Gas Vesicle Research Articles

Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria

Ultrasound allows imaging at a much greater depth than optical methods, but existing genetically encoded acoustic reporters for in vivo cellular imaging have been limited by poor sensitivity, specificity and in vivo expression. Here we describe two acoustic reporter genes (ARGs)—one for use in bacteria and one for use in mammalian cells—identified through a phylogenetic screen of candidate gas vesicle gene clusters from diverse bacteria and archaea that provide stronger ultrasound contrast, produce non-linear signals distinguishable from background tissue and have stable long-term expression. Compared to their first-generation counterparts, these improved bacterial and mammalian ARGs produce 9-fold and 38-fold stronger non-linear contrast, respectively. Using these new ARGs, we non-invasively imaged in situ tumor colonization and gene expression in tumor-homing therapeutic bacteria, tracked the progression of tumor gene expression and growth in a mouse model of breast cancer, and performed gene-expression-guided needle biopsies of a genetically mosaic tumor, demonstrating non-invasive access to dynamic biological processes at centimeter depth.

The buckling-condensation mechanism driving gas vesicle collapse.

Gas vesicles (GVs) are proteinaceous cylindrical shells found within bacteria or archea growing in aqueous environments and are composed primarily of two proteins, gas vesicle protein A and C (GvpA and GvpC). GVs exhibit strong performance as next-generation ultrasound contrast agents due to their gas-filled interior, tunable collapse pressure, stability in vivo and functionalizable exterior. However, the exact mechanism leading to GV collapse remains inconclusive, which leads to difficulty in predicting collapse pressures for different species of GVs and in extending favorable nonlinear response regimes. Here, we propose a two stage mechanism leading to GV loss of echogenicity and rupture under hydrostatic pressure: elastic buckling of the cylindrical shell coupled with condensation driven weakening of the GV membrane. Our goal is to therefore test whether the final fracture of the GV membrane occurs by the interplay of both mechanisms or purely through buckling failure as previously believed. To do so, we (1) compare the theoretical condensation and buckling pressures with that for experimental GV collapse and (2) describe how condensation can lead to plastic buckling failure. GV shell properties that are necessary input to this theoretical description, such as the elastic moduli and wettability of GvpA, are determined using molecular dynamics simulations of a novel structural model of GvpA that better represents the hydrophobic core. For GVs that are not reinforced by GvpC, this analytical framework shows that the experimentally observed pressures resulting in loss of echogenicity coincide with both the elastic buckling and condensation pressure regimes. We also found that the stress strain curve for GvpA wetted on both the interior and exterior exhibits a loss of mechanical stability compared to GvpA only wetted on the exterior by the bulk solution. We identify a pressure vs. vesicle size regime where condensation can occur prior to buckling, which may preclude nonlinear shell buckling responses in contrast imaging.

Toxicity effects of disinfection byproduct chloroacetic acid to Microcystis aeruginosa: Cytotoxicity and mechanisms

Chlorine-based disinfectants are widely used for disinfection in wastewater treatment. The mechanism of the effects of chlorinated disinfection by-products on cyanobacteria was unclear. Herein, the physiological effects of chloroacetic acid (CAA) on Microcystis aeruginosa (M. aeruginosa), including acute toxicity, oxidative stress, apoptosis, production of microcystin-LR (MC-LR), and the microcystin transportation-related gene mcyH transcript abundance have been investigated. CAA exposure resulted in a significant change in the cell ultrastructure, including thylakoid damage, disappearance of nucleoid, production of gas vacuoles, increase in starch granule, accumulation of lipid droplets, and disruption of cytoplasm membranes. Meanwhile, the apoptosis rate of M. aeruginosa increased with CAA concentration. The production of MC-LR was affected by CAA, and the transcript abundance of mcyH decreased. Our results suggested that CAA poses acute toxicity to M. aeruginosa, and it could cause oxidative damage, stimulate MC-LR production, and damage cell ultrastructure. This study may provide information about the minimum concentration of CAA in the water environment, which is safe for aquatic organisms, especially during the global coronavirus disease 2019 pandemic period.

