Toxin-Antitoxin Systems in Estuarine Synechococcus Strain CB0101 and Their Transcriptomic Responses to Environmental Stressors

Indole-3-acetic acid promotes growth in bloom-forming Microcystis via an antioxidant response

Interactions between bacteria and phytoplankton in the phycosphere facilitate and constrain biogeochemical cycling in aquatic ecosystems. Indole-3-acetic acid (IAA) is a bacterially produced chemical signal that promotes growth of phytoplankton and plants. Here, we explored the impact of IAA on bloom-forming cyanobacteria and their associated bacteria. Exposure to IAA and its precursor, tryptophan, resulted in a strong growth response in a bloom of the freshwater cyanobacterium, Microcystis. Metatranscriptome analysis revealed the induction of an antioxidant response in Microcystis upon exposure to IAA, potentially allowing populations to increase photosynthetic rate and overcome internally generated reactive oxygen. Our data reveal that co-occurring bacteria within the phycosphere microbiome exhibit a division of labor for supportive functions, such as nutrient mineralization and transport, vitamin synthesis, and reactive oxygen neutralization. These complex dynamics within the Microcystis phycosphere microbiome are an example of interactions within a microenvironment that can have ecosystem-scale consequences.

Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings

The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.

An Estuarine Cyanophage S-CREM1 Encodes Three Distinct Antitoxin Genes and a Large Number of Non-Coding RNA Genes

Cyanophages play important roles in regulating the population dynamics, community structure, metabolism, and evolution of cyanobacteria in aquatic ecosystems. Here, we report the genomic analysis of an estuarine cyanophage, S-CREM1, which represents a new genus of T4-like cyanomyovirus and exhibits new genetic characteristics. S-CREM1 is a lytic phage which infects estuarine Synechococcus sp. CB0101. In contrast to many cyanomyoviruses that usually have a broad host range, S-CREM1 only infected the original host strain. In addition to cyanophage-featured auxiliary metabolic genes (AMGs), S-CREM1 also contains unique AMGs, including three antitoxin genes, a MoxR family ATPase gene, and a pyrimidine dimer DNA glycosylase gene. The finding of three antitoxin genes in S-CREM1 implies a possible phage control of host cells during infection. One small RNA (sRNA) gene and three cis-regulatory RNA genes in the S-CREM1 genome suggest potential molecular regulations of host metabolism by the phage. In addition, S-CREM1 contains a large number of tRNA genes which may reflect a genomic adaption to the nutrient-rich environment. Our study suggests that we are still far from understanding the viral diversity in nature, and the complicated virus-host interactions remain to be discovered. The isolation and characterization of S-CREM1 further our understanding of the gene diversity of cyanophages and phage-host interactions in the estuarine environment.

HigBA toxin-antitoxin system of Weissella cibaria is involved in response to the bile salt stress

BACKGROUND

Toxin-antitoxin (TA) systems are prevalent adaptive genetic elements in bacterial genomes, which can respond to environmental stress. While, few studies have addressed TA systems in probiotics and their roles in the adaptation to gastrointestinal transit (GIT) environments.

RESULTS

The Weissella cibaria 018 could survive in pH 3.0-5.0 and 0.5-3.0 g L^-1 bile salt, and its HigBA system responded to the bile salt stress, but not to acid stress. The toxin protein HigB and its cognate antitoxin protein HigA had 85.1% and 100% similarity with those of Lactobacillus plantarum, respectively, and they formed the stable tetramer HigB-(HigA)₂ -HigB structure in W. cibaria 018. When exposed to 1.5-3.0 g L^-1 bile salt, the transcriptions of higB and higA were up-regulated with 4.39-19.29 and 5.94-30.91 folds, respectively. Meanwhile, W. cibaria 018 gathered into a mass with 48.07% survival rate and its persister cells were found to increase 8.21% under 3.0 g L^-1 bile salt.

CONCLUSION

The HigBA TA system of W. cibaria 018 responded to the bile salt stress, but not to acid stress, which might offer novel perspectives to understand the tolerant mechanism of probiotics to GIT environment. © 2022 Society of Chemical Industry.

