Environmental change, including global warming and chemical pollution, can compromise cnidarian-(e.g., coral-) dinoflagellate symbioses and cause coral bleaching. Understanding the mechanisms that regulate these symbioses will inform strategies for sustaining healthy coral-reef communities. A model system for corals is the symbiosis between the sea anemone Exaiptasia pallida (common name Aiptasia) and its dinoflagellate partners (family Symbiodiniaceae). To complement existing studies of the interactions between these organisms, we examined the impact of menthol, a reagent often used to render cnidarians aposymbiotic, on the dinoflagellate Breviolum minutum, both in culture and in hospite. In both environments, the growth and photosynthesis of this alga were compromised at either 100 or 300 mu M menthol. We observed reduction in PSII and PSI functions, the abundances of reaction-center proteins, and, at 300 mu M menthol, of total cellular proteins. Interestingly, for free-living algae exposed to 100 mu M menthol, an initial decline in growth, photosynthetic activities, pigmentation, and protein abundances reversed after 5-15 d, eventually approaching control levels. This behavior was observed in cells maintained in continuous light, but not in cells experiencing a light-dark regimen, suggesting that B. minutum can detoxify menthol or acclimate and repair damaged photosynthetic complexes in a light- and/or energy-dependent manner. Extended exposures of cultured algae to 300 mu M menthol ultimately resulted in algal death. Most symbiotic anemones were also unable to survive this menthol concentration for 30 d. Additionally, cells impaired for photosynthesis by pre-treatment with 300 mu M menthol exhibited reduced efficiency in re-populating the anemone host.

In cnidarian-Symbiodiniaceae symbioses, algal endosymbiont population control within the host is needed to sustain a symbiotic relationship. However, the molecular mechanisms that underlie such population control are unclear. Here we show that a cnidarian host uses nitrogen limitation as a primary mechanism to control endosymbiont populations. Nitrogen acquisition and assimilation transcripts become elevated in symbiotic Breviolum minutum algae as they reach high-densities within the sea anemone host Exaiptasia pallida. These same transcripts increase in free-living algae deprived of nitrogen. Symbiotic algae also have an elevated carbon-to-nitrogen ratio and shift metabolism towards scavenging nitrogen from purines relative to free-living algae. Exaiptasia glutamine synthetase and glutamate synthase transcripts concomitantly increase with the algal endosymbiont population, suggesting an increased ability of the host to assimilate ammonium. These results suggest algal growth and replication in hospite is controlled by access to nitrogen, which becomes limiting for the algae as their population within the host increases.

Photosynthesis is the dominant biotic carbon sink on earth and hence presents an opportunity for enhanced sequestration of CO2. If the average net carbon fixation efficiency of terrestrial plants could be increased by 3.3%, all anthropogenic CO2 accumulating in the atmosphere could instead be reduced and incorporated into terrestrial biomass. Plants make inefficient use of the overly abundant sunlight available to them, a result of having evolved to be competitive and survive highly dynamic environmental conditions rather than maximize photosynthetic productivity. We explore herein a phytophotonic approach to enhanced photosynthesis, whereby sunlight is redistributed by means of luminescent or persistent luminescent (PersL) materials. Phytophotonics has potential at varied scales, ranging from photobioreactors to greenhouses all the way to crops in the field, the latter having the potential to impact planetary CO2 levels. The approach is three-fold: a spectral redistribution to relieve high-light-stress at the top surface of leaves and increasingly drive photosynthesis deeper in leaves and canopies; a minute-scale temporal redistribution to bridge periods of intermittent shade and reduce shock associated with variable light conditions; and a multiple-hour temporal redistribution to shift a fraction of high-intensity midday lighting to evening hours. Based on simulations of photoluminescent materials and light quality experiments with a model algal system, it is shown that while lengthening daylight hours will require significant improvements in PersL materials, the other two approaches show more immediate promise. We demonstrate a means of concentrating PersL light from SrAl2O4:Eu,Dy, approaching levels needed to effectively bridge periods of natural shade, and outline the scientific questions and technical hurdles remaining to realize the benefits of the proposed spectral shift.

Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term 'dinoTADs') without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.

Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack. This arsenal has been expanded by the recent discovery of the versatile CRISPR-Cas system, which has two novel features. First, the host can specifically incorporate short sequences from invading genetic elements (virus or plasmid) into a region of its genome that is distinguished by clustered regularly interspaced short palindromic repeats (CRISPRs). Second, when these sequences are transcribed and precisely processed into small RNAs, they guide a multifunctional protein complex (Gas proteins) to recognize and cleave incoming foreign genetic material. This adaptive immunity system, which uses a library of small noncoding RNAs as a potent weapon against fast-evolving viruses, is also used as a regulatory system by the host. Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed.

The photosystem I (PSI) complex consisting of reaction center (RC) subunits, several peripheral subunits and many co-factors, is present in the thylakoid membranes of chloroplasts and cyanobacteria. The assembly of RC subunits (PsaA/B) that bind electron transfer co-factors and antenna pigments is an intricate process, and is mediated by several auxiliary factors such as Ycf3, Y3IP1/CGL59, Ycf4 and Ycf37/PYG7/CGL71. However, their precise molecular mechanisms in RC assembly remain to be addressed. Here we purified four PSI auxiliary factors by affinity chromatography, and characterized co-purified PSI assembly intermediates. We suggest that Ycf3 assists the initial assembly of newly synthesized PsaA/B subunits into an RC subcomplex, while Y3IP1 may be involved in transferring the RC subcomplex from Ycf3 to the Ycf4 module that stabilizes it. CGL71 may form an oligomer that transiently interacts with the PSI RC subcomplex, physically protecting it under oxic conditions until association with the peripheral PSI subunits occurs. Together, our results reveal the interplay among four auxiliary factors required for the stepwise assembly of the PSI RC.

In recent years there has been growing appreciation of the unexpected genetic diversity of microbes in the environment. This diversity has important implications for our understanding of photosynthesis in populations and in the environment. Conventional methodologies often cannot effectively capture this aspect. This chapter describes new approaches including comparative genomic and metagenomic approaches combined with a more detailed understanding of the metabolism and functionalities of cyanobacteria. This approach, which can be defined broadly as "functional ecogenomics" is partly motivated by the availability of high-throughput sequence data, which are steadily being acquired. The focus is on unicellular cyanobacteria in the hot spring microbial mats of Yellowstone National Park, which are primary producers in this prokaryotic community. We took a three-pronged approach, in which we (a) acquired complete genome sequences from two dominant Synechococcus sp. and carried out a comparative genomic analysis to understand the functional differences between these temperature adapted isolates; (b) produced a metagenome dataset that allows us to place genomic information in the context of the community within which these cyanobacteria grow and evolve; and (c) obtained pure isolates of some dominant organisms that allow us to manipulate them in a well-defined laboratory setting. In situ transcriptomics has allowed quantification of transcripts during the diel cycle. These diverse approaches and the ability to measure environmental parameters such as light and O-2 levels allow us detailed insight into the microbial mat system. Such an approach could be used to study a wide array of photosynthetic microorganisms as populations and interacting communities. As sequencing capacity, single cell capture techniques, proteomics and imaging techniques become more widely accessible we expect to obtain ever more detailed information about natural communities.