Recent Advances in the Study of Gas Vesicle Proteins and Application of Gas Vesicles in Biomedical Research.

The formation of gas vesicles has been investigated in bacteria and haloarchaea for more than 50 years. These air-filled nanostructures allow cells to stay at a certain height optimal for growth in their watery environment. Several gvp genes are involved and have been studied in Halobacterium salinarum, cyanobacteria, Bacillus megaterium, and Serratia sp. ATCC39006 in more detail. GvpA and GvpC form the gas vesicle shell, and additional Gvp are required as minor structural proteins, chaperones, an ATP-hydrolyzing enzyme, or as gene regulators. We analyzed the Gvp proteins of Hbt. salinarum with respect to their protein–protein interactions, and developed a model for the formation of these nanostructures. Gas vesicles are also used in biomedical research. Since they scatter waves and produce ultrasound contrast, they could serve as novel contrast agent for ultrasound or magnetic resonance imaging. Additionally, gas vesicles were engineered as acoustic biosensors to determine enzyme activities in cells. These applications are based on modifications of the surface protein GvpC that alter the mechanical properties of the gas vesicles. In addition, gas vesicles have been decorated with GvpC proteins fused to peptides of bacterial or viral pathogens and are used as tools for vaccine development.

Geometric effects in gas vesicle buckling under ultrasound

Acoustic reporter genes based on gas vesicles (GVs) have enabled the use of ultrasound to noninvasively visualize cellular function in vivo. The specific detection of GV signals relative to background acoustic scattering in tissues is facilitated by nonlinear ultrasound imaging techniques taking advantage of the sonomechanical buckling of GVs. However, the effect of geometry on the buckling behavior of GVs under exposure to ultrasound has not been studied. To understand such geometric effects, we developed computational models of GVs of various lengths and diameters and used finite element simulations to predict their threshold buckling pressures and postbuckling deformations. We demonstrated that the GV diameter has an inverse cubic relation to the threshold buckling pressure, whereas length has no substantial effect. To complement these simulations, we experimentally probed the effect of geometry on the mechanical properties of GVs and the corresponding nonlinear ultrasound signals. The results of these experiments corroborate our computational predictions. This study provides fundamental insights into how geometry affects the sonomechanical properties of GVs, which, in turn, can inform further engineering of these nanostructures for high-contrast, nonlinear ultrasound imaging.

Genome sequence of freshwater nontoxigenic Limnoraphis associated with microcystin-producing blooms.

A sample from a 2019 cyanobacterial bloom in a freshwater reservoir in eastern Oregon, USA, was used to produce a metagenome from which the complete, circular 7.3 Mbp genome of Limnoraphis sp. WC205 was assembled. The Limnoraphis sp. WC205 genome contains gas vesicle genes, genes for N2-fixation and genes for both phycocyanin- and phycoerythrin-containing phycobilisomes. Limnoraphis was present in Willow Creek Reservoir throughout the summer and fall, coexisting with various other cyanobacteria in blooms that were associated with microcystin. The absence of cyanotoxin genes from the Limnoraphis sp. WC205 genome showed this cyanobacterium to be non-toxigenic, although it is predicted to produce cyanobactins closely related to Microcystis aeruginosa microcyclamides. DNA sequence corresponding to the Microcystis mcyG gene identified Microcystis as the microcystin producer in this lake.

Development of a Potentially New Algaecide for Controlling Harmful Cyanobacteria Blooms Which is Ecologically Safe and Selective.