Comparative genome and transcriptome of Rhodococcus pyridinivorans GF3 for analyzing the detoxification mechanism of anthraquinone compounds

Anthraquinone compounds (ACs) could be efficiently degraded and detoxified by bacteria. However, the molecular mechanism of bacterial degradation and detoxification of ACs remains unclear. In this study, 1-aminoanthraquinone-2-sulfonate (ASA-2) was used as a model anthraquinone compound, the response mechanism of Rhodococcus pyridinivorans GF3 to ASA-2 using genomics and transcriptomics techniques was investigated. Comparative genome analysis showed that strain GF3 owned an especial gene region (Genes 1337-1399) containing the genes encoding cytochrome P450, monooxygenase, dehydrogenase and oxidoreductase, which did not commonly exist in Rhodococcus genus. The amino acid sequences of these genes were similar to those of the cleavage enzymes of anthraquinone ring in Aspergillus genus. Moreover, the transcriptions of Genes 1392-1394 (cytochrome 450 gene cluster) displayed 1.8-3.1-fold up-regulation under ASA-2 exposure. Meanwhile, as an intermediate product of ASA-2, catechol was degraded to acetyl-CoA, succinyl-CoA and pyruvate, resulting in the enhanced tricarboxylic acid cycle and ATP generation. This process also promoted the up-regulation of the genes encoding resistance, efflux, transporter and anti-oxidation pressure proteins, which were involved in resisting ASA-2 and maintaining the homeostasis of cells. These results provided us with a further understanding of the molecular mechanism of degradation and detoxification of ACs.

Isolation and Characterization of a Novel Cyanophage Encoding Multiple Auxiliary Metabolic Genes

As significant drivers of cyanobacteria mortality, cyanophages have been known to regulate the population dynamics, metabolic activities, and community structure of this most important marine autotrophic picoplankton and, therefore, influence the global primary production and biogeochemical cycle in aquatic ecosystems. In the present study, a lytic Synechococcus phage, namely S-SZBM1, was isolated and identified. Cyanophage S-SZBM1 has a double-stranded DNA genome of 177,834 bp with a G+C content of 43.31% and contains a total of 218 predicted ORFs and six tRNA genes. Phylogenetic analysis and nucleotide-based intergenomic similarity suggested that cyanophage S-SZBM1 belongs to a new genus under the family Kyanoviridae. A variety of auxiliary metabolic genes (AMGs) that have been proved or speculated to relate to photosynthesis, carbon metabolism, nucleotide synthesis and metabolism, cell protection, and other cell metabolism were identified in cyanophage S-SZBM1 genome and may affect host processes during infection. In addition, 24 of 32 predicted structural proteins were identified by a high-throughput proteome analysis which were potentially involved in the assembly processes of virion. The genomic and proteomic analysis features of cyanophage S-SZBM1 offer a valuable insight into the interactions between cyanophages and their hosts during infection.

Genome Sequence of Synechococcus sp. Strain LA31, Isolated from a Temperate Estuary

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.

Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology

Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications.

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Closed genome of the cyanobacteria Ca. P. alkaliphilum from high-pH photobioreactor

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Genetic factors lead this Phormidium to outcompete other cyanobacteria in photobioreactor

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Adaptation to high pH and alkalinity is not linked to specific genes

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Strain-level diversity contributes Ca. P. alkaliphilum success in changing conditions

Linkage between bacterial community-mediated hydrogen peroxide detoxification and the growth of Microcystis aeruginosa

Microcystis aeruginosa, an important cyanobloom-forming cyanobacterium, is sensitive to the high light intensity and consequent oxidative stress. Based on our genomic and transcriptomic analyses of H₂O₂-treated cells, many genes involved in photosynthesis, Calvin cycle, and microcystin synthesis were downregulated, whereas several toxin-antitoxin genes, DNA repair genes, and H₂O₂-defense systems such as peroxiredoxins and glutathione synthesis were upregulated. Axenic M. aeruginosa was then co-cultured with synthetic bacterial communities collected from 15 different freshwater samples with exhibiting different degrees of H₂O₂-production and catalase activities. Our analyses indicated that H₂O₂-resistant bacterial communities favored the growth and photosynthetic activity of M. aeruginosa cells under either H₂O₂ treatment or high light conditions. Nanopore-based bacterial community analyses indicated that these growth-promoting effects were likely attributable to a high proportion of Alphaproteobacteria (e.g., Brevundimonas and Ochrobactrum species), which protected M. aeruginosa cells from H₂O₂ toxicity. Further, these bacterial communities exhibited higher catalase activity levels and faster O₂ production rates upon H₂O₂ detoxification. Taken together, our findings newly suggest that the occurrence of catalase-less M. aeruginosa blooms is largely influenced by the surrounding microbiota during high light and organic-rich conditions.

