies have directly addressed their role in large lake systems. As part of an ongoing study of the microbial ecology of Lake Erie, we have examined the distribution and diversity of viruses in this system. One surprising result has been the pervasive distribution of cyanophages that infect the marine cyanobacterial isolate Synechococcus sp. strain WH7803. Viruses that lytically infect this cyanobacterium were identified throughout the western basin of Lake Erie, as well as in locations within the central and eastern basins. Analyses of the gene encoding the g20 viral capsid assembly protein (a conservative phylogenetic marker for the cyanophage) indicate that these viruses, as well as amplicons from natural populations and the ballast of commercial ships, are related to marine cyanophages but in some cases form a unique clade, leaving questions concerning the native hosts of these viruses. The results suggest that cyanophages may be as important in freshwater systems as they are known to be in marine systems.

Physiological diversity and niche adaptation in marine Synechococcus

During the twenty years or so since the discovery of tiny photosynthetic cells of the genus Synechococcus in marine oceanic systems, a tremendous expansion of interest has been seen in the literature pertaining to these organisms. The fact that they are ubiquitous and abundant in major oceanic regimes underlies their ecological importance as significant contributors to marine C fixation. Recent advances in the physiology and biochemistry of these organisms are presented here, focusing on strains of the MC-A and MC-B clusters; it is stressed that the data contained herein should be put into the context of the ecological niche occupied by particular genotypes in situ. This system is ripe for joining the often separate disciplines of molecular ecology and microbial physiology and provides a great opportunity to tease out the underlying processes that both mediate organism evolution and also the environmental factors that dictate this.