Harmful cyanobacterial blooms (HCBs) caused by Microcystis aeruginosa are of great concern as they negatively affect the aquatic environment and human health. Chemical methods could rapidly eradicate HCBs and have been used for many decades. However, many chemical reagents are not recommended to eliminate HCBs in the long term, given the possible destructive and toxic effects of the chemicals employed on non-target aquatic organisms. We developed a new algaecide, 2-((1,3,4-thiadiazol-2-yl)thio)-N-(4-chlorophenyl) acetamide (Q2), to control harmful cyanobacteria while being environmentally friendly and selective. In our study, Q2 effectively inhibited cyanobacterial growth, especially of M. aeruginosa, but did not affect eukaryotic algae in test concentrations. A critical mechanism was revealed by transcriptome and metagenomic results showing that Q2 affects multiple cellular targets of cyanobacteria for HCB control, including the destruction of organelles, damage in the photosynthesis center, as well as inhibition of gas vesicle growth, and these changes can be highly relevant to the decrease of quorum-sensing functional KEGG pathways. Furthermore, Q2 did not affect the microbial composition and could recover the disrupted aquatic functional pathways in a short period. This is different from the impact on ecosystem functioning of the traditionally used harmful algaecide diuron. All these results verified that Q2 could be friendly to the aquatic environment, providing a new directional choice in managing HCBs in the future.

Interaction of the gas vesicle proteins GvpA, GvpC, GvpN, and GvpO of Halobacterium salinarum.

The interactions of the four gas vesicle proteins GvpA, C, N, and O were investigated by split-GFP and pulldown assays. GvpA forms the ribs of the gas vesicle shell, whereas GvpC is attached to the exterior surface and stabilizes the gas vesicle structure. The AAA-ATPase GvpN as well as GvpO is found in much lower amounts. GvpN and GvpO formed homodimers and also the GvpN/GvpO heterodimer; both interacted with the C-terminal domain of GvpC when tested by split-GFP. When analyzed by pulldown assays, GvpN and GvpO also selected GvpA. The N-and C-terminal fragments of GvpC dimerized as Cterm/Cterm and Cterm/Nterm, but not as Nterm/Nterm. These interactions at both termini might lead to a network of GvpC molecules at the gas vesicle surface. However, a GvpA/GvpC interaction was not detectable, suggesting that the contact of both proteins is either mediated by another Gvp, or requires different structures that might form when GvpA is aggregated in the gas vesicle shell. Interactions of GvpA, C, N, and O were also studied with the accessory proteins GvpF through GvpM by split-GFP. GvpN bound GvpL only, whereas GvpO interacted with GvpF, I, and L, and the C-terminal domain of GvpC contacted GvpF, H, I, and L. GvpA/GvpA interactions were difficult to detect by split-GFP, but GvpA selected except for GvpI, K, and L all other accessory Gvp in pulldown assays. We will discuss the implications of these findings on gas-vesicle assembly.

Air-loaded Gas Vesicle Nanoparticles Promote Cell Growth in Three-dimensional Bioprinted Tissue Constructs.

Three-dimensional (3D) bioprinting has emerged as a promising method for the engineering of tissues and organs. Still, it faces challenges in its widespread use due to issues with the development of bioink materials and the nutrient diffusion barrier inherent to these scaffold materials. Herein, we introduce a method to promote oxygen diffusion throughout the printed constructs using genetically encoded gas vesicles derived from haloarchaea. These hollow nanostructures are composed of a protein shell that allows gases to permeate freely while excluding the water flow. After printing cells with gas vesicles of various concentrations, the cells were observed to have increased activity and proliferation. These results suggest that air-filled gas vesicles can help overcome the diffusion barrier throughout the 3D bioprinted constructs by increasing oxygen availability to cells within the center of the construct. The biodegradable nature of the gas vesicle proteins combined with our promising results encourage their potential use as oxygen-promoting materials in biological samples.