Complete Genome Sequences of Chesapeake Bay Synechococcus Strains CBW1002 and CBW1006 Isolated in Winter

Synechococcus are picocyanobacteria with a cosmopolitan distribution. They are capable of surviving in a wide variety of environmental conditions. Synechococcus have been isolated from the Chesapeake Bay during winter months, and they show an impressive tolerance to cold temperatures. Cold-adapted Synechococcus are unique and diverse, as they have complex phylogenetic lineages closely related to subalpine cluster II, Bornholm Sea cluster, CB7 cluster, and some novel lineages which are independent from summer estuarine strains in subcluster 5.2. CBW1002 and CBW1006 are the first complete genomes to represent Bornholm Sea cluster Synechococcus strains. They have some of the largest genomes among the Synechococcus (3.8 Mb) and share many unique and cryptic homologs which could give insight into their ability to tolerate such cold and dynamic conditions in the Chesapeake Bay estuary.

Picophytoplankton dynamics in a large temperate estuary and impacts of extreme storm events

Picophytoplankton (PicoP) are increasingly recognized as significant contributors to primary productivity and phytoplankton biomass in coastal and estuarine systems. Remarkably though, PicoP composition is unknown or not well-resolved in several large estuaries including the semi-lagoonal Neuse River Estuary (NRE), a tributary of the second largest estuary-system in the lower USA, the Pamlico-Albemarle Sound. The NRE is impacted by extreme weather events, including recent increases in precipitation and flooding associated with tropical cyclones. Here we examined the impacts of moderate to extreme (Hurricane Florence, September 2018) precipitation events on NRE PicoP abundances and composition using flow cytometry, over a 1.5 year period. Phycocyanin-rich Synechococcus-like cells were the most dominant PicoP, reaching ~ 106 cells mL-1, which highlights their importance as key primary producers in this relatively long residence-time estuary. Ephemeral "blooms" of picoeukaryotic phytoplankton (PEUK) during spring and after spikes in river flow were also detected, making PEUK periodically major contributors to PicoP biomass (up to ~ 80%). About half of the variation in PicoP abundance was explained by measured environmental variables. Temperature explained the most variation (24.5%). Change in total dissolved nitrogen concentration, an indication of increased river discharge, explained the second-most variation in PicoP abundance (15.9%). The short-term impacts of extreme river discharge from Hurricane Florence were particularly evident as PicoP biomass was reduced by ~ 100-fold for more than 2 weeks. We conclude that precipitation is a highly influential factor on estuarine PicoP biomass and composition, and show how 'wetter' future climate conditions will have ecosystem impacts down to the smallest of phytoplankton.

Presence of toxin-antitoxin systems in picocyanobacteria and their ecological implications

Picocyanobacteria (mainly Synechococcus and Prochlorococcus) contribute significantly to ocean's primary production. Toxin-Antitoxin (TA) systems present in bacteria and archaea are known to regulate cell growth in response to environmental stresses. However, little is known about the presence of TA systems in picocyanobacteria. This study investigated complete genomes of Synechococcus and Prochlorococcus to understand the prevalence of TA systems in picocyanobacteria. Using the TAfinder software, Type II TA systems were predicted in 27 of 33 (81%) Synechococcus strains, but none of 38 Prochlorococcus strains contain TA genes. Synechococcus strains with larger genomes tend to contain more putative type II TA systems. The number of TA pairs varies from 0 to 42 in Synechococcus strains isolated from various environments. A linear correlation between the genome size and the number of putative TA systems in both coastal and freshwater Synechococcus was established. In general, open ocean Synechococcus contain no or few TA systems, while coastal and freshwater Synechococcus contain more TA systems. The type II TA systems inhibit microbial translation via ribonucleases and allow cells to enter the "dormant" stage in adverse environments. Inheritance of TA genes in freshwater and coastal Synechococcus could confer a recoverable persister mechanism important to survive in variable environments.

