Here, we report the draft genome sequence of Bacillus cereus strain THSB-6-2, which was isolated from cyanobacterial blooms in Lake Taihu, China. The 5,496,658-bp genome assembly of Bacillus cereus consists of 28 contigs, with a GC content of 35% and with 5,587 protein-coding sequences and 58 RNA genes.
CyanoHABs are global environmental hazards, and their mechanisms of action are being intensively investigated. On an ecological scale, CyanoHABs are consequences of synergistic interactions between biological functions and elevated nutrients in eutrophic waters. On an evolutionary scale, one important question is how bloom-forming cyanobacteria acquire these superior biological functions.
Cyanobacterial harmful algal blooms (CyanoHABs) are longstanding aquatic hazards worldwide, of which the mechanism is not yet fully understood, i.e., the process in which cyanobacteria establish dominance over coexisting algae in the same eutrophic waters. The dominance of CyanoHABs represents a deviation from their low abundance under conventional evolution in the oligotrophic state, which has been the case since the origin of cyanobacteria on early Earth. To piece together a comprehensive mechanism of CyanoHABs, we revisit the origin and adaptive radiation of cyanobacteria in oligotrophic Earth, demonstrating ubiquitous adaptive radiation enabled by corresponding biological functions under various oligotrophic conditions. Next, we summarize the biological functions (ecophysiology) which drive CyanoHABs and ecological evidence to synthesize a working mechanism at the population level (the special mechanism) for CyanoHABs: CyanoHABs are the consequence of the synergistic interaction between superior cyanobacterial ecophysiology and elevated nutrients. Interestingly, these biological functions are not a result of positive selection by water eutrophication, but an adaptation to a longstanding oligotrophic state as all the genes in cyanobacteria are under strong negative selection. Last, to address the relative dominance of cyanobacteria over coexisting algae, we postulate a “general” mechanism of CyanoHABs at the community level from an energy and matter perspective: cyanobacteria are simpler life forms and thus have lower per capita nutrient demand for growth than coexisting eukaryotic algae. We prove this by comparing cyanobacteria and eukaryotic algae in cell size and structure, genome size, size of genome-scale metabolic networks, cell content, and finally the golden standard—field studies with nutrient supplementation in the same waters. To sum up, the comprehensive mechanism of CyanoHABs comprises a necessary condition, which is the general mechanism, and a sufficient condition, which is the special mechanism. One prominent prediction based on this tentative comprehensive mechanism is that eukaryotic algal blooms will coexist with or replace CyanoHABs if eutrophication continues and goes over the threshold nutrient levels for eukaryotic algae. This two-fold comprehensive mechanism awaits further theoretic and experimental testing and provides an important guide to control blooms of all algal species.
The mechanism of cyanobacterial harmful algal blooms (CyanoHABs) is complicated and confusing. One major reason is they are studied primarily from an ecological perspective and on bloom-forming species only. This narrow angle loses a broader evolutionary and ecological context in which CyanoHABs occur and fails to provide information on relevant components to achieve a wholistic understanding. To derive a comprehensive mechanism of CyanoHABs, we examine CyanoHABs through the overlooked evolutionary and ecological lenses: evolutionary radiation, ecological comparison with co-living algae, and recently identified genomic functional repertoire between blooming and non-blooming species. We found key factors: (1) elaborate diverse functional repertoire and low nutrient requirement in cyanobacteria molded by early adaptive evolution, (2) cyanobacteria having lower nutrient requirements than green algae indeed, (3) there is no directed evolution in biological functions toward water eutrophication in cyanobacteria, (4) the CyanoHAB-associated functional repertoire are more abundant and complete in blooming than non-blooming species. These factors lead us to postulate a preliminary mechanism of CyanoHABs as a synergistic quad: superior functional repertoire, established with long adaptive radiation under nutrient-deficient conditions and not evolved toward eutrophic conditions, enables cyanobacteria to efficiently utilize elevated nutrients under current eutrophic regime for excess growth and CyanoHABs thereof, due to their lower nutrient requirements than co-living algae. This preliminary synthesis without doubt needs further empirical testing, which can be undertaken with more comparative studies of multiple species using integrated systems biology approaches.
BackgroundMost organisms rely on a molecular circadian clock to orchestrate a wide range of physiological processes to match the 24-hour day. These molecular clocks are typically based on a negative feedback loop among a small set of proteins that govern the circadian output. Light or other environmental conditions can reset the circadian clock, but true circadian behaviors continue to cycle even in constant darkness, with an intrinsic period called the free-running period (FRP). Spiders have unusual FRPs, with some species having extremely short FRP (e.g. 18 hours for trashline orb weaver), and many having highly variable FRPs (intraspecific variation of up to 10 hours). In the absence of any genetic model of circadian rhythms in spiders, we developed a mathematical model to optimize experimental conditions for identifying circadian genes that also respond to light cues. ResultsOur mathematical model involved a single gene that encodes a protein that inhibits its own transcription. In our model, light degrades the circadian transcript, which allows a broad range of FRPs to be entrained to a 24-hour day. Our model predicted that exposing spiders to a pulse of light in the middle of the night would cause a pattern of expression between two later time points that was opposite the pattern exhibited by spiders who did not receive a pulse of light. RNA-sequencing of four groups of adult female orb weaving spiders, Metazygia wittfeldae, under these experimental conditions resulted in 528 significantly differentially expressed (DE) transcripts between the two collection times or between the light pulse and no light pulse. Consistent with our model, we found a cluster of transcripts with the flipped pattern of expression between the two collection times, dependent on the application of light.ConclusionsOur DE transcripts represent the first genetic evidence for circadian output in spiders. Furthermore, those transcripts with a flipped pattern of expression represent prime candidates for light-sensitive circadian genes, which may be involved in entraining the circadian clock to light. Functions of these genes varied from growth and development to reproduction to gene regulation, consistent with other circadian systems.
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