Bioengineering of Halobacterium sp. NRC-1 gas vesicle nanoparticles with GvpC fusion protein produced in E. coli

Gas vesicle nanoparticles (GVNPs) are hollow, buoyant prokaryotic organelles used for cell flotation. GVNPs are encoded by a large gas vesicle protein (gvp) gene cluster in the haloarchaeon, Halobacterium sp. NRC-1, including one gene, gvpC, specifying a protein bound to the surface of the nanoparticles. Genetically engineered GVNPs in the Halobacterium sp. have been produced by fusion of foreign sequences to gvpC. To improve the versatility of the GVNP platform, we developed a method for displaying exogenously produced GvpC fusion proteins on the haloarchaeal nanoparticles. The streptococcal IgG-binding protein domain was fused at or near the C-terminus of GvpC, expressed and purified from E. coli, and shown to bind to wild-type GVNPs. The two fusion proteins, GvpC3GB and GvpC4GB, without or with a highly acidic GvpC C-terminal region, were found to be able to bind nanoparticles equally well. The GVNP-bound GvpC-IgG-binding fusion protein was also capable of binding to an enzyme-linked IgG-HRP complex which retained enzyme activity, demonstrating the hybrid system capability for display and delivery of protein complexes. This is the first report demonstrating functional binding of exogenously produced GvpC fusion proteins to wild-type haloarchaeal GVNPs which significantly expands the capability of the platform to produce bioengineered nanoparticles for biomedical applications.Key points • Haloarchaeal gas vesicle nanoparticles (GVNPs) constitute a versatile display system. • GvpC-streptococcal IgG-binding fusion proteins expressed in E. coli bind to GVNPs. • IgG-binding proteins displayed on floating GVNPs bind and display IgG-HRP complex. Graphical abstract

A novel recombinant chimeric bio-adhesive protein consisting of mussel foot protein 3, 5, gas vesicle protein A, and CsgA curli protein expressed in Pichia pastoris

Despite various efforts to produce potent recombinant bio-adhesive proteins for medical purposes, efficient production of a safe and feasible bio-glue is not yet a commercial reality due to the weak properties or low expression levels. Here, a feasible expression system has been developed to produce strong recombinant fusion bioinspired protein using mussel foot protein 3 and 5 (Mfps) along with gas vesicle protein A (GvpA) of Anabaena flos-aquae, and a curli protein CsgA from E. coli, expressed under the control of alcohol oxidase (AOX1) promoter for high-level production in yeast P. pastoris using pPICZα vector. Purified chimeric proteins were first evaluated using western blotting, and their remaining dihydroxyphenylalanine (DOPA) was measured in the modified proteins by NBT assay. We further elucidated the mechanistic properties of obtained adhesive protein assembly in various pH levels based on its different subunits using atomic force microscopy (AFM) when adsorbed onto the mica surface. We found that both combinational structural features of subunits and post-translational changes during expression in yeast host have led to potent adherence due to higher DOPA residues specially in acidic condition and tetrad complex which is higher than that of earlier reports in prokaryotic systems. We believe that our obtained chimeric protein resulted from the fusion of GvpA and CsgA proteins with DOPA-containing Mfp proteins, expressed in the methylotrophic yeast, P. pastoris, not only presents a candidate for future biomedical applications but also provides novel biological clues used for high-performance bioinspired biomaterial designation.Graphical

Pathological features of hepatic portal venous gas in a cat

An 8-year 8-month-old castrated male Munchkin presented with vomiting, anorexia and hypoactivity. Computed tomography revealed excessive gas accumulation within the intestinal lumen and gas bubbles in the liver, spleen, and portal venous system, indicating hepatic portal venous gas. The cat died without any significant improvement, and mild splenomegaly was found at necropsy. Histologically, multiple gas vacuoles were diffusely observed in the liver and spleen. In the stomach, multiple gas vacuoles and scattered focal ulcers were detected within the mucosa. Multifocal hemorrhage was noted in the small and large intestines, whereas gas vacuoles were not present. Based on these findings, a gastric ulcer under high gas pressure may have provided an entry point for gas into the portal venous system.

Effect of Mutations in GvpJ and GvpM on Gas Vesicle Formation of Halobacterium salinarum.

