CRISPR systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats in type I and II CRISPR systems by the acquisition of short segments of DNA (spacers) from invasive elements. In several type III CRISPR systems, Cas1 is naturally fused to a reverse transcriptase (RT). In the marine bacterium Marinomonas mediterranea (MMB-1), we showed that a RT-Cas1 fusion protein enables the acquisition of RNA spacers in vivo in a RT-dependent manner. In vitro, the MMB-1 RT-Cas1 and Cas2 proteins catalyze the ligation of RNA segments into the CRISPR array, which is followed by reverse transcription. These observations outline a host-mediated mechanism for reverse information flow from RNA to DNA.

Bidirectional nutrient flow between partners is integral to the cnidarian-dinoflagellate endosymbiosis. However, our current knowledge of the transporter proteins that regulate nutrient and metabolite trafficking is nascent. Four transmembrane transporters that likely play an important role in interpartner nitrogen and carbon exchange were investigated with immunocytochemistry in the model sea anemone Exaiptasia diaphana ("Aiptasia"; strain NZ1): ammonium transporter 1 (AMT1), V-type proton ATPase (VHA), facilitated glucose transporter member 8 (GLUT8), and aquaporin-3 (AQP3). Anemones lacking symbionts were compared with those in symbiosis with either their typical, homologous dinoflagellate symbiont, Breviolum minutum, or the heterologous species, Durusdinium trenchii and Symbiodinium microadriaticum. AMT1 and VHA were only detected in symbiotic Aiptasia, irrespective of symbiont type. However, GLUT8 and AQP3 were detected in both symbiotic and aposymbiotic states. All transporters were localized to both the epidermis and gastrodermis, though localization patterns in host tissues were heavily influenced by symbiont identity, with S. microadriaticum-colonized anemones showing the most distinct patterns. These patterns suggested disruption of fixed carbon and inorganic nitrogen fluxes when in symbiosis with heterologous versus homologous symbionts. This study enhances our understanding of nutrient transport and host-symbiont integration, while providing a platform for further investigation of nutrient transporters and the host-symbiont interface in the cnidarian-dinoflagellate symbiosis. IMPORTANCE Coral reefs are in serious decline, in particular due to the thermally induced dysfunction of the cnidarian-dinoflagellate symbiosis that underlies their success. Yet our ability to react to this crisis is hindered by limited knowledge of how this symbiosis functions. Indeed, we still have much to learn about the cellular integration that determines whether a particular host-symbiont combination can persist, and hence whether corals might be able to adapt by acquiring new, more thermally resistant symbionts. Here, we employed immunocytochemistry to localize and quantify key nutrient transporters in tissues of the sea anemone Aiptasia, a globally adopted model system for this symbiosis, and compared the expression of these transporters when the host is colonized by native versus nonnative symbionts. We showed a clear link between transporter expression and symbiont identity, elucidating the cellular events that dictate symbiosis success, and we provide a methodological platform for further examination of cellular integration in this ecologically important symbiosis.

We provide here a news report on the 2015 Gordon Research Conference "Dynamics and regulation of photosynthesis: from the origin of biocatalysis to innovative solar conversion." It was held at Bentley University, Waltham, MA, USA, June 28-July 3, 2015, and offered a mix of traditional and emerging areas that highlighted new directions and methods of analyses. A major innovation was short (1 min) poster highlights that added an exciting dynamic to the interactions. Following the end of the formal sessions, three young scientists (Andrian Gutu, of Harvard University, USA; Alizee Malnoe of University of California, Berkeley, USA; and Yuval Mazor of Tel Aviv University, Israel) were recognized for their research; they also each received a recent volume of "Advances in photosynthesis and respiration including bioenergy and related processes" from Govindjee. We also provide at the end a brief report on the Gordon Research Seminar that preceded the conference.

Phototrophic microbial mat communities from 60 degrees C and 65 degrees C regions in the effluent channels of Mushroom and Octopus Springs (Yellowstone National Park, WY, USA) were investigated by shotgun metagenomic sequencing. Analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. Linkage of phylogenetic marker genes and functional genes showed novel chlorophototrophic bacteria belonging to uncharacterized lineages within the order Chlorobiales and within the Kingdom Chloroflexi. The latter is the first chlorophototrophic member of Kingdom Chloroflexi that lies outside the monophyletic group of chlorophototrophs of the Order Chloroflexales. Direct comparison of unassembled metagenomic sequences to genomes of representative isolates showed extensive genetic diversity, genomic rearrangements and novel physiological potential in native populations as compared with genomic references. Synechococcus spp. metagenomic sequences showed a high degree of synteny with the reference genomes of Synechococcus spp. strains A and B', but synteny declined with decreasing sequence relatedness to these references. There was evidence of horizontal gene transfer among native populations, but the frequency of these events was inversely proportional to phylogenetic relatedness. The ISME Journal (2011) 5, 1262-1278; doi: 10.1038/ismej.2011.73; published online 23 June 2011

Photosynthesis shapes the symbiotic relationships between cnidarians and Symbiodiniaceae algae-with many cnidarian hosts requiring symbiont photosynthate for survival-but little is known about how photosynthesis impacts symbiosis establishment. Here, we show that during symbiosis establishment, infection, proliferation, and maintenance can proceed without photosynthesis, but the ability to do so is dependent on specific cnidarian-Symbiodiniaceae relationships. The evaluation of 31 pairs of symbiotic relationships (five species of Symbiodiniaceae in sea anemone, coral, and jellyfish hosts) revealed that infection can occur without photosynthesis. A UV mutagenesis method for Symbiodiniaceae was established and used to generate six photosynthetic mutants that can infect these hosts. Without photosynthesis, Symbiodiniaceae cannot proliferate in the sea anemone Aiptasia or jellyfish Cassiopea but can proliferate in the juvenile polyps of the coral Acropora. After 6 months of darkness, Breviolum minutum is maintained within Aiptasia, indicating that Symbiodiniaceae maintenance can be independent of photosynthesis. Manipulating photosynthesis provides insights into cnidarian-Symbiodiniaceae symbiosis.