Complete Genome Sequence of Subcluster 5.2 Synechococcus sp. Strain CB0101, Isolated from the Chesapeake Bay

Synechococcus sp. strain CB0101 is a model strain for cyanobacteria living in the estuarine environment. It is also a representative member of marine Synechococcus subcluster 5.2. The draft genome sequence of CB0101 was reported in 2014 with 454 sequencing. Here, we report the complete genome sequence of CB0101, obtained with PacBio sequencing. CB0101 contains a specialized array of genes which are involved in sensing, responding to, and persisting in the presence of environmental stress.

Synechococcus sp. strain CB0101 is a model strain for cyanobacteria living in the estuarine environment. It is also a representative member of marine Synechococcus subcluster 5.2. The draft genome sequence of CB0101 was reported in 2014 with 454 sequencing. Here, we report the complete genome sequence of CB0101, obtained with PacBio sequencing. CB0101 contains a specialized array of genes which are involved in sensing, responding to, and persisting in the presence of environmental stress.

Characterization of Two Toxin-Antitoxin Systems in Deep-Sea Streptomyces sp. SCSIO 02999

Toxin-antitoxin (TA) systems are ubiquitous and abundant genetic elements in bacteria and archaea. Most previous TA studies have focused on commensal and pathogenic bacteria, but have rarely focused on marine bacteria, especially those isolated from the deep sea. Here, we identified and characterized three putative TA pairs in the deep-sea-derived Streptomyces sp. strain SCSIO 02999. Our results showed that Orf5461/Orf5462 and Orf2769/Orf2770 are bona fide TA pairs. We provide several lines of evidence to demonstrate that Orf5461 and Orf5462 constitute a type-II TA pair that are homologous to the YoeB/YefM TA pair from Escherichia coli. Although YoeB from SCSIO 02999 was toxic to an E. coli host, the homologous YefM antitoxin from SCSIO 02999 did not neutralize the toxic effect of YoeB from E. coli. For the Orf2769/Orf2770 TA pair, Orf2769 overexpression caused significant cell elongation and could lead to cell death in E. coli, and the neighboring Orf2770 could neutralize the toxic effect of Orf2769. However, no homologous toxin or antitoxin was found for this pair, and no direct interaction was found between Orf2769 and Orf2770. These results suggest that Orf2769 and Orf2770 may constitute a novel TA pair. Thus, deep-sea bacteria harbor typical and novel TA pairs. The biochemical and physiological functions of different TAs in deep-sea bacteria warrant further investigation.

Identification and Characterization of New Resistance-Conferring SGI1s (Salmonella Genomic Island 1) in Proteus mirabilis

Salmonella genomic island 1 (SGI1) is a resistance-conferring chromosomal genomic island that contains an antibiotic resistance gene cluster. The international spread of SGI1-containing strains drew attention to the role of genomic islands in the dissemination of antibiotic resistance genes in Salmonella and other Gram-negative bacteria. In this study, five SGI1 variants conferring multidrug and heavy metal resistance were identified and characterized in Proteus mirabilis strains: SGI1-PmCAU, SGI1-PmABB, SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48. The genetic structures of SGI1-PmCAU and SGI1-PmABB were identical to previously reported SGI1s, while structural analysis showed that SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48 are new SGI1 variants. SGI1-PmJN16 is derived from SGI1-Z with the MDR region containing a new gene cassette array dfrA12-orfF-aadA2-qacEΔ1-sul1-chrA-orf1. SGI1-PmJN40 has an unprecedented structure that contains two right direct repeat sequences separated by a transcriptional regulator-rich DNA fragment, and is predicted to form two different extrachromosomal mobilizable DNA circles for dissemination. SGI1-PmJN48 lacks a common ORF S044, and its right junction region exhibits a unique genetic organization due to the reverse integration of a P. mirabilis chromosomal gene cluster and the insertion of part of a P. mirabilis plasmid, making it the largest known SGI1 to date (189.1 kb). Further mobility functional analysis suggested that these SGIs can be excised from the chromosome for transfer between bacteria, which promotes the horizontal transfer of antibiotic and heavy metal resistance genes. The identification and characterization of the new SGI1 variants in this work suggested the diversity of SGI1 structures and their significant roles in the evolution of bacteria.