The two haloarchaeal proteins, GvpM and GvpJ, are homologous to GvpA, the major gas vesicle structural protein. All three are hydrophobic and essential for gas vesicle formation. The effect of mutations in GvpJ and GvpM was studied in Haloferax volcanii transformants by complementing the respective mutated gene with the remaining gvp genes and inspecting the cells for the presence of gas vesicles (Vac+). In case of GvpJ, 56 of 66 substitutions analyzed yielded Vac– ΔJ + Jmut transformants, indicating that GvpJ is very sensitive to alterations, whereas ten of the 38 GvpM variants resulted in Vac– ΔM + Mmut transformants. The variants were also tested by split-GFP for their ability to interact with their partner protein GvpL. Some of the alterations leading to a Vac– phenotype affected the J/L or M/L interaction. Also, the interactions J/A and J/M were studied using fragments to exclude an unspecific aggregation of these hydrophobic proteins. Both fragments of GvpJ interacted with the M1–25 and M60–84 fragments of GvpM, and fragment J1–56 of GvpJ interacted with the N-terminal fragment A1–22 of GvpA. A comparison of the results on the three homologous proteins indicates that despite their relatedness, GvpA, GvpJ, and GvpM have unique features and cannot substitute each other.

Self-assembling of chimeric mussel-inspired bio-adhesives originated from Mytilus californianus and Anabaena flos-aquae: A new approach to develop underwater adhesion

Bio-adhesives play a pivotal role in a wide range of medical applications. However, there are some problems about their application in different pH values and low adhesion force under wet conditions. Here, we report new recombinant fusion protein achieved by mussel foot proteins (Mfps) of Mytilus Californianus and gas vesicle protein A (GvpA) of Anabaena flos-aquae by genetic engineering methods. Transmission electron microscopy verified that these chimeric proteins self-assembled into β-sheet rich fibres because of GvpA amyloid structure. Also, in comparison to other studies, their adhesion forces were significantly increased, especially in the alkaline environments based on Mfp-3 and Mfp-5, confirmed by the colloidal probe atomic force microscope. This study illustrates that copolymer of Mfp-5-GvpA:GvpA-Mfp-3 can be used as a sturdy underwater adhesive with tolerance to auto-oxidation, especially at basic conditions.

Archaeosomes and Gas Vesicles as Tools for Vaccine Development.

Archaea are prokaryotic organisms that were classified as a new domain in 1990. Archaeal cellular components and metabolites have found various applications in the pharmaceutical industry. Some archaeal lipids can be used to produce archaeosomes, a new family of liposomes that exhibit high stability to temperatures, pH and oxidative conditions. Additionally, archaeosomes can be efficient antigen carriers and adjuvants promoting humoral and cellular immune responses. Some archaea produce gas vesicles, which are nanoparticles released by the archaea that increase the buoyancy of the cells and facilitate an upward flotation in water columns. Purified gas vesicles display a great potential for bioengineering, due to their high stability, immunostimulatory properties and uptake across cell membranes. Both archaeosomes and archaeal gas vesicles are attractive tools for the development of novel drug and vaccine carriers to control various diseases. In this review we discuss the current knowledge on production, preparation methods and potential applications of archaeosomes and gas vesicles as carriers for vaccines. We give an overview of the traditional structures of these carriers and their modifications. A comparative analysis of both vaccine delivery systems, including their advantages and limitations of their use, is provided. Gas vesicle- and archaeosome-based vaccines may be powerful next-generation tools for the prevention and treatment of a wide variety of infectious and non-infectious diseases.