The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2-13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.

In the cnidarian-dinoflagellate symbiosis, hosts show altered expression of genes involved in growth and proliferation when in the symbiotic state, but little is known about the molecular mechanisms that underlie the host's altered growth rate. Using tissue-specific transcriptomics, we determined how symbiosis affects expression of cell cycle-associated genes, in the model symbiotic cnidarian Exaiptasia diaphana (Aiptasia). The presence of symbionts within the gastrodermis elicited cell-cycle arrest in the G(1) phase in a larger proportion of host cells compared with the aposymbiotic gastrodermis. The symbiotic gastrodermis also showed a reduction in the amount of cells synthesizing their DNA and progressing through mitosis when compared with the aposymbiotic gastrodermis. Host apoptotic inhibitors (Mdm2) were elevated, while host apoptotic sensitizers (c-Myc) were depressed, in the symbiotic gastrodermis when compared with the aposymbiotic gastrodermis and epidermis of symbiotic anemones, respectively. This indicates that the presence of symbionts negatively regulates host apoptosis, possibly contributing to their persistence within the host. Transcripts (ATM/ATR) associated with DNA damage were also downregulated in symbiotic gastrodermal tissues. In epidermal cells, a single gene (Mob1) required for mitotic completion was upregulated in symbiotic compared with aposymbiotic anemones, suggesting that the presence of symbionts in the gastrodermis stimulates host cell division in the epidermis. To further corroborate this hypothesis, we performed microscopic analysis using an S-phase indicator (EdU), allowing us to evaluate cell cycling in host cells. Our results confirmed that there were significantly more proliferating host cells in both the gastrodermis and epidermis in the symbiotic state compared with the aposymbiotic state. Furthermore, when comparing between tissue layers in the presence of symbionts, the epidermis had significantly more proliferating host cells than the symbiont-containing gastrodermis. These results contribute to our understanding of the influence of symbionts on the mechanisms of cnidarian cell proliferation and mechanisms associated with symbiont maintenance.

Certain cyanobacteria look green if grown in red light and vice versa. This dramatic color change, called complementary chromatic adaptation (CCA), is caused by alterations of the major colored light-harvesting proteins. A major controller of CCA is the cyanobacteriochrome (CBCR) RcaE, a red-green reversible photoreceptor that triggers a complex signal transduction pathway. Now, a new study demonstrates that CCA is also modulated by DpxA, a CBCR that senses yellow and teal (greenish blue) light. DpxA acts to expand the range of wavelengths that can impact CCA, by fine-tuning the process. This dual control of CCA might positively impact the fitness of cells growing in the shade of competing algae or in a water column where light levels and spectral quality change gradually with depth. This discovery adds to the growing number of light-responsive phenomena controlled by multiple CBCRs. Furthermore, the diverse CBCRs which are exclusively found in cyanobacteria have significant biotechnological potential.

In microbial mat communities of Yellowstone hot springs, ribosomal RNA (rRNA) sequence diversity patterns indicate the presence of closely related bacterial populations along environmental gradients of temperature and light. To identify the functional bases for adaptation, we sequenced the genomes of two cyanobacterial (Synechococcus OS-A and OS-B') isolates representing ecologically distinct populations that dominate at different temperatures and are major primary producers in the mat. There was a marked lack of conserved large-scale gene order between the two Synechococcus genomes, indicative of extensive genomic rearrangements. Comparative genomic analyses showed that the isolates shared a large fraction of their gene content at high identity, yet, differences in phosphate and nitrogen utilization pathways indicated that they have adapted differentially to nutrient fluxes, possibly by the acquisition of genes by lateral gene transfer or their loss in certain populations. Comparisons of the Synechococcus genomes to metagenomic sequences derived from mats where these Synechococcus stains were originally isolated, revealed new facets of microbial diversity. First, Synechococcus populations at the lower temperature regions of the mat showed greater sequence diversity than those at high temperatures, consistent with a greater number of ecologically distinct populations at the lower temperature. Second, we found evidence of a specialized population that is apparently very closely related to Synechococcus OS-B', but contains genes that function in the uptake of reduced ferrous iron. In situ expression studies demonstrated that these genes are differentially expressed over the diel cycle, with highest expression when the mats are anoxic and iron may be in the reduced state. Genomic information from these mat-specific isolates and metagenomic information can be coupled to detect naturally occurring populations that are associated with different functionalities, not always represented by isolates, but which may nevertheless be important for niche partitioning and the establishment of microbial community structure.

Background: Cyanobacteria are important agents in global carbon and nitrogen cycling and hold great promise for biotechnological applications. Model organisms such as Synechocystis sp. and Synechococcus sp. have advanced our understanding of photosynthetic capacity and circadian behavior, mostly using population-level measurements in which the behavior of individuals cannot be monitored. Synechocystis sp. cells are small and divide slowly, requiring long-term experiments to track single cells. Thus, the cumulative effects of drift over long periods can cause difficulties in monitoring and quantifying cell growth and division dynamics.