Ultrasound-enhanced coagulation for cyanobacterial removal: Effects of ultrasound frequency and energy density on coagulation performance, leakage of intracellular organic matters and toxicity

Ultrasound-enhanced coagulation is capable of effectively removing algal cells in algae-laden water. However, study differences in ultrasound settings, algal cell conditions and coagulant properties complicate the accurate evaluation of this technique for practical applications. No study has yet compared algae (and algal organic matters) removal among different frequencies of ultrasound in the ultrasound-coagulation process. In this study, the ultrasound at three typical frequencies, 29.4, 470 and 780 kHz, were applied for this purpose. The results showed that high-frequency ultrasound at 470 and 780 kHz had substantially greater improvement of coagulation than low-frequency ultrasound at 29.4 kHz (For example, the turbidity removal at 1 mg-Al/L of polymeric aluminum chloride increased by 204.2%, 571.9% and 563.2% under 29.4, 470 and 780 kHz ultrasound-coagulation, respectively, at 3.42 J/mL). Algal cells exhibited irreversible physical damage and the release of intracellular organic matters (such as odorous compounds) under low-frequency ultrasound with energy densities ≥ 3.42 J/mL, whereas high-frequency ultrasound was characterized by nonviolent impairment, including oxidative degradation and gas vacuole destruction (particularly reversible) resulting from ultrasound-induced radicals and cell resonance, respectively. Avoiding the severe destruction of algal cells is crucial for minimizing the toxicity and secondary pollution of the treated water. To achieve satisfactory removal, protected safety and better economy, the optimal energy density for each frequency was also determined. The findings from the analyses of the laboratory-cultured sample were confirmed via real eutrophic surface water. This study provides new insights and guidance for the ongoing study of harmful algal removal by ultrasound-enhanced coagulation.

Escherichia coli expressing gas vesicles is safe for enhancing the ablation effect of highintensity focused ultrasound in tumor-bearing mice

To investigate the effect and safety of Escherichia coli (E.coli) expressing gas vesicle (GVs) for enhancing the efficacy of tumor ablation by high intensity focused ultrasound (HIFU) in tumor-bearing mice. Thirty-two female BALB/c mice were used to establish mouse models bearing 4T1 tumor, which were randomized into GVs group [E.coli BL21 (AI)-PET28a-Arg1] and control group (PBS), and the efficacy of HIFU ablation was evaluated by examining coagulative necrotic volume and pathology of the tumors. Another 104 BALB/c mice were also randomly divided into GVs group and control group, and body weight changes of the mice were recorded on days 1, 4 and 15 after intravenous injection of E.coli containing GVs or PBS. White blood cells, red blood cells, hemoglobin and platelet counts and liver and renal function parameters of the mice were detected, and serum levels of TNF-α and IL-1β were examined using ELISA. The pathological changes in the liver and spleen were evaluated using HE staining to assess the safety of the treatments. HIFU ablation resulted in a significantly greater volume of coagulative necrosis and severer tissue damage in GVs group than in the control group (P < 0.001). In the 104 BALB/c mice without tumor cell inoculation, intravenous injection of E.coli expressing GVs, as compared with PBS, did not significantly affect body weight or cause changes in white blood cell, red blood cell and platelet counts or hemoglobin level (P1=0.59, P2=0.27, P3=0.76, P4=0.81). The liver and kidney function parameters (P1=0.12, P2=0.46, P3=0.62, P4=0.86) and serum levels of TNF-α and IL-1β (P1=0.48, P2=0.56) were all comparable between GVs group and control group. No obvious pathological changes were detected in the liver and spleen tissues in either GVs group or the control group. E.coli expressing GVs is safe for enhancing the ablation effect of HIFU in tumor-bearing mice.

Ecological stoichiometry of functional traits in a colonial harmful cyanobacterium

AbstractTrait‐based approaches provide a mechanistic framework crossing scales from cellular traits to community dynamics, while ecological stoichiometry applies first principles to understand how the balance of energy and elements shape ecological interactions. However, few studies have explicitly linked both frameworks. In this study, we tested the stoichiometric regulation of a number of carbon (C) based (e.g., extracellular polysaccharides and colony formation) and nitrogen (N) containing traits (i.e., chlorophyll a, phycocyanin, and gas vesicle content) in cyanobacteria in laboratory experiments and in the field. We exposed the cosmopolitan colony forming freshwater cyanobacterium Microcystis sp. in batch experiments to light, N and phosphorus (P) limitation, and enhanced CO2 levels, and assessed the regulation of these traits. Cyanobacterial traits followed stoichiometrically predictable patterns, where N containing traits increased with cellular N content, and decreased with increasing C : N ratios. C‐based traits increased with cellular C content and C : N ratios under nutrient, particularly N, limitation. The pattern of colony formation was confirmed with field data from Lake Taihu (China), showing an increase in colony size when N was limiting and N : P ratios were low. These findings demonstrate how an explicit coupling of trait‐based approaches to ecological stoichiometry can support our mechanistic understanding of responses of cyanobacteria toward shifts in resource availability.

Comparative genomics of the ADA clade within the Nostocales

The ADA clade of Nostocales cyanobacteria, a group that is prominent in current harmful algal bloom events, now includes over 40 genome sequences with the recent addition of sixteen novel sequenced genomes (Dreher et al., Harmful Algae, 2021). Fourteen genomes are complete (closed), enabling highly detailed assessments of gene content and genome architecture. ADA genomes contain 5 rRNA operons, genes expected to support a photoautotrophic and diazotrophic lifestyle, and a varied array of genes for the synthesis of bioactive secondary metabolites. Genes for the production of the taste-and-odor compound geosmin and the four major classes of cyanotoxins — anatoxin-a, cylindrospermopsin, microcystin and saxitoxin — are represented in members of the ADA clade. Notably, the gene array for the synthesis of cylindrospermopsin by Dolichospermum sp. DET69 was located on a plasmid, raising the possibility of facile horizontal transmission. However, genes supporting independent conjugative transfer of this plasmid are lacking. Further, analysis of genomic loci containing this and other cyanotoxin gene arrays shows evidence that these arrays have long-term stability and do not appear to be genomic islands easily capable of horizontal transmission to other cells. There is considerable diversity in the gene complements of individual ADA genomes, including the variable presence of physiologically important genes: genomes in three species-level subclades lack the gas vesicle genes that facilitate a planktonic lifestyle, and, surprisingly, the genome of Cuspidothrix issatschenkoi CHARLIE-1, a reported diazotroph, lacks the genes for nitrogen fixation. Notably, phylogenetically related genomes possess limited synteny, indicating a prominent role for chromosome rearrangements during ADA strain evolution. The genomes contain abundant insertion sequences and repetitive transposase genes, which could be the main drivers of genome rearrangement through active transposition and homologous recombination. No prophages were found, and no evidence of viral infection was observed in the bloom population samples from which the genomes discussed here were derived. Phages thus seem to have a limited influence on ADA evolution.

Measuring gas vesicle dimensions by electron microscopy.

Gas vesicles (GVs) are cylindrical or spindle-shaped protein nanostructures filled with air and used for flotation by various cyanobacteria, heterotrophic bacteria, and Archaea. Recently, GVs have gained interest in biotechnology applications due to their ability to serve as imaging agents and actuators for ultrasound, magnetic resonance and several optical techniques. The diameter of GVs is a crucial parameter contributing to their mechanical stability, buoyancy function and evolution in host cells, as well as their properties in imaging applications. Despite its importance, reported diameters for the same types of GV differ depending on the method used for its assessment. Here, we provide an explanation for these discrepancies and utilize electron microscopy (EM) techniques to accurately estimate the diameter of the most commonly studied types of GVs. We show that during air drying on the EM grid, GVs flatten, leading to a ~1.5-fold increase in their apparent diameter. We demonstrate that GVs' diameter can be accurately determined by direct measurements from cryo-EM samples or alternatively indirectly derived from widths of flat collapsed and negatively stained GVs. Our findings help explain the inconsistency in previously reported data and provide accurate methods to measure GVs dimensions.